canu →
1.9+dfsg-1 →
armhf → 2019-12-15 11:54:23
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| canu 1.9+dfsg-1 (armhf) Sun, 15 Dec 2019 10:55:27 +0000 |
+==============================================================================+
Package: canu
Version: 1.9+dfsg-1
Source Version: 1.9+dfsg-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-c0335a31-0a6a-4b3b-9ce6-34670e6d4945' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.3 MB in 26s (924 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'canu' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/canu.git
Please use:
git clone https://salsa.debian.org/med-team/canu.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1232 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main canu 1.9+dfsg-1 (dsc) [1945 B]
Get:2 http://172.17.0.1/private bullseye-staging/main canu 1.9+dfsg-1 (tar) [1224 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main canu 1.9+dfsg-1 (diff) [6084 B]
Fetched 1232 kB in 0s (6022 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/canu-fojstL/canu-1.9+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/canu-fojstL' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-xjM5kS/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-xjM5kS/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-xjM5kS/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-xjM5kS/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-xjM5kS/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-xjM5kS/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-xjM5kS/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-xjM5kS/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (2860 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 21 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-xjM5kS/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12995 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap (>= 2.1.3)
Filtered Build-Depends: debhelper-compat (= 12), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap (>= 2.1.3)
dpkg-deb: building package 'sbuild-build-depends-canu-dummy' in '/<<BUILDDIR>>/resolver-xjM5kS/apt_archive/sbuild-build-depends-canu-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-canu-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-xjM5kS/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-xjM5kS/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-xjM5kS/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-xjM5kS/apt_archive ./ Sources [526 B]
Get:5 copy:/<<BUILDDIR>>/resolver-xjM5kS/apt_archive ./ Packages [609 B]
Fetched 2468 B in 1s (3187 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install canu build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev binfmt-support bsdmainutils
ca-certificates ca-certificates-java debhelper default-jre-headless
dh-autoreconf dh-strip-nondeterminism dwz fastjar file fontconfig-config
fonts-dejavu-core gettext gettext-base groff-base intltool-debian jaligner
jarwrapper java-common libapache-pom-java libarchive-zip-perl libasound2
libasound2-data libatinject-jsr330-api-java libavahi-client3
libavahi-common-data libavahi-common3 libboost-dev libboost1.67-dev libbsd0
libcommons-compress-java libcommons-parent-java libcroco3 libcups2
libdbus-1-3 libdebhelper-perl libelf1 libexpat1 libfastutil-java
libfile-stripnondeterminism-perl libfilesys-df-perl libfontconfig1
libfreetype6 libglib2.0-0 libgssapi-krb5-2 libguava-java libicu63
libjpeg62-turbo libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblcms2-2 libmagic-mgc libmagic1 libmeryl-dev libnspr4
libnss3 libpcsclite1 libpipeline1 libpng16-16 libsigsegv2 libssl1.1
libssw-java libsub-override-perl libtinfo5 libtool libuchardet0 libx11-6
libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1
libxtst6 m4 man-db mhap openjdk-11-jre-headless openssl po-debconf
sensible-utils ucf x11-common
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make default-jre gettext-doc libasprintf-dev libgettextpo-dev
groff libasound2-plugins alsa-utils libatinject-jsr330-api-java-doc
libboost-doc libboost1.67-doc libboost-atomic1.67-dev
libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev
libboost-coroutine1.67-dev libboost-date-time1.67-dev
libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
libxz-java cups-common krb5-doc krb5-user libjsr305-java-doc liblcms2-utils
pcscd libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic
fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic
libmail-box-perl
Recommended packages:
curl | wget | lynx dbus libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev binfmt-support bsdmainutils
ca-certificates ca-certificates-java debhelper default-jre-headless
dh-autoreconf dh-strip-nondeterminism dwz fastjar file fontconfig-config
fonts-dejavu-core gettext gettext-base groff-base intltool-debian jaligner
jarwrapper java-common libapache-pom-java libarchive-zip-perl libasound2
libasound2-data libatinject-jsr330-api-java libavahi-client3
libavahi-common-data libavahi-common3 libboost-dev libboost1.67-dev libbsd0
libcommons-compress-java libcommons-parent-java libcroco3 libcups2
libdbus-1-3 libdebhelper-perl libelf1 libexpat1 libfastutil-java
libfile-stripnondeterminism-perl libfilesys-df-perl libfontconfig1
libfreetype6 libglib2.0-0 libgssapi-krb5-2 libguava-java libicu63
libjpeg62-turbo libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblcms2-2 libmagic-mgc libmagic1 libmeryl-dev libnspr4
libnss3 libpcsclite1 libpipeline1 libpng16-16 libsigsegv2 libssl1.1
libssw-java libsub-override-perl libtinfo5 libtool libuchardet0 libx11-6
libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1
libxtst6 m4 man-db mhap openjdk-11-jre-headless openssl po-debconf
sbuild-build-depends-canu-dummy sensible-utils ucf x11-common
0 upgraded, 94 newly installed, 0 to remove and 21 not upgraded.
Need to get 87.9 MB of archives.
After this operation, 392 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-xjM5kS/apt_archive ./ sbuild-build-depends-canu-dummy 0.invalid.0 [900 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-1 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0038+nmu1 [69.0 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf binfmt-support armhf 2.2.0-2 [56.7 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1d-2 [806 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20190110 [157 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf java-common all 0.72 [14.5 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libavahi-common-data armhf 0.7-4+b2 [122 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libavahi-common3 armhf 0.7-4+b2 [51.0 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libdbus-1-3 armhf 1.12.16-2+b1 [189 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libavahi-client3 armhf 0.7-4+b2 [54.1 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libcups2 armhf 2.3.0-7 [304 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf liblcms2-2 armhf 2.9-3 [116 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-1 [274 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.1-2 [330 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-2 [280 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-2 [327 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libnspr4 armhf 2:4.23-1 [90.6 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libnss3 armhf 2:3.45-1 [957 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libasound2-data all 1.1.9-1 [60.6 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libasound2 armhf 1.1.9-1 [309 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libpcsclite1 armhf 1.8.25-3 [56.1 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.13.1-2 [132 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.8-1 [298 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.8-1 [691 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libxi6 armhf 2:1.7.9-1 [77.8 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+20 [252 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libxtst6 armhf 2:1.2.3-1 [26.3 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf openjdk-11-jre-headless armhf 11.0.5+10-2 [33.0 MB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf default-jre-headless armhf 2:1.11-72+b2 [11.2 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates-java all 20190909 [15.7 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.1 [173 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.3-2 [1137 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.1 [997 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf jaligner all 1.0+dfsg-6 [131 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf fastjar armhf 2:0.98-6 [42.6 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf jarwrapper all 0.72.10 [21.1 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libapache-pom-java all 18-1 [4676 B]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.2+b8 [4464 B]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libcommons-parent-java all 43-1 [10.8 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libcommons-compress-java all 1.18-3 [530 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libfastutil-java all 8.2.2-1 [15.4 MB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libfilesys-df-perl armhf 0.92-6+b5 [12.8 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libjsr305-java all 0.1~+svn49-11 [26.9 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libguava-java all 19.0-1 [2028 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libmeryl-dev armhf 0~20150903+r2013-6+b3 [64.7 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libssw-java armhf 1.1-6 [18.0 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf mhap all 2.1.3+dfsg-2 [160 kB]
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Setting up groff-base (1.22.4-3) ...
Setting up libx11-6:armhf (2:1.6.8-1) ...
Setting up libavahi-client3:armhf (0.7-4+b2) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libcommons-compress-java (1.18-3) ...
Setting up fontconfig-config (2.13.1-2) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up man-db (2.9.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libcups2:armhf (2.3.0-7) ...
Setting up libfontconfig1:armhf (2.13.1-2) ...
Setting up libxi6:armhf (2:1.7.9-1) ...
Setting up libxtst6:armhf (2:1.2.3-1) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up ca-certificates-java (20190909) ...
head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AddTrust_External_Root.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certigna.pem
Adding debian:Certinomis_-_Root_CA.pem
Adding debian:Certplus_Class_2_Primary_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Chambers_of_Commerce_Root_-_2008.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:Cybertrust_Global_Root.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DST_Root_CA_X3.pem
Adding debian:Deutsche_Telekom_Root_CA_2.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:EC-ACC.pem
Adding debian:EE_Certification_Centre_Root_CA.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GeoTrust_Global_CA.pem
Adding debian:GeoTrust_Primary_Certification_Authority.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem
Adding debian:GeoTrust_Universal_CA.pem
Adding debian:GeoTrust_Universal_CA_2.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R2.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:Global_Chambersign_Root_-_2008.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:LuxTrust_Global_Root_2.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:Network_Solutions_Certificate_Authority.pem
Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:QuoVadis_Root_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Sonera_Class_2_Root_CA.pem
Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:Taiwan_GRCA.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:TrustCor_ECA-1.pem
Adding debian:TrustCor_RootCert_CA-1.pem
Adding debian:TrustCor_RootCert_CA-2.pem
Adding debian:Trustis_FPS_Root_CA.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem
Adding debian:VeriSign_Universal_Root_Certification_Authority.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:thawte_Primary_Root_CA.pem
Adding debian:thawte_Primary_Root_CA_-_G2.pem
Adding debian:thawte_Primary_Root_CA_-_G3.pem
done.
Setting up default-jre-headless (2:1.11-72+b2) ...
Setting up debhelper (12.7.1) ...
Setting up jaligner (1.0+dfsg-6) ...
Setting up mhap (2.1.3+dfsg-2) ...
Setting up sbuild-build-depends-canu-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-3+rpi1) ...
Processing triggers for ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
done.
Setting up openjdk-11-jre-headless:armhf (11.0.5+10-2) ...
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.33.1-5+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-19+rpi1+b1 gcc-9_9.2.1-19+rpi1+b1 libc6-dev_2.29-3+rpi1 libstdc++-9-dev_9.2.1-19+rpi1+b1 libstdc++6_9.2.1-19+rpi1+b1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-5 binfmt-support_2.2.0-2 binutils_2.33.1-5+rpi1 binutils-arm-linux-gnueabihf_2.33.1-5+rpi1 binutils-common_2.33.1-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 ca-certificates_20190110 ca-certificates-java_20190909 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-19+rpi1+b1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1 debianutils_4.9 default-jre-headless_2:1.11-72+b2 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fastjar_2:0.98-6 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-19+rpi1+b1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-19+rpi1+b1 gcc-9-base_9.2.1-19+rpi1+b1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 jaligner_1.0+dfsg-6 jarwrapper_0.72.10 java-common_0.72 libacl1_2.2.53-5 libapache-pom-java_18-1 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-19+rpi1+b1 libasound2_1.1.9-1 libasound2-data_1.1.9-1 libassuan0_2.5.3-7 libatinject-jsr330-api-java_1.0+ds1-5 libatomic1_9.2.1-19+rpi1+b1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libavahi-client3_0.7-4+b2 libavahi-common-data_0.7-4+b2 libavahi-common3_0.7-4+b2 libbinutils_2.33.1-5+rpi1 libblkid1_2.34-0.1 libboost-dev_1.67.0.2+b8 libboost1.67-dev_1.67.0-13 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-3+rpi1 libc-dev-bin_2.29-3+rpi1 libc6_2.29-3+rpi1 libc6-dev_2.29-3+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-19+rpi1+b1 libcom-err2_1.45.4-1 libcommons-compress-java_1.18-3 libcommons-parent-java_43-1 libcroco3_0.6.13-1 libcups2_2.3.0-7 libdb5.3_5.3.28+dfsg1-0.6 libdbus-1-3_1.12.16-2+b1 libdebconfclient0_0.250 libdebhelper-perl_12.7.1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfastutil-java_8.2.2-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libfilesys-df-perl_0.92-6+b5 libfontconfig1_2.13.1-2 libfreetype6_2.10.1-2 libgcc-9-dev_9.2.1-19+rpi1+b1 libgcc1_1:9.2.1-19+rpi1+b1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.3-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-5 libgomp1_9.2.1-19+rpi1+b1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libguava-java_19.0-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libjpeg62-turbo_1:1.5.2-2+b1 libjsr305-java_0.1~+svn49-11 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 liblcms2-2_2.9-3 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmeryl-dev_0~20150903+r2013-6+b3 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libnspr4_2:4.23-1 libnss3_2:3.45-1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre3_2:8.39-12 libpcsclite1_1.8.25-3 libperl5.30_5.30.0-9 libpipeline1_1.5.1-2 libpng16-16_1.6.37-1 libreadline7_7.0-5 libreadline8_8.0-3 librust-bitflags-dev_1.2.1-1 librust-cloudabi+default-dev_0.0.3-1 librust-cloudabi-dev_0.0.3-1 librust-fuchsia-zircon-dev_0.3.3-2 librust-fuchsia-zircon-sys-dev_0.3.3-2 librust-libc-dev_0.2.62-1 librust-phf-codegen-dev_0.7.23-1 librust-phf-generator-dev_0.7.23-1 librust-phf-shared-dev_0.7.23-2+b1 librust-rand-0.5+alloc-dev_0.5.5-2+rpi1 librust-rand-0.5+std-dev_0.5.5-2+rpi1 librust-rand-0.5-dev_0.5.5-2+rpi1 librust-rand-core-0.2+alloc-dev_0.2.2-1 librust-rand-core-0.2+std-dev_0.2.2-1 librust-rand-core-0.2-dev_0.2.2-1 librust-rand-core-dev_0.3.0-1 librust-siphasher-dev_0.2.3-1 librust-winapi-dev_0.3.6-1 librust-winapi-i686-pc-windows-gnu-dev_0.4.0-1 librust-winapi-x86-64-pc-windows-gnu-dev_0.4.0-1 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.2-2+rpi1 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libssl1.1_1.1.1d-2 libssw-java_1.1-6 libstdc++-9-dev_9.2.1-19+rpi1+b1 libstdc++6_9.2.1-19+rpi1+b1 libsub-override-perl_0.09-2 libsystemd0_243-8+rpi1 libtasn1-6_4.14-3 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-19+rpi1+b1 libuchardet0_0.0.6-3 libudev1_243-8+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libx11-6_2:1.6.8-1 libx11-data_2:1.6.8-1 libxau6_1:1.0.8-1+b2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxi6_2:1.7.9-1 libxml2_2.9.4+dfsg1-8 libxrender1_1:0.9.10-1 libxtst6_2:1.2.3-1 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-1 mawk_1.3.3-17 mhap_2.1.3+dfsg-2 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_5.7 openjdk-11-jre-headless_11.0.5+10-2 openssl_1.1.1d-2 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-canu-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 ucf_3.0038+nmu1 util-linux_2.34-0.1 x11-common_1:7.7+20 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Nov 10 10:30:55 2019 UTC
gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1
gpgv: issuer "moeller@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./canu_1.9+dfsg-1.dsc
dpkg-source: info: extracting canu in /<<BUILDDIR>>/canu-1.9+dfsg
dpkg-source: info: unpacking canu_1.9+dfsg.orig.tar.xz
dpkg-source: info: unpacking canu_1.9+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use-debian-mhap-at-runtime.patch
dpkg-source: info: applying external-mhap.patch
dpkg-source: info: applying tell_version_properly.patch
dpkg-source: info: applying canu_version.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-c0335a31-0a6a-4b3b-9ce6-34670e6d4945
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package canu
dpkg-buildpackage: info: source version 1.9+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --sourcedirectory=src/
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/canu-1.9+dfsg'
rm -rf Linux-*
rm -f src/canu_version.H
make[1]: Leaving directory '/<<BUILDDIR>>/canu-1.9+dfsg'
dh_autoreconf_clean -O--sourcedirectory=src/
dh_clean -O--sourcedirectory=src/
debian/rules build-arch
dh build-arch --sourcedirectory=src/
dh_update_autotools_config -a -O--sourcedirectory=src/
dh_autoreconf -a -O--sourcedirectory=src/
dh_auto_configure -a -O--sourcedirectory=src/
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/canu-1.9+dfsg'
dh_auto_build
cd src && make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<BUILDDIR>>/canu-1.9+dfsg/src'
WARNING:
WARNING: g++ 9 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher.
WARNING:
Building for 'Linux' '4.9.0-0.bpo.2-armmp' as 'armv7l' into '/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/{bin,obj}'.
Using '/usr/bin/g++' version '9'.
Using user-supplied CXXFLAGS '-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security'.
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/edlib.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-buffered.C
Building release
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-compressed.C
utility/files.C: In function 'void writeToFile(void*, const char*, uint64, uint64, FILE*)':
utility/files.C:89:56: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
90 | nWritten, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:89:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
90 | nWritten, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:89:85: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
90 | nWritten, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:94:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
94 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): Short write\n",
| ~~^
| |
| long unsigned int
| %llu
95 | nWritten, nObjects, description, objectSize), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:94:65: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
94 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): Short write\n",
| ~~^
| |
| long unsigned int
| %llu
95 | nWritten, nObjects, description, objectSize), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:94:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
94 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): Short write\n",
| ~~^
| |
| long unsigned int
| %llu
95 | nWritten, nObjects, description, objectSize), exit(1);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C: In function 'uint64 loadFromFile(void*, const char*, uint64, uint64, FILE*, bool)':
utility/files.C:134:59: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
134 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): End of file\n",
| ~~^
| |
| long unsigned int
| %llu
135 | nLoaded, nObjects, description, objectSize);
| ~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:134:70: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
134 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): End of file\n",
| ~~^
| |
| long unsigned int
| %llu
135 | nLoaded, nObjects, description, objectSize);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:134:88: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
134 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): End of file\n",
| ~~^
| |
| long unsigned int
| %llu
135 | nLoaded, nObjects, description, objectSize);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:150:57: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
150 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
151 | nLoaded, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:150:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
150 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
151 | nLoaded, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:150:86: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
150 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
151 | nLoaded, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C: In function 'void AS_UTL_symlink(const char*, const char*)':
utility/files.C:311:10: warning: ignoring return value of 'int symlink(const char*, const char*)', declared with attribute warn_unused_result [-Wunused-result]
311 | symlink(pathToFile, pathToLink);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
utility/files.C: In function 'void AS_UTL_loadFileList(char*, std::vector<char*>&)':
utility/files.C:587:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
587 | fgets(line, FILENAME_MAX, F);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
utility/files.C:593:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
593 | fgets(line, FILENAME_MAX, F);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/strings.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system.C
utility/files-memoryMapped.C: In constructor 'memoryMappedFile::memoryMappedFile(const char*, memoryMappedFileType)':
utility/files-memoryMapped.C:76:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)', declared with attribute warn_unused_result [-Wunused-result]
76 | read(_fd, _data, _length);
| ~~~~^~~~~~~~~~~~~~~~~~~~~
utility/files-memoryMapped.C: In destructor 'memoryMappedFile::~memoryMappedFile()':
utility/files-memoryMapped.C:102:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result]
102 | write(_fd, _data, _length), close(_fd);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system-stackTrace.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sequence.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-reader.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer.C
utility/kmers-writer.C:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp]
58 | #warning how to set prefix size for streaming operations?
| ^~~~~~~
In file included from utility/kmers.H:32,
from utility/kmers-reader.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from utility/kmers.H:32,
from utility/kmers.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from utility/kmers-reader.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)':
utility/kmers-reader.C:208:46: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m);
| ~~~~~^ ~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
utility/kmers-reader.C:208:52: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m);
| ~~~~~^ ~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
In file included from utility/kmers.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-reader.C: In function 'void dumpMerylDataFile(char*)':
utility/kmers-reader.C:342:29: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2);
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-reader.C:342:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n",
| ~~~^
| |
| long unsigned int
| %8llu
343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2);
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-reader.C:342:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2);
| ~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-reader.C:342:68: warning: format '%lx' expects argument of type 'long unsigned int', but argument 10 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2);
| ~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-reader.C:342:77: warning: format '%lx' expects argument of type 'long unsigned int', but argument 11 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2);
| ~~
| |
| uint64 {aka long long unsigned int}
In file included from utility/kmers.H:32,
from utility/kmers-writer.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)':
utility/kmers-reader.C:143:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
143 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _inName);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from utility/kmers.H:29,
from utility/kmers-reader.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-block.C
In file included from utility/kmers-writer.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-writer.C: In member function 'void kmerCountFileWriter::initialize(uint32, bool)':
utility/kmers-writer.C:78:117: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
78 | fprintf(stderr, "kmerCountFileWriter()-- Creating '%s' for %u-mers, with prefixSize %u suffixSize %u numFiles %lu\n",
| ~~^
| |
| long unsigned int
| %llu
79 | _outName, (_prefixSize + _suffixSize) / 2, _prefixSize, _suffixSize, _numFiles);
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-writer.C: In member function 'uint32 kmerCountFileWriter::fileNumber(uint64)':
utility/kmers-writer.C:169:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
169 | fprintf(stderr, "kmerCountFileWriter()-- Formed invalid file number %lu >= number of files %lu:\n", oi, _numFiles);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers-writer.C:169:98: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
169 | fprintf(stderr, "kmerCountFileWriter()-- Formed invalid file number %lu >= number of files %lu:\n", oi, _numFiles);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/kmers-writer.C:170:71: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
170 | fprintf(stderr, "kmerCountFileWriter()-- prefix 0x%016lx\n", prefix);
| ~~~~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
utility/kmers-writer.C: In destructor 'kmerCountFileWriter::~kmerCountFileWriter()':
utility/kmers-writer.C:147:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
147 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _outName);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from utility/kmers.H:29,
from utility/kmers-writer.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-stream.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-statistics.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-exact.C
In file included from utility/kmers.H:32,
from utility/kmers-writer-block.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from utility/kmers-writer-block.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-writer-block.C: In member function 'void kmerCountBlockWriter::mergeBatches(uint32)':
utility/kmers-writer-block.C:325:84: warning: format '%lx' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
325 | fprintf(stderr, "ERROR: File %u segments 1 and %u differ in prefix: 0x%016lx vs 0x%016lx\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
326 | oi, ii, prefix, inBlocks[ii].prefix());
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-writer-block.C:325:96: warning: format '%lx' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
325 | fprintf(stderr, "ERROR: File %u segments 1 and %u differ in prefix: 0x%016lx vs 0x%016lx\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
326 | oi, ii, prefix, inBlocks[ii].prefix());
| ~~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-writer-block.C:370:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
370 | fprintf(stderr, "savnKmers %lu > nKmersMax %lu\n", savnKmers, nKmersMax);
| ~~^ ~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers-writer-block.C:370:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
370 | fprintf(stderr, "savnKmers %lu > nKmersMax %lu\n", savnKmers, nKmersMax);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from utility/kmers.H:32,
from utility/kmers-writer-stream.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from utility/kmers-writer-stream.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from utility/kmers.H:32,
from utility/kmers-statistics.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from utility/kmers-statistics.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from utility/kmers.H:32,
from utility/kmers-exact.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from utility/kmers-exact.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-exact.C: In member function 'bool kmerCountExactLookup::configure()':
utility/kmers-exact.C:171:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
171 | fprintf(stderr, " p prefixes bits gigabytes (allowed: %lu GB)\n", _maxMemory >> 33);
| ~~^ ~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers-exact.C:185:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
185 | fprintf(stderr, "%2u %14lu %16lu %9.3f (smallest)\n", pb, nprefix, space, bitsToGB(space));
| ~~~~^ ~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %14llu
utility/kmers-exact.C:185:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
185 | fprintf(stderr, "%2u %14lu %16lu %9.3f (smallest)\n", pb, nprefix, space, bitsToGB(space));
| ~~~~^ ~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %16llu
utility/kmers-exact.C:188:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
188 | fprintf(stderr, "%2u %14lu %16lu %9.3f (used)\n", pb, nprefix, space, bitsToGB(space));
| ~~~~^ ~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %14llu
utility/kmers-exact.C:188:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
188 | fprintf(stderr, "%2u %14lu %16lu %9.3f (used)\n", pb, nprefix, space, bitsToGB(space));
| ~~~~^ ~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %16llu
utility/kmers-exact.C:191:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
191 | fprintf(stderr, "%2u %14lu %16lu %9.3f\n", pb, nprefix, space, bitsToGB(space));
| ~~~~^ ~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %14llu
utility/kmers-exact.C:191:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
191 | fprintf(stderr, "%2u %14lu %16lu %9.3f\n", pb, nprefix, space, bitsToGB(space));
| ~~~~^ ~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %16llu
utility/kmers-exact.C:198:52: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
198 | fprintf(stderr, "Not enough memory to load %lu distinct %u-kmers.\n", _nSuffix, _Kbits / 2);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers-exact.C:203:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
203 | fprintf(stderr, "For %lu distinct %u-mers (with %u bits used for indexing and %u bits for tags):\n", _nSuffix, _Kbits / 2, _prefixBits, _suffixBits);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers-exact.C:205:55: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
205 | fprintf(stderr, " %7.3f GB memory for index (%lu elements %u bits wide)\n", bitsToGB(_nPrefix * _prePtrBits), _nPrefix, _prePtrBits);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers-exact.C:206:55: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
206 | fprintf(stderr, " %7.3f GB memory for tags (%lu elements %u bits wide)\n", bitsToGB(_nSuffix * _suffixBits), _nSuffix, _suffixBits);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers-exact.C:207:55: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
207 | fprintf(stderr, " %7.3f GB memory for data (%lu elements %u bits wide)\n", bitsToGB(_nSuffix * _valueBits), _nSuffix, _valueBits);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers-exact.C: In member function 'void kmerCountExactLookup::allocate()':
utility/kmers-exact.C:342:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
342 | fprintf(stderr, "Allocating space for %lu suffixes of %u bits each -> %lu bits (%.3f GB) in blocks of %.3f MB\n",
| ~~^
| |
| long unsigned int
| %llu
343 | _nSuffix, _suffixBits, arraySize, bitsToGB(arraySize), bitsToMB(arrayBlockMin));
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-exact.C:342:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
342 | fprintf(stderr, "Allocating space for %lu suffixes of %u bits each -> %lu bits (%.3f GB) in blocks of %.3f MB\n",
| ~~^
| |
| long unsigned int
| %llu
343 | _nSuffix, _suffixBits, arraySize, bitsToGB(arraySize), bitsToMB(arrayBlockMin));
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-exact.C:354:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
354 | fprintf(stderr, " %lu values of %u bits each -> %lu bits (%.3f GB) in blocks of %.3f MB\n",
| ~~^
| |
| long unsigned int
| %llu
355 | _nSuffix, _valueBits, arraySize, bitsToGB(arraySize), bitsToMB(arrayBlockMin));
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-exact.C:354:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
354 | fprintf(stderr, " %lu values of %u bits each -> %lu bits (%.3f GB) in blocks of %.3f MB\n",
| ~~^
| |
| long unsigned int
| %llu
355 | _nSuffix, _valueBits, arraySize, bitsToGB(arraySize), bitsToMB(arrayBlockMin));
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-exact.C: In member function 'void kmerCountExactLookup::load()':
utility/kmers-exact.C:412:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
412 | fprintf(stderr, "minValue " F_U32 " maxValue " F_U32 " value " F_U64 " bits " F_U32 "\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
413 | _minValue, _maxValue, value, _valueBits);
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-exact.C:412:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
utility/kmers-exact.C: In member function 'bool kmerCountExactLookup::exists_test(kmer)':
utility/kmers-exact.C:501:41: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
501 | fprintf(stderr, "FAILED kmer 0x%016lx\n", kmer);
| ~~~~~^ ~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
utility/kmers-exact.C:502:41: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
502 | fprintf(stderr, "FAILED prefix 0x%016lx\n", prefix);
| ~~~~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
utility/kmers-exact.C:503:41: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
503 | fprintf(stderr, "FAILED suffix 0x%016lx\n", suffix);
| ~~~~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
utility/kmers-exact.C:505:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
505 | fprintf(stderr, "original %9lu %9lu\n", _suffixBgn[prefix], _suffixBgn[prefix + 1]);
| ~~~^ ~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %9llu
utility/kmers-exact.C:505:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
505 | fprintf(stderr, "original %9lu %9lu\n", _suffixBgn[prefix], _suffixBgn[prefix + 1]);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %9llu
utility/kmers-exact.C:506:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "final %9lu %9lu\n", bgn, end);
| ~~~^ ~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %9llu
utility/kmers-exact.C:506:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "final %9lu %9lu\n", bgn, end);
| ~~~^ ~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %9llu
utility/kmers-exact.C:517:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
517 | fprintf(stderr, "TEST bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix);
| ~~~^ ~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %8llu
utility/kmers-exact.C:517:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
517 | fprintf(stderr, "TEST bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix);
| ~~~^ ~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %8llu
utility/kmers-exact.C:517:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
517 | fprintf(stderr, "TEST bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix);
| ~~~^ ~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %8llu
utility/kmers-exact.C:517:59: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
517 | fprintf(stderr, "TEST bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix);
| ~~^ ~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers-exact.C:517:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
517 | fprintf(stderr, "TEST bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix);
| ~~^ ~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers-exact.C:532:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
532 | fprintf(stderr, "ITER bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix);
| ~~~^ ~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %8llu
utility/kmers-exact.C:532:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
532 | fprintf(stderr, "ITER bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix);
| ~~~^ ~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %8llu
utility/kmers-exact.C:532:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
532 | fprintf(stderr, "ITER bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix);
| ~~~^ ~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %8llu
utility/kmers-exact.C:532:59: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
532 | fprintf(stderr, "ITER bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix);
| ~~^ ~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers-exact.C:532:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
532 | fprintf(stderr, "ITER bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix);
| ~~^ ~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/bits.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/hexDump.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/md5.C
In file included from utility/bits.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/objectStore.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C
utility/objectStore.C: In function 'bool fetchFromObjectStore(char*)':
utility/objectStore.C:257:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
257 | args[1] = "download";
| ^~~~~~~~~~
utility/objectStore.C:258:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
258 | args[2] = "--overwrite";
| ^~~~~~~~~~~~~
utility/objectStore.C:259:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
259 | args[3] = "--no-progress";
| ^~~~~~~~~~~~~~~
utility/objectStore.C:260:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
260 | args[4] = "--output";
| ^~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from correction/falconConsensus.H:75,
from correction/falconConsensus.C:73:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from correction/falconConsensus.H:75,
from correction/falconConsensus-alignTag.C:73:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from stores/sqCache.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C
stores/sqCache.C: In constructor 'sqCache::sqCache(sqStore*, sqRead_version, uint64)':
stores/sqCache.C:95:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
95 | fprintf(stderr, "sqCache: found %u %s reads with %lu bases.\n", nReads, toString(_version), nBases);
| ~~^ ~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
stores/sqCache.C: In member function 'void sqCache::sqCache_loadReads(bool)':
stores/sqCache.C:328:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
328 | fprintf(stderr, "Loading %u reads and %lu bases out of %u reads in the store.\n",
| ~~^
| |
| long unsigned int
| %llu
329 | nReads, nBases, _nReads);
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreEncode.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreEncode.C
In file included from stores/sqStore.H:89,
from stores/sqStore.C:38:
stores/sqStoreBlobWriter.H: In member function 'void sqStore::sqStore_stashReadData(sqReadData*)':
stores/sqStoreBlobWriter.H:68:39: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
68 | snprintf(_blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , _storePath, _bufferCount);
stores/sqStoreBlobWriter.H:68:39: note: using the range [0, 4294967295] for directive argument
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStore.C:38:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_deletePartitions()':
stores/sqStoreConstructor.C:405:35: warning: '/partitions/map' directive output may be truncated writing 15 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
405 | snprintf(path, FILENAME_MAX, "%s/partitions/map", _storePath);
| ^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4112 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreInfo.C: In member function 'bool sqStoreInfo::checkInfo()':
stores/sqStoreInfo.C:82:31: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 4 has type 'long unsigned int' [-Wformat=]
82 | failed += fprintf(stderr, "ERROR: sqVersion in store = 0x%016" F_X64P ", differs from executable = 0x%016" F_X64P "\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:423:37: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
423 | snprintf(path, FILENAME_MAX, "%s/partitions/reads.%04u", _storePath, ii+1); AS_UTL_unlink(path);
| ^~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:423:34: note: using the range [0, 4294967295] for directive argument
423 | snprintf(path, FILENAME_MAX, "%s/partitions/reads.%04u", _storePath, ii+1); AS_UTL_unlink(path);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:424:37: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
424 | snprintf(path, FILENAME_MAX, "%s/partitions/blobs.%04u", _storePath, ii+1); AS_UTL_unlink(path);
| ^~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:424:34: note: using the range [0, 4294967295] for directive argument
424 | snprintf(path, FILENAME_MAX, "%s/partitions/blobs.%04u", _storePath, ii+1); AS_UTL_unlink(path);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:429:35: warning: '/partitions' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
429 | snprintf(path, FILENAME_MAX, "%s/partitions", _storePath);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_delete()':
stores/sqStoreConstructor.C:391:35: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
391 | snprintf(path, FILENAME_MAX, "%s/info", _storePath); AS_UTL_unlink(path);
| ^~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:392:35: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
392 | snprintf(path, FILENAME_MAX, "%s/libraries", _storePath); AS_UTL_unlink(path);
| ^~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4107 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:393:35: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
393 | snprintf(path, FILENAME_MAX, "%s/reads", _storePath); AS_UTL_unlink(path);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:394:35: warning: '/blobs' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
394 | snprintf(path, FILENAME_MAX, "%s/blobs", _storePath); AS_UTL_unlink(path);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C: In constructor 'sqStore::sqStore(const char*, const char*, sqStore_mode, uint32)':
stores/sqStoreConstructor.C:115:36: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
115 | snprintf(nameI, FILENAME_MAX, "%s/info", _storePath);
| ^~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:208:36: warning: '/partitions/map' directive output may be truncated writing 15 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
208 | snprintf(nameI, FILENAME_MAX, "%s/partitions/map", _storePath);
| ^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4112 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:227:36: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
227 | snprintf(nameL, FILENAME_MAX, "%s/libraries", _storePath);
| ^~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4107 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:228:33: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
228 | snprintf(nameR, FILENAME_MAX, "%s/partitions/reads.%04" F_U32P, _storePath, _partitionID);
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:229:33: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
229 | snprintf(nameB, FILENAME_MAX, "%s/partitions/blobs.%04" F_U32P, _storePath, _partitionID);
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/sqStore.H:89,
from stores/sqStoreConstructor.C:39:
stores/sqStoreBlobWriter.H:68:39: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
68 | snprintf(_blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , _storePath, _bufferCount);
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/sqStore.H:89,
from stores/sqStoreConstructor.C:39:
stores/sqStoreBlobWriter.H:68:39: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
68 | snprintf(_blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , _storePath, _bufferCount);
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStorePartition.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C
stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()':
stores/sqStoreConstructor.C:258:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
258 | snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, _storePath, V);
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 13 and 4109 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:266:35: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
266 | snprintf(No, FILENAME_MAX, "%s/libraries", _storePath);
| ^~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4107 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:267:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
267 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/libraries", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:270:35: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
270 | snprintf(No, FILENAME_MAX, "%s/reads", _storePath);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:271:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
271 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 19 and 4122 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:274:35: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
274 | snprintf(No, FILENAME_MAX, "%s/info", _storePath);
| ^~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:275:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
275 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/info", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 18 and 4121 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:278:35: warning: '/info.txt' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
278 | snprintf(No, FILENAME_MAX, "%s/info.txt", _storePath);
| ^~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 10 and 4106 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:279:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
279 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/info.txt", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4125 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:261:34: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
261 | snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, _storePath, V);
stores/sqStoreConstructor.C:261:34: note: using the range [0, 4294967295] for directive argument
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 13 and 4116 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C
stores/ovOverlap.C:217:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp]
217 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C
stores/ovStoreWriter.C:71:2: warning: #warning not failing if a valid store [-Wcpp]
71 | #warning not failing if a valid store
| ^~~~~~~
stores/sqStorePartition.C: In member function 'void sqStore::sqStore_buildPartitions(uint32*)':
stores/sqStorePartition.C:94:35: warning: '/partitions' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
94 | snprintf(name, FILENAME_MAX, "%s/partitions", _clonePath);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStorePartition.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStorePartition.C:107:37: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
107 | snprintf(name, FILENAME_MAX, "%s/partitions/blobs.%04d", _clonePath, i);
| ^~~~~~~~~~~~~~~~~~
stores/sqStorePartition.C:107:34: note: directive argument in the range [1, 536870912]
107 | snprintf(name, FILENAME_MAX, "%s/partitions/blobs.%04d", _clonePath, i);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStorePartition.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4124 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStorePartition.C:111:37: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
111 | snprintf(name, FILENAME_MAX, "%s/partitions/reads.%04d", _clonePath, i);
| ^~~~~~~~~~~~~~~~~~
stores/sqStorePartition.C:111:34: note: directive argument in the range [1, 536870912]
111 | snprintf(name, FILENAME_MAX, "%s/partitions/reads.%04d", _clonePath, i);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStorePartition.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4124 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/sqStore.H:88,
from stores/sqStorePartition.C:39:
stores/sqStoreBlobReader.H:66:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
66 | snprintf(N, FILENAME_MAX, "%s/blobs.%04u", storePath, file);
| ^~~~~~~
stores/sqStoreBlobReader.H:66:33: note: directive argument in the range [0, 65535]
66 | snprintf(N, FILENAME_MAX, "%s/blobs.%04u", storePath, file);
| ^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStorePartition.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4109 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStorePartition.C:199:37: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
199 | snprintf(name, FILENAME_MAX, "%s/partitions/blobs.%04d", _clonePath, i);
| ^~~~~~~~~~~~~~~~~~
stores/sqStorePartition.C:199:34: note: directive argument in the range [1, 1073741824]
199 | snprintf(name, FILENAME_MAX, "%s/partitions/blobs.%04d", _clonePath, i);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStorePartition.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStorePartition.C:202:37: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
202 | snprintf(name, FILENAME_MAX, "%s/partitions/reads.%04d", _clonePath, i);
| ^~~~~~~~~~~~~~~~~~
stores/sqStorePartition.C:202:34: note: directive argument in the range [1, 1073741824]
202 | snprintf(name, FILENAME_MAX, "%s/partitions/reads.%04d", _clonePath, i);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStore.H:37,
from stores/sqStorePartition.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStore.C: In member function 'void ovStore::dumpMetaData(uint32, uint32)':
stores/ovStore.C:415:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
415 | fprintf(stdout, "%9u %5u %5u %9u %9u %9lu\n", ii,
| ~~~^
| |
| long unsigned int
| %9llu
......
420 | _index[ii]._overlapID);
| ~~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C
In file included from stores/ovStore.C:59:
stores/ovStore.H: In constructor 'ovStore::ovStore(const char*, sqStore*)':
stores/ovStore.H:77:39: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
77 | snprintf(name, FILENAME_MAX, "%s/info", path);
| ^~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStore.C:59:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStore.C:109:35: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
109 | snprintf(name, FILENAME_MAX, "%s/evalues", _storePath);
| ^~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStore.C:59:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C: In member function 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)':
stores/ovStoreWriter.C:228:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
228 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum);
| ^~~~~~~
stores/ovStoreWriter.C:228:34: note: directive argument in the range [0, 536870910]
228 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4129 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:237:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
237 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i);
| ^~~~~~~
stores/ovStoreWriter.C:237:34: note: directive argument in the range [0, 536870910]
237 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4124 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)':
stores/ovStoreWriter.C:260:35: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
260 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bucket, _sliceNum);
| ^~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeOverlapSlice()':
stores/ovStoreWriter.C:486:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
486 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, _sliceNum);
| ^~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::checkSortingIsComplete()':
stores/ovStoreWriter.C:505:38: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
505 | snprintf(nameF, FILENAME_MAX, "%s/%04u.info", _storePath, i);
| ^
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:506:38: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
506 | snprintf(nameI, FILENAME_MAX, "%s/%04u.index", _storePath, i);
| ^
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C
stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()':
stores/ovStoreWriter.C:537:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
537 | snprintf(name, FILENAME_MAX, "%s/%04u.index", _storePath, ss);
| ^
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:540:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
540 | snprintf(name, FILENAME_MAX, "%s/%04u.info", _storePath, ss);
| ^
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:557:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
557 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, bb);
| ^~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:561:39: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
561 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, ss);
| ^~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:565:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
565 | snprintf(name, FILENAME_MAX, "%s/bucket%04u", _storePath, bb);
| ^~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)':
stores/ovStoreWriter.C:344:40: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
344 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, _sliceNum);
| ^
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/ovStoreWriter.C:56:
stores/ovStore.H:104:39: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
104 | snprintf(name, FILENAME_MAX, "%s/%04u.info", path, index);
| ^
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C
In file included from stores/ovStoreWriter.C:56:
stores/ovStore.H: In member function 'void ovStoreSliceWriter::mergeInfoFiles()':
stores/ovStore.H:79:39: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
79 | snprintf(name, FILENAME_MAX, "%s/%04u.info", path, index);
| ^
stores/ovStore.H:79:36: note: directive argument in the range [1, 107374183]
79 | snprintf(name, FILENAME_MAX, "%s/%04u.info", path, index);
| ^~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4112 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:404:42: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
404 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, ss);
| ^
stores/ovStoreWriter.C:404:39: note: directive argument in the range [1, 107374184]
404 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, ss);
| ^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4113 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/ovStoreWriter.C:56:
stores/ovStore.H:102:39: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
102 | snprintf(name, FILENAME_MAX, "%s/info", path);
| ^~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/tgStore.C:44:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from stores/ovStore.H:43,
from stores/ovStoreFile.C:47:
stores/ovStoreFile.H: In member function 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)':
stores/ovStoreFile.H:89:40: warning: '.oc' directive output may be truncated writing 3 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
89 | snprintf(_name, FILENAME_MAX, "%s.oc", prefix);
| ^~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/ovStore.H:37,
from stores/ovStoreFile.C:47:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 4 and 4100 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C
stores/tgStore.C: In member function 'void tgStore::purgeVersion(uint32)':
stores/tgStore.C:191:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
191 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name);
| ^~~~~~~~
stores/tgStore.C:191:33: note: using the range [-2147483648, 2147483647] for directive argument
191 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C:192:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
192 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name);
| ^~~~~~~~
stores/tgStore.C:192:33: note: using the range [-2147483648, 2147483647] for directive argument
192 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C:193:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
193 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name);
| ^~~~~~~~
stores/tgStore.C:193:33: note: using the range [-2147483648, 2147483647] for directive argument
193 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C: In member function 'void tgStore::dumpMASR(tgStore::tgStoreEntry*&, uint32&, uint32)':
stores/tgStore.C:594:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
594 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V);
| ^~~~~~~~
stores/tgStore.C:594:33: note: using the range [-2147483648, 2147483647] for directive argument
594 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C: In member function 'void tgStore::loadMASR(tgStore::tgStoreEntry*&, uint32&, uint32&, uint32)':
stores/tgStore.C:626:40: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
626 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, i);
| ^~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C:637:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
637 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V);
| ^~~~~~~~
stores/tgStore.C:637:33: note: using the range [-2147483648, 2147483647] for directive argument
637 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C:641:38: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
641 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V);
| ^~~~~~~~
stores/tgStore.C:641:35: note: using the range [-2147483648, 2147483647] for directive argument
641 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C: In member function 'FILE* tgStore::openDB(uint32)':
stores/tgStore.C:695:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
695 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version);
| ^~~~~~~~
stores/tgStore.C:695:33: note: using the range [-2147483648, 2147483647] for directive argument
695 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgTig.C:34:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
stores/tgTig.C: In member function 'void tgTig::dumpLayout(FILE*)':
stores/tgTig.C:452:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
452 | fprintf(stderr, "ERROR: _bases length %ld\n", strlen(_bases));
| ~~^ ~~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
stores/tgTig.C: In member function 'void tgTig::dumpFASTA(FILE*)':
stores/tgTig.C:707:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
707 | ">tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestCircular=%s\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgTig.C: In member function 'void tgTig::dumpFASTQ(FILE*)':
stores/tgTig.C:726:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
726 | "@tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestCircular=%s\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc
In file included from stores/tgTig.H:36,
from stores/tgTigSizeAnalysis.H:41,
from stores/tgTigSizeAnalysis.C:38:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc
stores/tgTig.C: In member function 'bool tgTig::loadLayout(FILE*)':
stores/tgTig.C:470:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
470 | fgets(LINE, LINEmax, F); LINEnum++;
| ~~~~~^~~~~~~~~~~~~~~~~~
stores/tgTig.C:594:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
594 | fgets(LINE, LINEmax, F); LINEnum++;
| ~~~~~^~~~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)':
stores/tgTigSizeAnalysis.C:129:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
129 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat);
| ^~~~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C:130:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
130 | printSummary(out, "lenSuggestCircular", lenSuggestCircular);
| ^~~~~~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C:132:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
132 | printSummary(out, "lenUnassembled", lenUnassembled);
| ^~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C:133:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
133 | printSummary(out, "lenBubble", lenBubble);
| ^~~~~~~~~~~
stores/tgTigSizeAnalysis.C:134:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
134 | printSummary(out, "lenContig", lenContig);
| ^~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/tgTigMultiAlignDisplay.C:42:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from overlapInCore/overlapReadCache.H:37,
from overlapInCore/overlapReadCache.C:30:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C
In file included from utgcns/libNDalign/NDalign.C:36:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utgcns/libNDalign/NDalign.C: In member function 'bool NDalign::processHits()':
utgcns/libNDalign/NDalign.C:660:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
660 | display("NDalign::processHits()-- ", false);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libNDalign/NDalign.C: In member function 'bool NDalign::scanDeltaForBadness(bool, bool)':
utgcns/libNDalign/NDalign.C:724:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
724 | display("NDalign::scanForDeltaBadness()-- ", true);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libNDalign/NDalign.C: In member function 'void NDalign::realignForward(bool, bool)':
utgcns/libNDalign/NDalign.C:774:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
774 | display("NDalign::realignForward()-- ", displayAlign);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libNDalign/NDalign.C: In member function 'void NDalign::realignBackward(bool, bool)':
utgcns/libNDalign/NDalign.C:838:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
838 | display("NDalign::realignBackward()-- ", displayAlign);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C
In file included from /usr/include/c++/9/set:60,
from utility/strings.H:37,
from stores/ovOverlap.H:41,
from stores/ovStore.H:42,
from utgcns/libNDalign/NDalign.H:39,
from utgcns/libNDalign/NDalign.C:34:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const long long unsigned int&>, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair<const long long unsigned int, int>; _KeyOfValue = std::_Select1st<std::pair<const long long unsigned int, int> >; _Compare = std::less<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, int> >]':
/usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, int>, std::_Select1st<std::pair<const long long unsigned int, int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from utgcns/libNDalign/NDalign.H:45,
from utgcns/libNDalign/NDalign.C:34:
/usr/include/c++/9/bits/stl_map.h: In member function 'bool NDalign::findHits()':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, int>, std::_Select1st<std::pair<const long long unsigned int, int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function 'void NDalign::fastFindMersA(bool)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, int>, std::_Select1st<std::pair<const long long unsigned int, int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, int>, std::_Select1st<std::pair<const long long unsigned int, int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function 'void NDalign::fastFindMersB(bool)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, int>, std::_Select1st<std::pair<const long long unsigned int, int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, int>, std::_Select1st<std::pair<const long long unsigned int, int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, int>, std::_Select1st<std::pair<const long long unsigned int, int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C
gfa/gfa.C: In member function 'void gfaSequence::load(char*)':
gfa/gfa.C:123:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
123 | findGFAtokenI(_features, "LN:i:", _length);
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/dumpBlob.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/ovStoreBuild.C
stores/ovStoreBuild.C: In function 'int main(int, char**)':
stores/ovStoreBuild.C:125:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
125 | err.push_back("ERROR: No overlap store (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreBuild.C:128:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
128 | err.push_back("ERROR: No sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/ovStoreConfig.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/ovStoreBucketizer.C
stores/ovStoreConfig.C: In member function 'void ovStoreConfig::assignReadsToSlices(sqStore*, uint64, uint64)':
stores/ovStoreConfig.C:288:76: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
288 | fprintf(stderr, "ERROR: expected %u slices, generated %u instead. %lu overlaps per slice allowed.\n",
| ~~^
| |
| long unsigned int
| %llu
289 | _numSlices, slice, olapsPerSlice);
| ~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
stores/ovStoreConfig.C: In function 'int main(int, char**)':
stores/ovStoreConfig.C:372:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
372 | err.push_back("ERROR: No sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreConfig.C:375:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
375 | err.push_back("ERROR: No input overlap files (-L or last on the command line) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreConfig.C:378:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
378 | err.push_back("ERROR: Can't both -create -describe a config.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreConfig.C:381:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
381 | err.push_back("ERROR: Must supply one of -create or -describe.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreConfig.C:385:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
385 | err.push_back("ERROR: Memory (-M) must be at least 0.25 GB to account for overhead.\n"); // , OVSTORE_MEMORY_OVERHEAD / 1024.0 / 1024.0 / 1024.0
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/ovStoreSorter.C
stores/ovStoreBucketizer.C: In function 'int main(int, char**)':
stores/ovStoreBucketizer.C:139:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
139 | err.push_back("ERROR: No overlap store (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreBucketizer.C:142:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
142 | err.push_back("ERROR: No sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreBucketizer.C:145:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
145 | err.push_back("ERROR: No store configuration (-C) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreBucketizer.C:148:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
148 | err.push_back("ERROR: Invalid or no bucket (-b) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreSorter.C: In function 'int main(int, char**)':
stores/ovStoreSorter.C:167:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
167 | err.push_back("ERROR: No overlap store (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreSorter.C:170:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
170 | err.push_back("ERROR: no slice number (-F) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/ovStoreIndexer.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/ovStoreDump.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/ovStoreStats.C
stores/ovStoreIndexer.C: In function 'int main(int, char**)':
stores/ovStoreIndexer.C:80:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
80 | err.push_back("ERROR: No overlap store (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreIndexer.C:83:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
83 | err.push_back("ERROR: No sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreIndexer.C:86:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
86 | err.push_back("ERROR: No config (-C) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreDump.C: In function 'int main(int, char**)':
stores/ovStoreDump.C:754:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
754 | err.push_back("ERROR: no input seqStore (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreDump.C:757:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
757 | err.push_back("ERROR: no input ovlStore (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreDump.C:760:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
760 | err.push_back("ERROR: -prefix is necessary for -binary output.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/sqStoreCreate.C
In file included from stores/ovStoreStats.C:35:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
stores/ovStoreDump.C: In member function 'void dumpParameters::loadBogartStatus(const char*, uint32)':
stores/ovStoreDump.C:283:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
283 | fgets(NN, FILENAME_MAX, E);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
stores/ovStoreDump.C:299:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
299 | fgets(NN, FILENAME_MAX, E);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
stores/ovStoreDump.C:305:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
305 | fgets(NN, FILENAME_MAX, S);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
stores/ovStoreDump.C:321:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
321 | fgets(NN, FILENAME_MAX, S);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
stores/ovStoreDump.C:327:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
327 | fgets(NN, FILENAME_MAX, G);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
stores/ovStoreDump.C:343:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
343 | fgets(NN, FILENAME_MAX, G);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreate.C: In function 'int main(int, char**)':
stores/sqStoreCreate.C:904:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
904 | err.push_back("ERROR: no seqStore (-o) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreate.C:907:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
907 | err.push_back("ERROR: no input files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreate.C:910:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
910 | err.push_back("ERROR: no genome size (-genomesize) set, needed for coverage filtering (-coverage) to work.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreate.C: In function 'uint32 loadFASTA(char*, char*, char*, int32&, uint8*, compressedFileReader*, FILE*, uint32&)':
stores/sqStoreCreate.C:104:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
104 | fgets(L, AS_MAX_READLEN+1, F->file()); nLines++;
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreate.C:159:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
159 | fgets(L, AS_MAX_READLEN+1, F->file()); nLines++;
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreate.C: In function 'uint32 loadFASTQ(char*, char*, char*, int32&, uint8*, compressedFileReader*, FILE*, uint32&)':
stores/sqStoreCreate.C:220:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
220 | fgets(S, AS_MAX_READLEN+1, F->file());
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreate.C:233:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
233 | fgets(overflow, 1048576, F->file());
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreate.C:289:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
289 | fgets(L, AS_MAX_READLEN+1, F->file()); // NOTE: Using L, not Q, since L is char and Q is uint8
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreate.C:290:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
290 | fgets(L, AS_MAX_READLEN+1, F->file());
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreate.C:302:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
302 | fgets(overflow, 1048576, F->file());
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreate.C: In function 'void loadReads(sqStore*, sqLibrary*, uint32, uint32, FILE*, FILE*, FILE*, char*, uint32&, uint32&, uint64&, uint32&, uint64&)':
stores/sqStoreCreate.C:423:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
423 | fgets(L, AS_MAX_READLEN+1, F->file());
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreate.C:535:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
535 | fgets(L, AS_MAX_READLEN+1, F->file()); lineNumber++;
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sqStoreCreatePartition/stores/sqStoreCreatePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/sqStoreCreatePartition.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqStoreCreatePartition.C:37:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
stores/sqStoreDumpFASTQ.C: In function 'int main(int, char**)':
stores/sqStoreDumpFASTQ.C:502:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
502 | ">%s id=" F_U32 " clr=" F_U32 "," F_U32 "\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreDumpFASTQ.C:506:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
506 | ">read" F_U32 " clr=" F_U32 "," F_U32 "\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreDumpFASTQ.C:512:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
512 | "@%s id=" F_U32 " clr=" F_U32 "," F_U32 "\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreDumpFASTQ.C:517:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
517 | "@read" F_U32 " clr=" F_U32 "," F_U32 "\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreatePartition.C: In function 'int main(int, char**)':
stores/sqStoreCreatePartition.C:193:48: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
193 | (doDelete == false)) err.push_back("ERROR: no seqStore (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreCreatePartition.C:194:48: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
194 | if (tigStorePath == NULL) err.push_back("ERROR: no tigStore (-T) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from stores/ovStoreDump.C:51:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<ovOverlap, int>}; _Tp = std::pair<ovOverlap, int>; _Alloc = std::allocator<std::pair<ovOverlap, int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<ovOverlap, int>}; _Tp = std::pair<ovOverlap, int>; _Alloc = std::allocator<std::pair<ovOverlap, int> >]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from stores/ovStoreDump.C:51:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >; _Distance = int; _Tp = std::pair<ovOverlap, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_LexicographicReverse<ovOverlap, int, sortByPosition> >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTQ()':
stores/sqStoreDumpFASTQ.C:89:36: warning: '.fastq' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
89 | snprintf(N, FILENAME_MAX, "%s.fastq%s", _p, _s);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStoreDumpFASTQ.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 7 and 8197 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreDumpFASTQ.C:87:37: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size between 0 and 4095 [-Wformat-truncation=]
87 | snprintf(N, FILENAME_MAX, "%s.%s.fastq%s", _p, _n, _s);
| ^~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStoreDumpFASTQ.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 8 and 12293 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTA()':
stores/sqStoreDumpFASTQ.C:119:36: warning: '.fasta' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
119 | snprintf(N, FILENAME_MAX, "%s.fasta%s", _p, _s);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStoreDumpFASTQ.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 7 and 8197 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreDumpFASTQ.C:117:37: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size between 0 and 4095 [-Wformat-truncation=]
117 | snprintf(N, FILENAME_MAX, "%s.%s.fasta%s", _p, _n, _s);
| ^~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/sqStoreDumpFASTQ.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 8 and 12293 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >; _Distance = int; _Tp = std::pair<ovOverlap, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_Lexicographic<ovOverlap, int, sortByPosition> >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/sqStoreDumpMetaData.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/tgStoreCompress.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/tgStoreCompress.C:45:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >; _Distance = int; _Tp = std::pair<ovOverlap, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_LexicographicReverse<ovOverlap, int, sortByPosition> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >; _Distance = int; _Tp = std::pair<ovOverlap, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<ovOverlap, int, sortByPosition> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/tgStoreDump.C
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<ovOverlap, int, sortByPosition> >]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
stores/tgStoreDump.C:643:2: warning: #warning replace this with genericStatistics [-Wcpp]
643 | #warning replace this with genericStatistics
| ^~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from stores/ovStoreDump.C:51:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<ovOverlap, int, sortByPosition> >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/tgTigSizeAnalysis.C
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<__gnu_parallel::_Lexicographic<ovOverlap, int, sortByPosition> >]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<ovOverlap, int, sortByPosition> >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/tgStoreDump.C:55:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
stores/tgStoreDump.C: In function 'int main(int, char**)':
stores/tgStoreDump.C:1115:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1115 | err.push_back("No sequence store (-S option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:1118:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1118 | err.push_back("No tig store (-T option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:1121:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1121 | err.push_back("No tig store version (-T option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:1124:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1124 | err.push_back("-coverage needs and output prefix (-o option).\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:1127:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1127 | err.push_back("No DUMP TYPE supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgTigSizeAnalysis.H:41,
from stores/tgTigSizeAnalysis.C:38:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)':
stores/tgTigSizeAnalysis.C:129:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
129 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat);
| ^~~~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C:130:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
130 | printSummary(out, "lenSuggestCircular", lenSuggestCircular);
| ^~~~~~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C:132:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
132 | printSummary(out, "lenUnassembled", lenUnassembled);
| ^~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C:133:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
133 | printSummary(out, "lenBubble", lenBubble);
| ^~~~~~~~~~~
stores/tgTigSizeAnalysis.C:134:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
134 | printSummary(out, "lenContig", lenContig);
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void __gnu_parallel::multiseq_partition(_RanSeqs, _RanSeqs, _RankType, _RankIterator, _Compare) [with _RanSeqs = __gnu_cxx::__normal_iterator<std::pair<ovOverlap*, ovOverlap*>*, std::vector<std::pair<ovOverlap*, ovOverlap*>, std::allocator<std::pair<ovOverlap*, ovOverlap*> > > >; _RankType = int; _RankIterator = __gnu_cxx::__normal_iterator<ovOverlap**, std::vector<ovOverlap*, std::allocator<ovOverlap*> > >; _Compare = sortByPosition]':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from stores/ovStoreDump.C:51:
/usr/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<ovOverlap, int>*, std::vector<std::pair<ovOverlap, int>, std::allocator<std::pair<ovOverlap, int> > > >' changed in GCC 7.1
397 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/tgStoreLoad.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/tgStoreLoad.C:33:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
stores/tgStoreLoad.C: In function 'int main(int, char**)':
stores/tgStoreLoad.C:194:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
194 | err.push_back("ERROR: no sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreLoad.C:196:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
196 | err.push_back("ERROR: no tig store (-T) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreLoad.C:198:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
198 | err.push_back("ERROR: no input tig files supplied on command line or via -L option.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/tgStoreFilter.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/tgTigDisplay.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/loadCorrectedReads.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/tgStoreFilter.C:45:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/tgTigDisplay.C:33:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/loadCorrectedReads.C:29:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility stores/loadErates.C
stores/loadCorrectedReads.C: In function 'int main(int, char**)':
stores/loadCorrectedReads.C:80:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
80 | err.push_back("ERROR: no sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadCorrectedReads.C:82:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
82 | err.push_back("ERROR: no tig store (-T) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadCorrectedReads.C:84:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
84 | err.push_back("ERROR: no input tigs supplied on command line and no -L file supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadCorrectedReads.C:182:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'std::vector<char*>::size_type' {aka 'unsigned int'} [-Wformat=]
182 | fprintf(stderr, "%9" F_U64P " %9" F_U64P " %35" F_U64P "\n", nLoadTot, nSkipTot, corInputs.size());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~
| |
| std::vector<char*>::size_type {aka unsigned int}
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores meryl/meryl.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores meryl/merylCountArray.C
stores/loadTrimmedReads.C: In function 'int main(int, char**)':
stores/loadTrimmedReads.C:76:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
76 | err.push_back("ERROR: no sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp]
261 | #warning HARD CODED NUMBER OF FILES!
| ^~~~~~~
stores/loadErates.C: In function 'int main(int, char**)':
stores/loadErates.C:214:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
214 | err.push_back("ERROR: No overlap store (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadErates.C:217:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
217 | err.push_back("ERROR: No sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadErates.C:220:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
220 | err.push_back("ERROR: No input erate files (-L or last on the command line) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores meryl/merylInput.C
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/meryl.C:46:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/meryl.C:46:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/meryl.C:46:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
In file included from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:97,
from meryl/meryl.H:49,
from meryl/merylCountArray.C:26:
meryl/merylCountArray.H: In instantiation of 'void swv<VALUE>::set(uint64, VALUE) [with VALUE = unsigned int; uint64 = long long unsigned int]':
meryl/merylCountArray.C:205:7: required from 'swv<VALUE>* merylCountArray<VALUE>::unpackSuffixesAndValues(uint64) [with VALUE = unsigned int; uint64 = long long unsigned int]'
meryl/merylCountArray.C:411:16: required from here
utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow]
77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X)))
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK'
41 | _s2 = suffix & uint64MASK(32);
| ^~~~~~~~~~
meryl/merylCountArray.H: In instantiation of 'void swv<VALUE>::set(uint64, VALUE) [with VALUE = long long unsigned int; uint64 = long long unsigned int]':
meryl/merylCountArray.C:205:7: required from 'swv<VALUE>* merylCountArray<VALUE>::unpackSuffixesAndValues(uint64) [with VALUE = long long unsigned int; uint64 = long long unsigned int]'
meryl/merylCountArray.C:412:16: required from here
utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow]
77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X)))
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK'
41 | _s2 = suffix & uint64MASK(32);
| ^~~~~~~~~~
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylInput.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylInput.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylInput.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
meryl/meryl.C: In member function 'void merylOpStack::addPrinter(char*)':
meryl/meryl.C:193:38: warning: '%0*d' directive output may be truncated writing between 1 and 2147483648 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
193 | snprintf(N, FILENAME_MAX, "%s%0*d%s", pre, len, ff, suf);
| ^~~~
meryl/meryl.C:193:35: note: using the range [-2147483648, 2147483647] for directive argument
193 | snprintf(N, FILENAME_MAX, "%s%0*d%s", pre, len, ff, suf);
| ^~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from meryl/meryl.H:49,
from meryl/meryl.C:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output 2 or more bytes (assuming 4098) into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadErates.C: In member function 'void ovStore::addEvalues(std::vector<char*>&)':
stores/loadErates.C:86:41: warning: '/evalues.WORKING' directive output may be truncated writing 16 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
86 | snprintf(evalueTemp, FILENAME_MAX, "%s/evalues.WORKING", _storePath);
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/loadErates.C:43:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 17 and 4113 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadErates.C:87:41: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
87 | snprintf(evalueName, FILENAME_MAX, "%s/evalues", _storePath);
| ^~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from stores/loadErates.C:43:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from stores/loadErates.C:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<evalueFileMap, int>}; _Tp = std::pair<evalueFileMap, int>; _Alloc = std::allocator<std::pair<evalueFileMap, int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<evalueFileMap, int>}; _Tp = std::pair<evalueFileMap, int>; _Alloc = std::allocator<std::pair<evalueFileMap, int> >]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
meryl/meryl.C: In function 'int main(int, char**)':
meryl/meryl.C:331:42: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
331 | snprintf(indexName, FILENAME_MAX, "%s/merylIndex", optString);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from meryl/meryl.H:49,
from meryl/meryl.C:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl.C:332:42: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
332 | snprintf(sqInfName, FILENAME_MAX, "%s/info", optString);
| ^~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from meryl/meryl.H:49,
from meryl/meryl.C:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl.C:333:42: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
333 | snprintf(sqRdsName, FILENAME_MAX, "%s/reads", optString);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from meryl/meryl.H:49,
from meryl/meryl.C:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl.C:594:54: warning: '%s' directive output may be truncated writing up to 4096 bytes into a region of size 996 [-Wformat-truncation=]
594 | snprintf(s, 1024, "Don't know what to do with '%s'.", optString);
| ^~ ~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from meryl/meryl.H:49,
from meryl/meryl.C:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 31 and 4127 bytes into a destination of size 1024
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from stores/loadErates.C:43:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >; _Distance = int; _Tp = std::pair<evalueFileMap, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_LexicographicReverse<evalueFileMap, int, std::less<evalueFileMap> > >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >; _Distance = int; _Tp = std::pair<evalueFileMap, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_Lexicographic<evalueFileMap, int, std::less<evalueFileMap> > >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores meryl/merylOp-count.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores meryl/merylOp-countSimple.C
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-count.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-count.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores meryl/merylOp-histogram.C
In file included from meryl/meryl.H:51,
from meryl/merylOp-count.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >; _Distance = int; _Tp = std::pair<evalueFileMap, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_LexicographicReverse<evalueFileMap, int, std::less<evalueFileMap> > >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
meryl/merylOp-count.C: In function 'uint64 findMaxInputSizeForMemorySize(uint32, uint64)':
meryl/merylOp-count.C:69:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
69 | fprintf(stderr, "For memory size %lu bytes\n", memSize);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
meryl/merylOp-count.C:112:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %10llu
113 | wp, nKmers,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C:112:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %10llu
113 | wp, nKmers,
114 | nPrefix, nSeg,
| ~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C:112:42: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %10llu
113 | wp, nKmers,
114 | nPrefix, nSeg,
| ~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C:112:48: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %10llu
......
115 | mersPerSeg,
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C:112:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %10llu
......
116 | basicMem, ptrMem, dataMem,
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C:112:60: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %10llu
......
116 | basicMem, ptrMem, dataMem,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C:112:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %12llu
......
116 | basicMem, ptrMem, dataMem,
| ~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C: In function 'void findExpectedSimpleSize(uint64, uint64&)':
meryl/merylOp-count.C:157:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
157 | fprintf(stderr, " -> %lu entries for counts up to %u.\n", nEntries, ((uint32)1 << lowBitsSize) - 1);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C:158:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
158 | fprintf(stderr, " -> %lu %cbits memory used\n", scaledNumber(lowMem), scaledUnit(lowMem));
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C:160:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
160 | fprintf(stderr, " %lu input bases\n", nKmerEstimate);
| ~~^ ~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C:161:51: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
161 | fprintf(stderr, " -> expected max count of %lu, needing %lu extra bits.\n", expMaxCount, extraBits);
| ~~^ ~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C:161:64: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
161 | fprintf(stderr, " -> expected max count of %lu, needing %lu extra bits.\n", expMaxCount, extraBits);
| ~~^ ~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C:163:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
163 | fprintf(stderr, " -> %lu %cbits memory used\n", scaledNumber(highMem), scaledUnit(highMem));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C:167:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
167 | fprintf(stderr, " %lu %cB memory needed\n", scaledNumber(totMem), scaledUnit(totMem));
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C: In member function 'void merylOperation::configureCounting(uint64, bool&, uint32&, uint64&, uint32&, uint64&)':
meryl/merylOp-count.C:378:19: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
378 | fprintf(stderr, "Counting %lu (estimated) %s %s%s%s " F_U32 "-mers from " F_SIZE_T " input file%s:\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
379 | scaledNumber(_expNumKmers), scaledName(_expNumKmers),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C: In member function 'void merylOperation::count(uint32, uint64, uint32, uint64)':
meryl/merylOp-count.C:596:69: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
596 | fprintf(stderr, "Used %3.3f GB out of %3.3f GB to store %12lu kmers.\n",
| ~~~~^
| |
| long unsigned int
| %12llu
......
599 | kmersAdded);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >; _Distance = int; _Tp = std::pair<evalueFileMap, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<evalueFileMap, int, std::less<evalueFileMap> > >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<evalueFileMap, int, std::less<evalueFileMap> > >]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from stores/loadErates.C:43:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<evalueFileMap, int, std::less<evalueFileMap> > >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<__gnu_parallel::_Lexicographic<evalueFileMap, int, std::less<evalueFileMap> > >]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<evalueFileMap, int, std::less<evalueFileMap> > >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void __gnu_parallel::multiseq_partition(_RanSeqs, _RanSeqs, _RankType, _RankIterator, _Compare) [with _RanSeqs = __gnu_cxx::__normal_iterator<std::pair<evalueFileMap*, evalueFileMap*>*, std::vector<std::pair<evalueFileMap*, evalueFileMap*>, std::allocator<std::pair<evalueFileMap*, evalueFileMap*> > > >; _RankType = int; _RankIterator = __gnu_cxx::__normal_iterator<evalueFileMap**, std::vector<evalueFileMap*, std::allocator<evalueFileMap*> > >; _Compare = std::less<evalueFileMap>]':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from stores/loadErates.C:43:
/usr/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<evalueFileMap, int>*, std::vector<std::pair<evalueFileMap, int>, std::allocator<std::pair<evalueFileMap, int> > > >' changed in GCC 7.1
397 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-countSimple.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-countSimple.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylOp-countSimple.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-histogram.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-countSimple.C: In member function 'void merylOperation::countSimple()':
meryl/merylOp-countSimple.C:107:76: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
107 | fprintf(stderr, "Increasing to %u-bit storage (for kmer 0x%016lx).\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
108 | lowBitsSize + hib + 1, kidx);
| ~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-countSimple.C:150:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
150 | fprintf(stderr, " nPrefix %lu\n", nPrefix);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
meryl/merylOp-countSimple.C:151:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
151 | fprintf(stderr, " nSuffix %lu\n", nSuffix);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
meryl/merylOp-countSimple.C:152:38: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
152 | fprintf(stderr, " sMask 0x%016lx\n", sMask);
| ~~~~~^ ~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-histogram.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylOp-histogram.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores meryl/merylOp.C
meryl/merylOp-nextMer.C:98:2: warning: #warning "need to decide whic direction we're going?" [-Wcpp]
98 | #warning "need to decide whic direction we're going?"
| ^~~~~~~
meryl/merylOp-nextMer.C:116:2: warning: #warning "rounding issues in word-frequency!" [-Wcpp]
116 | #warning "rounding issues in word-frequency!"
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl-import/meryl/meryl-import.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores meryl/meryl-import.C
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-nextMer.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-nextMer.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylOp-nextMer.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-nextMer.C: In member function 'void merylOperation::initializeThreshold()':
meryl/merylOp-nextMer.C:113:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
113 | fprintf(stderr, "For fraction-distinct %f, found threshold %lu\n", _fracDist, _threshold);
| ~~^ ~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
meryl/merylOp-nextMer.C:121:63: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
121 | fprintf(stderr, "For word-frequency %f, found threshold %lu\n", _wordFreq, _threshold);
| ~~^ ~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
meryl/merylOp-nextMer.C: In member function 'bool merylOperation::nextMer()':
meryl/merylOp-nextMer.C:612:46: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n",
| ~~^
| |
| long unsigned int
| %llu
613 | _kmer.toString(str), _actCount[0], _actCount[1]);
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-nextMer.C:612:70: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n",
| ~~^
| |
| long unsigned int
| %llu
613 | _kmer.toString(str), _actCount[0], _actCount[1]);
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylOp.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
In file included from utility/kmers.H:32,
from meryl/meryl-import.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl-import/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores meryl/merylCountArray.C
In file included from meryl/meryl-import.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylCountArray.H:29,
from meryl/meryl-import.C:31:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
meryl/meryl-import.C: In function 'int main(int, char**)':
meryl/meryl-import.C:92:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
92 | err.push_back("No input kmer file (-kmers) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-import.C:94:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
94 | err.push_back("No output database name (-output) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-import.C:96:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
96 | err.push_back("No kmer size (-k) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-import.C:233:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
233 | fprintf(stderr, "Found %lu kmers in the input.\n", nKmers);
| ~~^ ~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl-lookup/meryl/meryl-lookup.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores meryl/meryl-lookup.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility sequence/sequence.C
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-extract.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility sequence/sequence-extract.C
In file included from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:97,
from meryl/meryl.H:49,
from meryl/merylCountArray.C:26:
meryl/merylCountArray.H: In instantiation of 'void swv<VALUE>::set(uint64, VALUE) [with VALUE = unsigned int; uint64 = long long unsigned int]':
meryl/merylCountArray.C:205:7: required from 'swv<VALUE>* merylCountArray<VALUE>::unpackSuffixesAndValues(uint64) [with VALUE = unsigned int; uint64 = long long unsigned int]'
meryl/merylCountArray.C:411:16: required from here
utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow]
77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X)))
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK'
41 | _s2 = suffix & uint64MASK(32);
| ^~~~~~~~~~
meryl/merylCountArray.H: In instantiation of 'void swv<VALUE>::set(uint64, VALUE) [with VALUE = long long unsigned int; uint64 = long long unsigned int]':
meryl/merylCountArray.C:205:7: required from 'swv<VALUE>* merylCountArray<VALUE>::unpackSuffixesAndValues(uint64) [with VALUE = long long unsigned int; uint64 = long long unsigned int]'
meryl/merylCountArray.C:412:16: required from here
utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow]
77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X)))
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK'
41 | _s2 = suffix & uint64MASK(32);
| ^~~~~~~~~~
In file included from utility/kmers.H:32,
from meryl/meryl-lookup.C:32:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/meryl-lookup.C:32:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C: In function 'void dumpExistence(dnaSeqFile*, kmerCountExactLookup*)':
meryl/meryl-lookup.C:67:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
67 | fprintf(stdout, "%s\t%lu\t%c\t%s\t%lu\t%s\t%lu\n",
| ~~^
| |
| long unsigned int
| %llu
68 | name,
69 | kiter.position(),
| ~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C:67:43: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
67 | fprintf(stdout, "%s\t%lu\t%c\t%s\t%lu\t%s\t%lu\n",
| ~~^
| |
| long unsigned int
| %llu
......
71 | kiter.fmer().toString(fString), fValue,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C:67:52: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
67 | fprintf(stdout, "%s\t%lu\t%c\t%s\t%lu\t%s\t%lu\n",
| ~~^
| |
| long unsigned int
| %llu
......
72 | kiter.rmer().toString(rString), rValue);
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C: In function 'void reportExistence(dnaSeqFile*, kmerCountExactLookup*)':
meryl/meryl-lookup.C:107:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
107 | fprintf(stdout, "%s\t%lu\t%lu\t%lu\n", name, nKmer, kl->nKmers(), nKmerFound);
| ~~^ ~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C:107:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
107 | fprintf(stdout, "%s\t%lu\t%lu\t%lu\n", name, nKmer, kl->nKmers(), nKmerFound);
| ~~^ ~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C:107:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
107 | fprintf(stdout, "%s\t%lu\t%lu\t%lu\n", name, nKmer, kl->nKmers(), nKmerFound);
| ~~^ ~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C: In function 'int main(int, char**)':
meryl/meryl-lookup.C:166:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
166 | err.push_back("No input sequences (-sequence) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-lookup.C:168:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
168 | err.push_back("No query meryl database (-mers) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-lookup.C:170:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
170 | err.push_back("No report-type (-existence, etc) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C: In function 'int main(int, char**)':
sequence/sequence.C:377:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
377 | err.push_back("ERROR: No mode (summarize, extract, generate or simulate) specified.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:381:21: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
381 | err.push_back("ERROR: No input sequence files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:385:21: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
385 | err.push_back("ERROR: No input sequence files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:391:21: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
391 | err.push_back("ERROR: No reference genome sequence (-genome) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:395:21: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
395 | err.push_back("ERROR: No input sequence files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence.C:26:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence.C:26:
/usr/include/c++/9/bits/stl_vector.h: In function 'void decodeRange(char*, std::vector<_Tp>&, std::vector<_Tp>&) [with T = long long unsigned int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-generate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility sequence/sequence-generate.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-mutate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility sequence/sequence-mutate.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-sample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility sequence/sequence-sample.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility sequence/sequence-shiftregister.C
sequence/sequence-generate.C: In function 'void doGenerate(generateParameters&)':
sequence/sequence-generate.C:92:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
92 | ">random%08 " F_U64P "\n", nSeqs);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-simulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility sequence/sequence-simulate.C
sequence/sequence-mutate.C: In function 'void doMutate(std::vector<char*>&, mutateParameters&)':
sequence/sequence-mutate.C:160:50: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
160 | AS_UTL_writeFastA(stdout, nBases, oLen, 0, ">%s\n", seq.name());
| ^~~~~~~
sequence/sequence-sample.C: In function 'void doSample_paired(std::vector<char*>&, sampleParameters&)':
sequence/sequence-sample.C:212:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
212 | AS_UTL_writeFastA(outFile1, seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name());
| ^~~~~~~
sequence/sequence-sample.C:213:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
213 | AS_UTL_writeFastA(outFile2, seq2.bases(), seq2.length(), 0, ">%s\n", seq2.name());
| ^~~~~~~
sequence/sequence-sample.C: In function 'void doSample_single(std::vector<char*>&, sampleParameters&)':
sequence/sequence-sample.C:289:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
289 | AS_UTL_writeFastA(outFile1, seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name());
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility sequence/sequence-summarize.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C
sequence/sequence-simulate.C: In member function 'void simulateParameters::finalize()':
sequence/sequence-simulate.C:42:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
42 | char *path = findSharedFile("share/sequence", distribName);
| ^~~~~~~~~~~~~~~~
sequence/sequence-simulate.C: In function 'void doSimulate_loadSequences(simulateParameters&, std::vector<dnaSeq*>&, uint64&)':
sequence/sequence-simulate.C:86:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<dnaSeq*>::size_type' {aka 'unsigned int'} [-Wformat=]
86 | fprintf(stderr, "Loaded %lu sequences.\n", seqs.size());
| ~~^ ~~~~~~~~~~~
| | |
| long unsigned int std::vector<dnaSeq*>::size_type {aka unsigned int}
| %u
sequence/sequence-simulate.C: In function 'void doSimulate_extract(simulateParameters&, std::vector<dnaSeq*>&, uint64, mtRandom&, uint64, uint64)':
sequence/sequence-simulate.C:191:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
191 | fprintf(stdout, ">read=%lu,%s,position=%lu,length=%u,%s\n",
| ~~^
| |
| long unsigned int
| %llu
192 | nReads+1,
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
sequence/sequence-simulate.C:191:48: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
191 | fprintf(stdout, ">read=%lu,%s,position=%lu,length=%u,%s\n",
| ~~^
| |
| long unsigned int
| %llu
......
194 | position,
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
sequence/sequence-summarize.C: In function 'void doSummarize(std::vector<char*>&, summarizeParameters&)':
sequence/sequence-summarize.C:224:26: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=]
224 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn);
| ~~^
| |
| long unsigned int
| %llu
sequence/sequence-summarize.C:224:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
224 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn);
| ~~^ ~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
sequence/sequence-summarize.C:238:26: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=]
238 | fprintf(stdout, "%lu\n", lengths[ii]);
| ~~^
| |
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {seqEntry}; _Tp = seqEntry; _Alloc = std::allocator<seqEntry>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqEntry>::iterator' {aka '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {seqEntry}; _Tp = seqEntry; _Alloc = std::allocator<seqEntry>]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/parallel/multiway_mergesort.h: In function 'void __gnu_parallel::parallel_sort_mwms(_RAIter, _RAIter, _Compare, __gnu_parallel::_ThreadIndex) [with bool __stable = false; bool __exact = true; _RAIter = __gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >; _Compare = bool (*)(const seqEntry&, const seqEntry&)]':
/usr/include/c++/9/parallel/multiway_mergesort.h:395:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
395 | parallel_sort_mwms(_RAIter __begin, _RAIter __end,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/parallel/multiway_mergesort.h:395:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const seqEntry&, const seqEntry&)>]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const seqEntry&, const seqEntry&)>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >; _Distance = int; _Tp = seqEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const seqEntry&, const seqEntry&)>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const seqEntry&, const seqEntry&)>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/parallel/algo.h: In function 'void std::__parallel::sort(_RAIter, _RAIter, _Compare, _Parallelism) [with _RAIter = __gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >; _Compare = bool (*)(const seqEntry&, const seqEntry&); _Parallelism = __gnu_parallel::default_parallel_tag]':
/usr/include/c++/9/parallel/algo.h:1633:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1633 | sort(_RAIter __begin, _RAIter __end, _Compare __comp,
| ^~~~
/usr/include/c++/9/parallel/algo.h:1633:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
In file included from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/parallel/sort.h:106:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
105 | parallel_sort_mwms<__stable, true>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
106 | (__begin, __end, __comp, __parallelism.__get_num_threads());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/parallel/algo.h: In function 'void doSample_sample(sampleParameters&, uint64, uint64, std::vector<long long unsigned int>&, std::vector<seqEntry>&)':
/usr/include/c++/9/parallel/algo.h:1736:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1736 | sort(__begin, __end, __comp, __gnu_parallel::default_parallel_tag());
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/parallel/algo.h:1736:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1736 | sort(__begin, __end, __comp, __gnu_parallel::default_parallel_tag());
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/bits/stl_vector.h: In function 'void doSample_paired(std::vector<char*>&, sampleParameters&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C
/usr/include/c++/9/bits/stl_vector.h: In function 'void doSample_single(std::vector<char*>&, sampleParameters&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<seqEntry, int>}; _Tp = std::pair<seqEntry, int>; _Alloc = std::allocator<std::pair<seqEntry, int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<seqEntry, int>}; _Tp = std::pair<seqEntry, int>; _Alloc = std::allocator<std::pair<seqEntry, int> >]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >; _Distance = int; _Tp = std::pair<seqEntry, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_LexicographicReverse<seqEntry, int, bool (*)(const seqEntry&, const seqEntry&)> >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >; _Distance = int; _Tp = std::pair<seqEntry, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_Lexicographic<seqEntry, int, bool (*)(const seqEntry&, const seqEntry&)> >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/9/parallel/algo.h:57,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/parallel/merge.h: In function '_OutputIterator __gnu_parallel::__merge_advance_movc(_RAIter1&, _RAIter1, _RAIter2&, _RAIter2, _OutputIterator, _DifferenceTp, _Compare) [with _RAIter1 = seqEntry*; _RAIter2 = seqEntry*; _OutputIterator = __gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >; _DifferenceTp = int; _Compare = bool (*)(const seqEntry&, const seqEntry&)]':
/usr/include/c++/9/parallel/merge.h:105:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
105 | __merge_advance_movc(_RAIter1& __begin1, _RAIter1 __end1,
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/multiway_mergesort.h:40,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::multiway_merge_3_variant(_RAIterIterator, _RAIterIterator, _RAIter3, _DifferenceTp, _Compare) [with iterator = __gnu_parallel::_GuardedIterator; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<seqEntry*, seqEntry*>*, std::vector<std::pair<seqEntry*, seqEntry*>, std::allocator<std::pair<seqEntry*, seqEntry*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >; _DifferenceTp = int; _Compare = bool (*)(const seqEntry&, const seqEntry&)]':
/usr/include/c++/9/parallel/multiway_merge.h:241:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
241 | multiway_merge_3_variant(_RAIterIterator __seqs_begin,
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/parallel/multiway_mergesort.h: In function 'void __gnu_parallel::parallel_sort_mwms(_RAIter, _RAIter, _Compare, __gnu_parallel::_ThreadIndex) [with bool __stable = false; bool __exact = true; _RAIter = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Compare = std::greater<long long unsigned int>]':
/usr/include/c++/9/parallel/multiway_mergesort.h:395:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
395 | parallel_sort_mwms(_RAIter __begin, _RAIter __end,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/parallel/multiway_mergesort.h:395:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<long long unsigned int> >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<long long unsigned int> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
overlapInCore/overlapInCore-Build_Hash_Index.C: In function 'void Mark_Skip_Kmers()':
overlapInCore/overlapInCore-Build_Hash_Index.C:258:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
258 | fgets(line, 1024, F);
| ~~~~~^~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<long long unsigned int> >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/parallel/algo.h: In function 'void std::__parallel::sort(_RAIter, _RAIter, _Compare, _Parallelism) [with _RAIter = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Compare = std::greater<long long unsigned int>; _Parallelism = __gnu_parallel::default_parallel_tag]':
/usr/include/c++/9/parallel/algo.h:1633:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1633 | sort(_RAIter __begin, _RAIter __end, _Compare __comp,
| ^~~~
/usr/include/c++/9/parallel/algo.h:1633:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
In file included from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/parallel/sort.h:106:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
105 | parallel_sort_mwms<__stable, true>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
106 | (__begin, __end, __comp, __parallelism.__get_num_threads());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::multiway_merge_4_variant(_RAIterIterator, _RAIterIterator, _RAIter3, _DifferenceTp, _Compare) [with iterator = __gnu_parallel::_GuardedIterator; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<seqEntry*, seqEntry*>*, std::vector<std::pair<seqEntry*, seqEntry*>, std::allocator<std::pair<seqEntry*, seqEntry*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >; _DifferenceTp = int; _Compare = bool (*)(const seqEntry&, const seqEntry&)]':
/usr/include/c++/9/parallel/multiway_merge.h:360:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
360 | multiway_merge_4_variant(_RAIterIterator __seqs_begin,
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/bits/stl_vector.h: In function 'void doSummarize(std::vector<char*>&, summarizeParameters&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/parallel/algo.h:1736:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1736 | sort(__begin, __end, __comp, __gnu_parallel::default_parallel_tag());
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >; _Distance = int; _Tp = std::pair<seqEntry, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_LexicographicReverse<seqEntry, int, bool (*)(const seqEntry&, const seqEntry&)> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >; _Distance = int; _Tp = std::pair<seqEntry, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<seqEntry, int, bool (*)(const seqEntry&, const seqEntry&)> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<seqEntry, int, bool (*)(const seqEntry&, const seqEntry&)> >]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<seqEntry, int, bool (*)(const seqEntry&, const seqEntry&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<long long unsigned int, int>}; _Tp = std::pair<long long unsigned int, int>; _Alloc = std::allocator<std::pair<long long unsigned int, int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<long long unsigned int, int>}; _Tp = std::pair<long long unsigned int, int>; _Alloc = std::allocator<std::pair<long long unsigned int, int> >]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Distance = int; _Tp = std::pair<long long unsigned int, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_LexicographicReverse<long long unsigned int, int, std::greater<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Distance = int; _Tp = std::pair<long long unsigned int, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::greater<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<__gnu_parallel::_Lexicographic<seqEntry, int, bool (*)(const seqEntry&, const seqEntry&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/multiway_mergesort.h:40,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::multiway_merge_3_variant(_RAIterIterator, _RAIterIterator, _RAIter3, _DifferenceTp, _Compare) [with iterator = __gnu_parallel::_GuardedIterator; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int*, long long unsigned int*>*, std::vector<std::pair<long long unsigned int*, long long unsigned int*>, std::allocator<std::pair<long long unsigned int*, long long unsigned int*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _DifferenceTp = int; _Compare = std::greater<long long unsigned int>]':
/usr/include/c++/9/parallel/multiway_merge.h:241:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
241 | multiway_merge_3_variant(_RAIterIterator __seqs_begin,
| ^~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<seqEntry, int, bool (*)(const seqEntry&, const seqEntry&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void __gnu_parallel::multiseq_partition(_RanSeqs, _RanSeqs, _RankType, _RankIterator, _Compare) [with _RanSeqs = __gnu_cxx::__normal_iterator<std::pair<seqEntry*, seqEntry*>*, std::vector<std::pair<seqEntry*, seqEntry*>, std::allocator<std::pair<seqEntry*, seqEntry*> > > >; _RankType = int; _RankIterator = __gnu_cxx::__normal_iterator<seqEntry**, std::vector<seqEntry*, std::allocator<seqEntry*> > >; _Compare = bool (*)(const seqEntry&, const seqEntry&)]':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<seqEntry, int>*, std::vector<std::pair<seqEntry, int>, std::allocator<std::pair<seqEntry, int> > > >' changed in GCC 7.1
397 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::multiway_merge_4_variant(_RAIterIterator, _RAIterIterator, _RAIter3, _DifferenceTp, _Compare) [with iterator = __gnu_parallel::_GuardedIterator; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int*, long long unsigned int*>*, std::vector<std::pair<long long unsigned int*, long long unsigned int*>, std::allocator<std::pair<long long unsigned int*, long long unsigned int*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _DifferenceTp = int; _Compare = std::greater<long long unsigned int>]':
/usr/include/c++/9/parallel/multiway_merge.h:360:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
360 | multiway_merge_4_variant(_RAIterIterator __seqs_begin,
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/multiway_mergesort.h:40,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::multiway_merge_loser_tree(_RAIterIterator, _RAIterIterator, _RAIter3, _DifferenceTp, _Compare) [with _LT = __gnu_parallel::_LoserTree<false, seqEntry, bool (*)(const seqEntry&, const seqEntry&)>; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<seqEntry*, seqEntry*>*, std::vector<std::pair<seqEntry*, seqEntry*>, std::allocator<std::pair<seqEntry*, seqEntry*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >; _DifferenceTp = int; _Compare = bool (*)(const seqEntry&, const seqEntry&)]':
/usr/include/c++/9/parallel/multiway_merge.h:491:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
491 | multiway_merge_loser_tree(_RAIterIterator __seqs_begin,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Distance = int; _Tp = std::pair<long long unsigned int, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_LexicographicReverse<long long unsigned int, int, std::greater<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Distance = int; _Tp = std::pair<long long unsigned int, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::greater<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::greater<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::greater<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
78 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::greater<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1920:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1920 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1921 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1920:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::greater<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::greater<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void __gnu_parallel::multiseq_partition(_RanSeqs, _RanSeqs, _RankType, _RankIterator, _Compare) [with _RanSeqs = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int*, long long unsigned int*>*, std::vector<std::pair<long long unsigned int*, long long unsigned int*>, std::allocator<std::pair<long long unsigned int*, long long unsigned int*> > > >; _RankType = int; _RankIterator = __gnu_cxx::__normal_iterator<long long unsigned int**, std::vector<long long unsigned int*, std::allocator<long long unsigned int*> > >; _Compare = std::greater<long long unsigned int>]':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
397 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C
/usr/include/c++/9/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::__sequential_multiway_merge(_RAIterIterator, _RAIterIterator, _RAIter3, const typename std::iterator_traits<typename std::iterator_traits<_OI>::value_type::first_type>::value_type&, _DifferenceTp, _Compare) [with bool __stable = false; bool __sentinels = false; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<seqEntry*, seqEntry*>*, std::vector<std::pair<seqEntry*, seqEntry*>, std::allocator<std::pair<seqEntry*, seqEntry*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >; _DifferenceTp = int; _Compare = bool (*)(const seqEntry&, const seqEntry&)]':
/usr/include/c++/9/parallel/multiway_merge.h:920:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
920 | __sequential_multiway_merge(_RAIterIterator __seqs_begin,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/algo.h:57,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/9/parallel/merge.h:178:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
178 | return __merge_advance_movc(__begin1, __end1, __begin2, __end2,
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
179 | __target, __max_length, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/multiway_mergesort.h:40,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/9/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::multiway_merge_loser_tree(_RAIterIterator, _RAIterIterator, _RAIter3, _DifferenceTp, _Compare) [with _LT = __gnu_parallel::_LoserTree<false, long long unsigned int, std::greater<long long unsigned int> >; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int*, long long unsigned int*>*, std::vector<std::pair<long long unsigned int*, long long unsigned int*>, std::allocator<std::pair<long long unsigned int*, long long unsigned int*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _DifferenceTp = int; _Compare = std::greater<long long unsigned int>]':
/usr/include/c++/9/parallel/multiway_merge.h:491:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
491 | multiway_merge_loser_tree(_RAIterIterator __seqs_begin,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::__sequential_multiway_merge(_RAIterIterator, _RAIterIterator, _RAIter3, const typename std::iterator_traits<typename std::iterator_traits<_OI>::value_type::first_type>::value_type&, _DifferenceTp, _Compare) [with bool __stable = false; bool __sentinels = false; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int*, long long unsigned int*>*, std::vector<std::pair<long long unsigned int*, long long unsigned int*>, std::allocator<std::pair<long long unsigned int*, long long unsigned int*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _DifferenceTp = int; _Compare = std::greater<long long unsigned int>]':
/usr/include/c++/9/parallel/multiway_merge.h:920:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
920 | __sequential_multiway_merge(_RAIterIterator __seqs_begin,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
overlapInCore/overlapInCorePartition.C: In function 'int main(int, char**)':
overlapInCore/overlapInCorePartition.C:436:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
436 | FILE *BAT = openOutput(outputPrefix, "ovlbat");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:437:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
437 | FILE *JOB = openOutput(outputPrefix, "ovljob");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:438:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
438 | FILE *OPT = openOutput(outputPrefix, "ovlopt");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:451:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
451 | renameToFinal(outputPrefix, "ovlbat");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:452:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
452 | renameToFinal(outputPrefix, "ovljob");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:453:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
453 | renameToFinal(outputPrefix, "ovlopt");
| ^~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C
overlapInCore/overlapPair.C:479:2: warning: #warning do we need to check for contained too? [-Wcpp]
479 | #warning do we need to check for contained too?
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C
overlapInCore/overlapImport.C: In function 'int main(int, char**)':
overlapInCore/overlapImport.C:158:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
158 | err.push_back("ERROR: no input seqStore (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
overlapInCore/overlapImport.C:161:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
161 | err.push_back("ERROR: no input overlap files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from overlapInCore/overlapReadCache.H:37,
from overlapInCore/overlapPair.C:44:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
overlapInCore/overlapPair.C: In function 'void* recomputeOverlaps(void*)':
overlapInCore/overlapPair.C:429:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
429 | if (extendAlignment(bRead, bbgn, bend, blen, "B", bID,
| ^~~
overlapInCore/overlapPair.C:430:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
430 | aRead, abgn, aend, alen, "A", aID,
| ^~~
overlapInCore/overlapPair.C:437:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
437 | if (extendAlignment(aRead, abgn, aend, alen, "A", aID,
| ^~~
overlapInCore/overlapPair.C:438:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
438 | bRead, bbgn, bend, blen, "B", bID,
| ^~~
overlapInCore/overlapPair.C:506:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
506 | if (extendAlignment(bRead, bbgn, bend, blen, "Bb5", bID,
| ^~~~~
overlapInCore/overlapPair.C:507:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
507 | aRead, abgn, aend, alen, "Ab5", aID,
| ^~~~~
overlapInCore/overlapPair.C:532:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
532 | if (extendAlignment(aRead, abgn, aend, alen, "Aa5", aID,
| ^~~~~
overlapInCore/overlapPair.C:533:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
533 | bRead, bbgn, bend, blen, "Ba5", bID,
| ^~~~~
overlapInCore/overlapPair.C:560:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
560 | if (extendAlignment(aRead, abgn, aend, alen, "Aa3", aID,
| ^~~~~
overlapInCore/overlapPair.C:561:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
561 | bRead, bbgn, bend, blen, "Ba3", bID,
| ^~~~~
overlapInCore/overlapPair.C:586:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
586 | if (extendAlignment(bRead, bbgn, bend, blen, "Bb3", bID,
| ^~~~~
overlapInCore/overlapPair.C:587:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
587 | aRead, abgn, aend, alen, "Ab3", aID,
| ^~~~~
overlapInCore/overlapImport.C:274:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
274 | fgets(S, 1024, in->file());
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
overlapInCore/overlapImport.C:304:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
304 | fgets(S, 1024, in->file());
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
overlapInCore/edalign.C: In function 'bool readLine(FILE*, char*, int32, int32&, splitToWords&)':
overlapInCore/edalign.C:38:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
38 | fgets(line, lineMax, file);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores correction/filterCorrectionOverlaps.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from wtdbg/wtdbgConvert.C:33:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores correction/filterCorrectionLayouts.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from correction/generateCorrectionLayouts.C:37:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
correction/generateCorrectionLayouts.C: In function 'void generateLayout(tgTig*, uint16*, uint32, double, double, ovOverlap*, uint32, FILE*)':
correction/generateCorrectionLayouts.C:118:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
118 | fprintf(logFile, " filter read %9u at position %6u,%6u length %5lu erate %.3f - low quality (threshold %.2f)\n",
| ~~~^
| |
| long unsigned int
| %5llu
119 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate(), maxEvidenceErate);
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
correction/generateCorrectionLayouts.C:125:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
125 | fprintf(logFile, " filter read %9u at position %6u,%6u length %5lu erate %.3f - too short (threshold %u)\n",
| ~~~^
| |
| long unsigned int
| %5llu
126 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate(), minEvidenceLength);
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
correction/generateCorrectionLayouts.C:133:26: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
133 | fprintf(logFile, " filter read %9u at position %6u,%6u length %5lu erate %.3f - filtered by global filter (threshold " F_U16 ")\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
134 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate(), olapThresh[ovl[oo].b_iid]);
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
correction/generateCorrectionLayouts.C:140:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
140 | fprintf(logFile, " filter read %9u at position %6u,%6u length %5lu erate %.3f - duplicate\n",
| ~~~^
| |
| long unsigned int
| %5llu
141 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate());
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
correction/generateCorrectionLayouts.C:146:73: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
146 | fprintf(logFile, " allow read %9u at position %6u,%6u length %5lu erate %.3f\n",
| ~~~^
| |
| long unsigned int
| %5llu
147 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate());
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from utgcns/stashContains.H:35,
from utgcns/stashContains.C:30:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from /usr/include/c++/9/set:60,
from utility/strings.H:37,
from stores/ovOverlap.H:41,
from stores/ovStore.H:42,
from wtdbg/wtdbgConvert.C:31:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const unsigned int&>, std::tuple<>}; _Key = unsigned int; _Val = std::pair<const unsigned int, double>; _KeyOfValue = std::_Select1st<std::pair<const unsigned int, double> >; _Compare = std::less<unsigned int>; _Alloc = std::allocator<std::pair<const unsigned int, double> >]':
/usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const unsigned int, double> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from correction/filterCorrectionLayouts.C:29:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C
In file included from /usr/include/c++/9/map:61,
from stores/tgTig.H:38,
from stores/tgStore.H:43,
from wtdbg/wtdbgConvert.C:33:
/usr/include/c++/9/bits/stl_map.h: In function 'void save_tig(sqStore*, tgStore*, tgTig*, std::map<unsigned int, std::map<unsigned int, int> >&, std::map<unsigned int, std::map<unsigned int, int> >&, std::map<unsigned int, std::map<unsigned int, bool> >&, std::map<unsigned int, bool>&, std::map<unsigned int, std::map<unsigned int, double> >&, std::map<unsigned int, std::map<unsigned int, unsigned int> >&)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const unsigned int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const unsigned int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const unsigned int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from correction/falconsense.C:32:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
correction/falconsense.C: In function 'void generateFalconConsensus(falconConsensus*, tgTig*, sqCache*, std::map<unsigned int, sqRead*>&, std::map<unsigned int, sqReadData*>&, bool, uint32)':
correction/falconsense.C:209:41: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
209 | fprintf(stdout, "(%6u) memory act %10lu est %10lu act/est %.2f", len, fc->getRSS(), mem, fc->getRSS() * 100.0 / mem);
| ~~~~^ ~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %10llu
correction/falconsense.C:209:51: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
209 | fprintf(stdout, "(%6u) memory act %10lu est %10lu act/est %.2f", len, fc->getRSS(), mem, fc->getRSS() * 100.0 / mem);
| ~~~~^ ~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %10llu
correction/falconsense.C: In function 'int main(int, char**)':
correction/falconsense.C:365:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
365 | err.push_back("ERROR: no seqStore input (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
correction/falconsense.C:368:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
368 | err.push_back("ERROR: no corStore input (-C) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
correction/falconsense.C: In function 'void loadReadList(char*, uint32, uint32, std::set<unsigned int>&)':
correction/falconsense.C:70:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
70 | for (fgets(L, 1024, R);
| ~~~~~^~~~~~~~~~~~
correction/falconsense.C:72:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
72 | fgets(L, 1024, R)) {
| ~~~~~^~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from utgcns/stashContains.H:35,
from utgcns/stashContains.C:30:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from correction/filterCorrectionLayouts.C:26:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<readStatus, int>}; _Tp = std::pair<readStatus, int>; _Alloc = std::allocator<std::pair<readStatus, int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<readStatus, int>}; _Tp = std::pair<readStatus, int>; _Alloc = std::allocator<std::pair<readStatus, int> >]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from correction/filterCorrectionLayouts.C:26:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >; _Distance = int; _Tp = std::pair<readStatus, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_LexicographicReverse<readStatus, int, bool (*)(const readStatus&, const readStatus&)> >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >; _Distance = int; _Tp = std::pair<readStatus, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_Lexicographic<readStatus, int, bool (*)(const readStatus&, const readStatus&)> >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
In file included from correction/errorEstimate.C:34:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >; _Distance = int; _Tp = std::pair<readStatus, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_LexicographicReverse<readStatus, int, bool (*)(const readStatus&, const readStatus&)> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >; _Distance = int; _Tp = std::pair<readStatus, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<readStatus, int, bool (*)(const readStatus&, const readStatus&)> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<readStatus, int, bool (*)(const readStatus&, const readStatus&)> >]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from correction/filterCorrectionLayouts.C:26:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<readStatus, int, bool (*)(const readStatus&, const readStatus&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/set:60,
from utility/strings.H:37,
from stores/ovOverlap.H:41,
from stores/ovStore.H:42,
from correction/errorEstimate.C:31:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const unsigned int&>, std::tuple<>}; _Key = unsigned int; _Val = std::pair<const unsigned int, double>; _KeyOfValue = std::_Select1st<std::pair<const unsigned int, double> >; _Compare = std::less<unsigned int>; _Alloc = std::allocator<std::pair<const unsigned int, double> >]':
/usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const unsigned int, double> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from correction/errorEstimate.C:38:
/usr/include/c++/9/bits/stl_map.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<unsigned int, std::pair<const unsigned int, double>, std::_Select1st<std::pair<const unsigned int, double> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const unsigned int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from correction/errorEstimate.C:30:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<double, int>}; _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<double, int>}; _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from correction/errorEstimate.C:30:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Distance = int; _Tp = std::pair<double, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_LexicographicReverse<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Distance = int; _Tp = std::pair<double, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<__gnu_parallel::_Lexicographic<readStatus, int, bool (*)(const readStatus&, const readStatus&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<readStatus, int, bool (*)(const readStatus&, const readStatus&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void __gnu_parallel::multiseq_partition(_RanSeqs, _RanSeqs, _RankType, _RankIterator, _Compare) [with _RanSeqs = __gnu_cxx::__normal_iterator<std::pair<readStatus*, readStatus*>*, std::vector<std::pair<readStatus*, readStatus*>, std::allocator<std::pair<readStatus*, readStatus*> > > >; _RankType = int; _RankIterator = __gnu_cxx::__normal_iterator<readStatus**, std::vector<readStatus*, std::allocator<readStatus*> > >; _Compare = bool (*)(const readStatus&, const readStatus&)]':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from correction/filterCorrectionLayouts.C:26:
/usr/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<readStatus, int>*, std::vector<std::pair<readStatus, int>, std::allocator<std::pair<readStatus, int> > > >' changed in GCC 7.1
397 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Distance = int; _Tp = std::pair<double, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_LexicographicReverse<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Distance = int; _Tp = std::pair<double, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from correction/errorEstimate.C:30:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
78 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1920:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1920 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1921 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1920:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void __gnu_parallel::multiseq_partition(_RanSeqs, _RanSeqs, _RankType, _RankIterator, _Compare) [with _RanSeqs = __gnu_cxx::__normal_iterator<std::pair<double*, double*>*, std::vector<std::pair<double*, double*>, std::allocator<std::pair<double*, double*> > > >; _RankType = int; _RankIterator = __gnu_cxx::__normal_iterator<double**, std::vector<double*, std::allocator<double*> > >; _Compare = std::less<double>]':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from correction/errorEstimate.C:30:
/usr/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
397 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C
In file included from utility/kmers.H:32,
from haplotyping/splitHaplotype.C:30:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from haplotyping/splitHaplotype.C:30:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:520:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
521 | prefix,
522 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:520:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
520 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
523 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
haplotyping/splitHaplotype.C: In member function 'void hapData::initializeKmerTable(uint32)':
haplotyping/splitHaplotype.C:430:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
430 | fprintf(stderr, "-- loaded %lu kmers.\n", nKmers);
| ~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
haplotyping/splitHaplotype.C: In function 'void outputReadBatch(void*, void*)':
haplotyping/splitHaplotype.C:681:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
681 | ">%s\n", s->_names[ii].string());
| ^~~~~~~
haplotyping/splitHaplotype.C: In function 'int main(int, char**)':
haplotyping/splitHaplotype.C:745:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
745 | err.push_back("No input sequences supplied with either (-S) or (-R).\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplotyping/splitHaplotype.C:747:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
747 | err.push_back("Only one type of input reads (-S or -R) supported.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplotyping/splitHaplotype.C:749:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
749 | err.push_back("Not enough haplotypes (-H) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplotyping/splitHaplotype.C:828:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
828 | fprintf(stdout, "-- %8u reads %12lu bases written to haplotype file %s.\n", G->_haps[ii]->nReads, G->_haps[ii]->nBases, G->_haps[ii]->outputName);
| ~~~~^
| |
| long unsigned int
| %12llu
haplotyping/splitHaplotype.C:829:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
829 | fprintf(stdout, "-- %8u reads %12lu bases written to haplotype file %s.\n", G->_ambiguousReads, G->_ambiguousBases, G->_ambiguousName);
| ~~~~^ ~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %12llu
haplotyping/splitHaplotype.C:831:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
831 | fprintf(stdout, "-- %8u reads %12lu bases filtered for being too short.\n", G->_filteredReads, G->_filteredBases);
| ~~~~^ ~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %12llu
overlapBasedTrimming/trimReads.C: In function 'int main(int, char**)':
overlapBasedTrimming/trimReads.C:476:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
476 | readsIn .generatePlots(outputPrefix, "inputReads", 250);
| ^~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:477:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
477 | deletedIn.generatePlots(outputPrefix, "inputDeletedReads", 250);
| ^~~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:478:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
478 | noTrimIn .generatePlots(outputPrefix, "inputNoTrimReads", 250);
| ^~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:488:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
488 | readsOut .generatePlots(outputPrefix, "outputTrimmedReads", 250);
| ^~~~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:489:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
489 | noOvlOut .generatePlots(outputPrefix, "outputNoOvlReads", 250);
| ^~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:490:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
490 | deletedOut .generatePlots(outputPrefix, "outputDeletedReads", 250);
| ^~~~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:491:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
491 | noChangeOut.generatePlots(outputPrefix, "outputUnchangedReads", 250);
| ^~~~~~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:499:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
499 | trim5.generatePlots(outputPrefix, "trim5", 25);
| ^~~~~~~
overlapBasedTrimming/trimReads.C:500:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
500 | trim3.generatePlots(outputPrefix, "trim3", 25);
| ^~~~~~~
In file included from overlapBasedTrimming/trimReads.C:31:
overlapBasedTrimming/trimStat.H: In member function 'void trimStat::generatePlots(char*, char*, uint32)':
overlapBasedTrimming/trimStat.H:78:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
78 | system(N);
| ~~~~~~^~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-quality.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-quality.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustFlipped.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores overlapBasedTrimming/mergeRanges.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C
overlapBasedTrimming/mergeRanges.C: In function 'int main(int, char**)':
overlapBasedTrimming/mergeRanges.C:77:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
77 | err.push_back("ERROR: no sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapAlign/overlapAlign.C:39:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapAlign/computeOverlapAlignment.C:33:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
overlapAlign/computeOverlapAlignment.C: In member function 'void maComputation::computeOverlapAlignment(uint32, uint32, double, uint32, uint32)':
overlapAlign/computeOverlapAlignment.C:246:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
246 | if (computeAlignment(_bRead, bbgn, bend, blen, "B", _bID, // Align all of sequence B into
| ^~~
overlapAlign/computeOverlapAlignment.C:247:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
247 | _aRead, abgn, aend, alen, "A", _aID, // sequence A with free ends.
| ^~~
overlapAlign/computeOverlapAlignment.C:291:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
291 | if (computeAlignment(_aRead, abgn, aend, alen, "A", _aID, // Align all of sequence A into
| ^~~
overlapAlign/computeOverlapAlignment.C:292:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
292 | _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends.
| ^~~
overlapAlign/computeOverlapAlignment.C:339:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
339 | if (computeAlignment(_bRead, bbgn, bend, blen, "B", _bID, // Align all of sequence B into
| ^~~
overlapAlign/computeOverlapAlignment.C:340:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
340 | _aRead, abgn, aend, alen, "A", _aID, // sequence A with free ends.
| ^~~
overlapAlign/computeOverlapAlignment.C:384:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
384 | if (computeAlignment(_aRead, abgn, aend, alen, "A", _aID, // Align all of sequence A into
| ^~~
overlapAlign/computeOverlapAlignment.C:385:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
385 | _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends.
| ^~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapAlign/trimRead.C:33:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapAlign/computeAlignments.C:36:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from overlapErrorAdjustment/findErrors.H:34,
from overlapErrorAdjustment/findErrors.C:30:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = Olap_Info_t*; _Distance = int; _Tp = Olap_Info_t; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<Olap_Info_t> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type 'Olap_Info_t' changed in GCC 9.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = Olap_Info_t*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<Olap_Info_t> >]':
/usr/include/c++/9/bits/stl_heap.h:342:22: note: parameter passing for argument of type '_ValueType' {aka 'Olap_Info_t'} changed in GCC 9.1
342 | std::__adjust_heap(__first, __parent, __len, _GLIBCXX_MOVE(__value),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
343 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:253:25: note: parameter passing for argument of type '_ValueType' {aka 'Olap_Info_t'} changed in GCC 9.1
253 | std::__adjust_heap(__first, _DistanceType(0),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | _DistanceType(__last - __first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
255 | _GLIBCXX_MOVE(__value), __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = Olap_Info_t*; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<Olap_Info_t> >]':
/usr/include/c++/9/bits/stl_heap.h:253:25: note: parameter passing for argument of type '_ValueType' {aka 'Olap_Info_t'} changed in GCC 9.1
253 | std::__adjust_heap(__first, _DistanceType(0),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | _DistanceType(__last - __first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
255 | _GLIBCXX_MOVE(__value), __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from overlapErrorAdjustment/findErrors.H:34,
from overlapErrorAdjustment/findErrors.C:30:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<Olap_Info_t, int>}; _Tp = std::pair<Olap_Info_t, int>; _Alloc = std::allocator<std::pair<Olap_Info_t, int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<Olap_Info_t, int>}; _Tp = std::pair<Olap_Info_t, int>; _Alloc = std::allocator<std::pair<Olap_Info_t, int> >]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from overlapErrorAdjustment/findErrors.H:34,
from overlapErrorAdjustment/findErrors.C:30:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >; _Distance = int; _Tp = std::pair<Olap_Info_t, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_LexicographicReverse<Olap_Info_t, int, std::less<Olap_Info_t> > >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >; _Distance = int; _Tp = std::pair<Olap_Info_t, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_Lexicographic<Olap_Info_t, int, std::less<Olap_Info_t> > >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >; _Distance = int; _Tp = std::pair<Olap_Info_t, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_LexicographicReverse<Olap_Info_t, int, std::less<Olap_Info_t> > >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >; _Distance = int; _Tp = std::pair<Olap_Info_t, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<Olap_Info_t, int, std::less<Olap_Info_t> > >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<Olap_Info_t, int, std::less<Olap_Info_t> > >]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from overlapErrorAdjustment/findErrors.H:34,
from overlapErrorAdjustment/findErrors.C:30:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<Olap_Info_t, int, std::less<Olap_Info_t> > >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<__gnu_parallel::_Lexicographic<Olap_Info_t, int, std::less<Olap_Info_t> > >]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<Olap_Info_t, int, std::less<Olap_Info_t> > >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
overlapErrorAdjustment/findErrors-Dump.C: In function 'int main(int, char**)':
overlapErrorAdjustment/findErrors-Dump.C:66:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
66 | char *typeName[13] = { "IDENT",
| ^~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:67:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
67 | "DELETE",
| ^~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:68:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
68 | "A_SUBST",
| ^~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:69:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
69 | "C_SUBST",
| ^~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:70:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
70 | "G_SUBST",
| ^~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:71:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
71 | "T_SUBST",
| ^~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:72:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
72 | "A_INSERT",
| ^~~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:73:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
73 | "C_INSERT",
| ^~~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:74:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
74 | "G_INSERT",
| ^~~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:75:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
75 | "T_INSERT",
| ^~~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:76:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
76 | "NO_VOTE",
| ^~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:77:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
77 | "EXTENSION",
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void __gnu_parallel::multiseq_partition(_RanSeqs, _RanSeqs, _RankType, _RankIterator, _Compare) [with _RanSeqs = __gnu_cxx::__normal_iterator<std::pair<Olap_Info_t*, Olap_Info_t*>*, std::vector<std::pair<Olap_Info_t*, Olap_Info_t*>, std::allocator<std::pair<Olap_Info_t*, Olap_Info_t*> > > >; _RankType = int; _RankIterator = __gnu_cxx::__normal_iterator<Olap_Info_t**, std::vector<Olap_Info_t*, std::allocator<Olap_Info_t*> > >; _Compare = std::less<Olap_Info_t>]':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from overlapErrorAdjustment/findErrors.H:34,
from overlapErrorAdjustment/findErrors.C:30:
/usr/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<Olap_Info_t, int>*, std::vector<std::pair<Olap_Info_t, int>, std::allocator<std::pair<Olap_Info_t, int> > > >' changed in GCC 7.1
397 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/bogart.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C
bogart/AS_BAT_BestOverlapGraph.C:863:2: warning: #warning what is the error rate of the 'best contained' overlap? [-Wcpp]
863 | #warning what is the error rate of the 'best contained' overlap?
| ^~~~~~~
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/bogart.C:46:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
bogart/bogart.C: In function 'int main(int, char**)':
bogart/bogart.C:280:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
280 | if (erateGraph < 0.0) err.push_back("Invalid overlap error threshold (-eg option); must be at least 0.0.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:281:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
281 | if (erateMax < 0.0) err.push_back("Invalid overlap error threshold (-eM option); must be at least 0.0.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:282:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
282 | if (prefix == NULL) err.push_back("No output prefix name (-o option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:283:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
283 | if (seqStorePath == NULL) err.push_back("No sequence store (-S option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:284:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
284 | if (ovlStorePath == NULL) err.push_back("No overlap store (-O option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:624:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
624 | writeTigsToStore(contigs, prefix, "ctg", true);
| ^~~~~
bogart/bogart.C:644:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
644 | writeTigsToStore(unitigs, prefix, "utg", true);
| ^~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_BestOverlapGraph.C:46:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/AS_BAT_AssemblyGraph.C:28:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C
bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp]
486 | #warning deviationGraph hard coded
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_AssemblyGraph.C:26:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BestPlacement&}; _Tp = BestPlacement; _Alloc = std::allocator<BestPlacement>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BestPlacement>::iterator' {aka '__gnu_cxx::__normal_iterator<BestPlacement*, std::vector<BestPlacement> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BestPlacement>::iterator' {aka '__gnu_cxx::__normal_iterator<BestPlacement*, std::vector<BestPlacement> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_AssemblyGraph.C:26:
/usr/include/c++/9/bits/stl_vector.h: In function '_ZN13AssemblyGraph10buildGraphEPKcdR9TigVectorb._omp_fn.0':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BestPlacement*, std::vector<BestPlacement> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/AS_BAT_CreateUnitigs.C:29:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_AssemblyGraph.C:26:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BestPlacement}; _Tp = BestPlacement; _Alloc = std::allocator<BestPlacement>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BestPlacement>::iterator' {aka '__gnu_cxx::__normal_iterator<BestPlacement*, std::vector<BestPlacement> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void AssemblyGraph::rebuildGraph(TigVector&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BestPlacement*, std::vector<BestPlacement> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_DetectSpurs.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_DetectSpurs.C:31:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<double, int>}; _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<double, int>}; _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Distance = int; _Tp = std::pair<double, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_LexicographicReverse<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Distance = int; _Tp = std::pair<double, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Distance = int; _Tp = std::pair<double, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_LexicographicReverse<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Distance = int; _Tp = std::pair<double, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
78 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1920:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1920 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1921 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1920:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<double, int, std::less<double> > >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void __gnu_parallel::multiseq_partition(_RanSeqs, _RanSeqs, _RankType, _RankIterator, _Compare) [with _RanSeqs = __gnu_cxx::__normal_iterator<std::pair<double*, double*>*, std::vector<std::pair<double*, double*>, std::allocator<std::pair<double*, double*> > > >; _RankType = int; _RankIterator = __gnu_cxx::__normal_iterator<double**, std::vector<double*, std::allocator<double*> > >; _Compare = std::less<double>]':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > > >' changed in GCC 7.1
397 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/AS_BAT_DropDeadEnds.C:29:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_Instrumentation.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_Instrumentation.C:43:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C
bogart/AS_BAT_Instrumentation.C: In function 'void reportTigs(TigVector&, const char*, const char*, uint64)':
bogart/AS_BAT_Instrumentation.C:408:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
408 | writeTigsToStore(tigs, getLogFilePrefix(), "tig", false);
| ^~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/AS_BAT_MarkRepeatReads.C:29:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
bogart/AS_BAT_Logging.C: In member function 'void logFileInstance::open()':
bogart/AS_BAT_Logging.C:91:37: warning: '.num' directive output may be truncated writing 4 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
91 | snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part);
| ^~~~
bogart/AS_BAT_Logging.C:91:34: note: using the range [-2147483648, 2147483647] for directive argument
91 | snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part);
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from bogart/AS_BAT_Logging.H:41,
from bogart/AS_BAT_Logging.C:38:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4115 bytes into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_MergeOrphans.C:35:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_OptimizePositions.C
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_MergeOrphans.C:30:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const overlapPlacement&}; _Tp = overlapPlacement; _Alloc = std::allocator<overlapPlacement>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<overlapPlacement>::iterator' {aka '__gnu_cxx::__normal_iterator<overlapPlacement*, std::vector<overlapPlacement> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_MergeOrphans.C:30:
/usr/include/c++/9/bits/stl_vector.h: In function 'void assignReadsToTargets(Unitig*, std::vector<overlapPlacement>*, std::vector<candidatePop*>)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<overlapPlacement*, std::vector<overlapPlacement> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_OptimizePositions.C:40:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
/usr/include/c++/9/bits/stl_vector.h: In function '_Z24findOrphanReadPlacementsR9TigVectorRSt3mapIjSt6vectorIjSaIjEESt4lessIjESaISt4pairIKjS4_EEEd._omp_fn.0':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<overlapPlacement*, std::vector<overlapPlacement> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_Outputs.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_Outputs.C:47:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_OverlapCache.C:49:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from bogart/AS_BAT_Outputs.C:51:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_PlaceContains.C:43:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_OverlapCache.C:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<long long unsigned int, int>}; _Tp = std::pair<long long unsigned int, int>; _Alloc = std::allocator<std::pair<long long unsigned int, int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<long long unsigned int, int>}; _Tp = std::pair<long long unsigned int, int>; _Alloc = std::allocator<std::pair<long long unsigned int, int> >]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_OverlapCache.C:46:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Distance = int; _Tp = std::pair<long long unsigned int, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_LexicographicReverse<long long unsigned int, int, std::less<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Distance = int; _Tp = std::pair<long long unsigned int, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::less<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Distance = int; _Tp = std::pair<long long unsigned int, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_LexicographicReverse<long long unsigned int, int, std::less<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Distance = int; _Tp = std::pair<long long unsigned int, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::less<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::less<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_OverlapCache.C:46:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::less<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
78 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::less<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1920:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1920 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1921 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1920:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::less<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<long long unsigned int, int, std::less<long long unsigned int> > >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void __gnu_parallel::multiseq_partition(_RanSeqs, _RanSeqs, _RankType, _RankIterator, _Compare) [with _RanSeqs = __gnu_cxx::__normal_iterator<std::pair<long long unsigned int*, long long unsigned int*>*, std::vector<std::pair<long long unsigned int*, long long unsigned int*>, std::allocator<std::pair<long long unsigned int*, long long unsigned int*> > > >; _RankType = int; _RankIterator = __gnu_cxx::__normal_iterator<long long unsigned int**, std::vector<long long unsigned int*, std::allocator<long long unsigned int*> > >; _Compare = std::less<long long unsigned int>]':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_OverlapCache.C:46:
/usr/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<long long unsigned int, int>*, std::vector<std::pair<long long unsigned int, int>, std::allocator<std::pair<long long unsigned int, int> > > >' changed in GCC 7.1
397 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_PlaceReadUsingOverlaps.C:43:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_PopulateUnitig.C:42:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_PromoteToSingleton.C
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const overlapPlacement&}; _Tp = overlapPlacement; _Alloc = std::allocator<overlapPlacement>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<overlapPlacement>::iterator' {aka '__gnu_cxx::__normal_iterator<overlapPlacement*, std::vector<overlapPlacement> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_ReadInfo.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_PromoteToSingleton.C:40:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'bool placeReadUsingOverlaps(TigVector&, Unitig*, uint32, std::vector<overlapPlacement>&, uint32)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<overlapPlacement*, std::vector<overlapPlacement> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_SetParentAndHang.C
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<overlapPlacement, int>}; _Tp = std::pair<overlapPlacement, int>; _Alloc = std::allocator<std::pair<overlapPlacement, int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<overlapPlacement, int>}; _Tp = std::pair<overlapPlacement, int>; _Alloc = std::allocator<std::pair<overlapPlacement, int> >]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >; _Distance = int; _Tp = std::pair<overlapPlacement, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_LexicographicReverse<overlapPlacement, int, bool (*)(const overlapPlacement&, const overlapPlacement&)> >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >; _Distance = int; _Tp = std::pair<overlapPlacement, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_Lexicographic<overlapPlacement, int, bool (*)(const overlapPlacement&, const overlapPlacement&)> >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_SplitDiscontinuous.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_TigGraph.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_SetParentAndHang.C:41:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_SplitDiscontinuous.C:41:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >; _Distance = int; _Tp = std::pair<overlapPlacement, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_LexicographicReverse<overlapPlacement, int, bool (*)(const overlapPlacement&, const overlapPlacement&)> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >; _Distance = int; _Tp = std::pair<overlapPlacement, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<overlapPlacement, int, bool (*)(const overlapPlacement&, const overlapPlacement&)> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<overlapPlacement, int, bool (*)(const overlapPlacement&, const overlapPlacement&)> >]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<overlapPlacement, int, bool (*)(const overlapPlacement&, const overlapPlacement&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<__gnu_parallel::_Lexicographic<overlapPlacement, int, bool (*)(const overlapPlacement&, const overlapPlacement&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<overlapPlacement, int, bool (*)(const overlapPlacement&, const overlapPlacement&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void __gnu_parallel::multiseq_partition(_RanSeqs, _RanSeqs, _RankType, _RankIterator, _Compare) [with _RanSeqs = __gnu_cxx::__normal_iterator<std::pair<overlapPlacement*, overlapPlacement*>*, std::vector<std::pair<overlapPlacement*, overlapPlacement*>, std::allocator<std::pair<overlapPlacement*, overlapPlacement*> > > >; _RankType = int; _RankIterator = __gnu_cxx::__normal_iterator<overlapPlacement**, std::vector<overlapPlacement*, std::allocator<overlapPlacement*> > >; _Compare = bool (*)(const overlapPlacement&, const overlapPlacement&)]':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39:
/usr/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<overlapPlacement, int>*, std::vector<std::pair<overlapPlacement, int>, std::allocator<std::pair<overlapPlacement, int> > > >' changed in GCC 7.1
397 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_TigVector.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/AS_BAT_TigGraph.C:28:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_TigVector.C:28:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_AddRead.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_Unitig.C:39:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogus/bogus/bogus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogus/bogus.C
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_Unitig_AddRead.C:43:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from bogart/AS_BAT_Unitig.H:45,
from bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C:43:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:506:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:506:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
506 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:507:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
507 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:508:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogus/bogus/bogusUtil.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores bogus/bogusUtil.C
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C
bogus/bogusUtil.C: In function 'void loadNucmer(char*, std::vector<genomeAlignment>&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<referenceSequence>&, std::map<std::__cxx11::basic_string<char>, unsigned int>&, double)':
bogus/bogusUtil.C:125:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
125 | fgets(inLine, 1024, inFile); // (file paths)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
bogus/bogusUtil.C:126:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
126 | fgets(inLine, 1024, inFile); // NUCMER
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
bogus/bogusUtil.C:127:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
127 | fgets(inLine, 1024, inFile); // (blank)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
bogus/bogusUtil.C:128:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
128 | fgets(inLine, 1024, inFile); // (header)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
bogus/bogusUtil.C:142:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
142 | fgets(inLine, 1024, inFile);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
bogus/bogusUtil.C:200:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
200 | fgets(inLine, 1024, inFile);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
bogus/bogusUtil.C: In function 'void loadSnapper(char*, std::vector<genomeAlignment>&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<referenceSequence>&, std::map<std::__cxx11::basic_string<char>, unsigned int>&, double)':
bogus/bogusUtil.C:226:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
226 | fgets(inLine, 1024, inFile);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
bogus/bogusUtil.C:274:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
274 | fgets(inLine, 1024, inFile);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
bogus/bogusUtil.C: In function 'void loadReferenceSequence(char*, std::vector<referenceSequence>&, std::map<std::__cxx11::basic_string<char>, unsigned int>&)':
bogus/bogusUtil.C:300:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
300 | fgets(refhdr, 1024, F); chomp(refhdr);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogus/bogusUtil.C:301:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
301 | fgets(refseq, MAX_GENOME_SIZE_INPUT, F); chomp(refseq);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogus/bogusUtil.C:326:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
326 | fgets(refhdr, 1024, F); chomp(refhdr);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogus/bogusUtil.C:327:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
327 | fgets(refseq, MAX_GENOME_SIZE_INPUT, F); chomp(refseq);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from utgcns/utgcns.C:46:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/parallel/multiway_mergesort.h: In function 'void __gnu_parallel::parallel_sort_mwms(_RAIter, _RAIter, _Compare, __gnu_parallel::_ThreadIndex) [with bool __stable = false; bool __exact = true; _RAIter = __gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >; _Compare = bool (*)(const genomeAlignment&, const genomeAlignment&)]':
/usr/include/c++/9/parallel/multiway_mergesort.h:395:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
395 | parallel_sort_mwms(_RAIter __begin, _RAIter __end,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/parallel/multiway_mergesort.h:395:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
utgcns/utgcns.C: In function 'int main(int, char**)':
utgcns/utgcns.C:231:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
231 | err.push_back("ERROR: No seqStore (-S) and no package (-p) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/utgcns.C:234:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
234 | err.push_back("ERROR: No tigStore (-T) OR no test tig (-t) OR no package (-p) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const genomeAlignment&, const genomeAlignment&)>]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const genomeAlignment&, const genomeAlignment&)>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogusUtil.C:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const genomeAlignment&}; _Tp = genomeAlignment; _Alloc = std::allocator<genomeAlignment>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<genomeAlignment>::iterator' {aka '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogusUtil.C:43:
/usr/include/c++/9/bits/stl_vector.h: In function 'void addAlignment(std::vector<genomeAlignment>&, int32, int32, int32, bool, int32, int32, double, int32, int32, int32)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >; _Distance = int; _Tp = genomeAlignment; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const genomeAlignment&, const genomeAlignment&)>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const genomeAlignment&, const genomeAlignment&)>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/parallel/algo.h: In function 'void std::__parallel::sort(_RAIter, _RAIter, _Compare, _Parallelism) [with _RAIter = __gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >; _Compare = bool (*)(const genomeAlignment&, const genomeAlignment&); _Parallelism = __gnu_parallel::default_parallel_tag]':
/usr/include/c++/9/parallel/algo.h:1633:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1633 | sort(_RAIter __begin, _RAIter __end, _Compare __comp,
| ^~~~
/usr/include/c++/9/parallel/algo.h:1633:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
In file included from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/parallel/sort.h:106:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
105 | parallel_sort_mwms<__stable, true>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
106 | (__begin, __end, __comp, __parallelism.__get_num_threads());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/parallel/algo.h: In function 'int main(int, char**)':
/usr/include/c++/9/parallel/algo.h:1736:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1736 | sort(__begin, __end, __comp, __gnu_parallel::default_parallel_tag());
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/parallel/algo.h:1736:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1736 | sort(__begin, __end, __comp, __gnu_parallel::default_parallel_tag());
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void loadSnapper(char*, std::vector<genomeAlignment>&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<referenceSequence>&, std::map<std::__cxx11::basic_string<char>, unsigned int>&, double)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/parallel/multiway_mergesort.h:35,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<genomeAlignment, int>}; _Tp = std::pair<genomeAlignment, int>; _Alloc = std::allocator<std::pair<genomeAlignment, int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<genomeAlignment, int>}; _Tp = std::pair<genomeAlignment, int>; _Alloc = std::allocator<std::pair<genomeAlignment, int> >]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >; _Distance = int; _Tp = std::pair<genomeAlignment, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_LexicographicReverse<genomeAlignment, int, bool (*)(const genomeAlignment&, const genomeAlignment&)> >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >; _Distance = int; _Tp = std::pair<genomeAlignment, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<__gnu_parallel::_Lexicographic<genomeAlignment, int, bool (*)(const genomeAlignment&, const genomeAlignment&)> >]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/9/parallel/algo.h:57,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/parallel/merge.h: In function '_OutputIterator __gnu_parallel::__merge_advance_movc(_RAIter1&, _RAIter1, _RAIter2&, _RAIter2, _OutputIterator, _DifferenceTp, _Compare) [with _RAIter1 = genomeAlignment*; _RAIter2 = genomeAlignment*; _OutputIterator = __gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >; _DifferenceTp = int; _Compare = bool (*)(const genomeAlignment&, const genomeAlignment&)]':
/usr/include/c++/9/parallel/merge.h:105:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
105 | __merge_advance_movc(_RAIter1& __begin1, _RAIter1 __end1,
| ^~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void loadNucmer(char*, std::vector<genomeAlignment>&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<referenceSequence>&, std::map<std::__cxx11::basic_string<char>, unsigned int>&, double)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C
In file included from /usr/include/c++/9/parallel/multiway_mergesort.h:40,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::multiway_merge_3_variant(_RAIterIterator, _RAIterIterator, _RAIter3, _DifferenceTp, _Compare) [with iterator = __gnu_parallel::_GuardedIterator; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<genomeAlignment*, genomeAlignment*>*, std::vector<std::pair<genomeAlignment*, genomeAlignment*>, std::allocator<std::pair<genomeAlignment*, genomeAlignment*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >; _DifferenceTp = int; _Compare = bool (*)(const genomeAlignment&, const genomeAlignment&)]':
/usr/include/c++/9/parallel/multiway_merge.h:241:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
241 | multiway_merge_3_variant(_RAIterIterator __seqs_begin,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::multiway_merge_4_variant(_RAIterIterator, _RAIterIterator, _RAIter3, _DifferenceTp, _Compare) [with iterator = __gnu_parallel::_GuardedIterator; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<genomeAlignment*, genomeAlignment*>*, std::vector<std::pair<genomeAlignment*, genomeAlignment*>, std::allocator<std::pair<genomeAlignment*, genomeAlignment*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >; _DifferenceTp = int; _Compare = bool (*)(const genomeAlignment&, const genomeAlignment&)]':
/usr/include/c++/9/parallel/multiway_merge.h:360:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
360 | multiway_merge_4_variant(_RAIterIterator __seqs_begin,
| ^~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from utgcns/stashContains.H:35,
from utgcns/stashContains.C:30:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >; _Distance = int; _Tp = std::pair<genomeAlignment, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_LexicographicReverse<genomeAlignment, int, bool (*)(const genomeAlignment&, const genomeAlignment&)> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >; _Distance = int; _Tp = std::pair<genomeAlignment, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<genomeAlignment, int, bool (*)(const genomeAlignment&, const genomeAlignment&)> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<genomeAlignment, int, bool (*)(const genomeAlignment&, const genomeAlignment&)> >]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<genomeAlignment, int, bool (*)(const genomeAlignment&, const genomeAlignment&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<__gnu_parallel::_Lexicographic<genomeAlignment, int, bool (*)(const genomeAlignment&, const genomeAlignment&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<__gnu_parallel::_Lexicographic<genomeAlignment, int, bool (*)(const genomeAlignment&, const genomeAlignment&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void __gnu_parallel::multiseq_partition(_RanSeqs, _RanSeqs, _RankType, _RankIterator, _Compare) [with _RanSeqs = __gnu_cxx::__normal_iterator<std::pair<genomeAlignment*, genomeAlignment*>*, std::vector<std::pair<genomeAlignment*, genomeAlignment*>, std::allocator<std::pair<genomeAlignment*, genomeAlignment*> > > >; _RankType = int; _RankIterator = __gnu_cxx::__normal_iterator<genomeAlignment**, std::vector<genomeAlignment*, std::allocator<genomeAlignment*> > >; _Compare = bool (*)(const genomeAlignment&, const genomeAlignment&)]':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/bits/stl_heap.h:397:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<genomeAlignment, int>*, std::vector<std::pair<genomeAlignment, int>, std::allocator<std::pair<genomeAlignment, int> > > >' changed in GCC 7.1
397 | std::__make_heap(__first, __last, __cmp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/multiway_mergesort.h:40,
from /usr/include/c++/9/parallel/sort.h:44,
from /usr/include/c++/9/parallel/algo.h:45,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::multiway_merge_loser_tree(_RAIterIterator, _RAIterIterator, _RAIter3, _DifferenceTp, _Compare) [with _LT = __gnu_parallel::_LoserTreePointer<false, genomeAlignment, bool (*)(const genomeAlignment&, const genomeAlignment&)>; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<genomeAlignment*, genomeAlignment*>*, std::vector<std::pair<genomeAlignment*, genomeAlignment*>, std::allocator<std::pair<genomeAlignment*, genomeAlignment*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >; _DifferenceTp = int; _Compare = bool (*)(const genomeAlignment&, const genomeAlignment&)]':
/usr/include/c++/9/parallel/multiway_merge.h:491:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
491 | multiway_merge_loser_tree(_RAIterIterator __seqs_begin,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from utgcns/unitigConsensus.H:67,
from utgcns/unitigConsensus.C:74:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C
/usr/include/c++/9/parallel/multiway_merge.h: In function '_RAIter3 __gnu_parallel::__sequential_multiway_merge(_RAIterIterator, _RAIterIterator, _RAIter3, const typename std::iterator_traits<typename std::iterator_traits<_OI>::value_type::first_type>::value_type&, _DifferenceTp, _Compare) [with bool __stable = false; bool __sentinels = false; _RAIterIterator = __gnu_cxx::__normal_iterator<std::pair<genomeAlignment*, genomeAlignment*>*, std::vector<std::pair<genomeAlignment*, genomeAlignment*>, std::allocator<std::pair<genomeAlignment*, genomeAlignment*> > > >; _RAIter3 = __gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >; _DifferenceTp = int; _Compare = bool (*)(const genomeAlignment&, const genomeAlignment&)]':
/usr/include/c++/9/parallel/multiway_merge.h:920:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
920 | __sequential_multiway_merge(_RAIterIterator __seqs_begin,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/parallel/algo.h:57,
from /usr/include/c++/9/parallel/algorithm:37,
from /usr/include/c++/9/algorithm:80,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:113,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/9/parallel/merge.h:178:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
178 | return __merge_advance_movc(__begin1, __end1, __begin2, __end2,
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
179 | __target, __max_length, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from gfa/alignGFA.C:28:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:719:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
719 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
gfa/alignGFA.C: In function 'bool checkRecord(bedRecord*, sequences&, sequences&, bool, bool)':
gfa/alignGFA.C:481:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
481 | success &= checkRecord_align("ALL",
| ^~~~~
gfa/alignGFA.C:509:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
509 | success &= checkRecord_align("LEFT",
| ^~~~~~
gfa/alignGFA.C:515:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
515 | success &= checkRecord_align("RIGHT",
| ^~~~~~~
gfa/alignGFA.C: In function 'void processBEDtoGFA(char*, uint32, char*, char*, uint32)':
gfa/alignGFA.C:740:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
740 | gfaFile *gfa = new gfaFile("H\tVN:Z:1.0");
| ^~~~~~~~~~~~~
cp -pf pipelines/canu.pl /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/canu
chmod +x /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/canu
cp -pf pipelines/canu-time.pl /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/canu-time
chmod +x /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/canu-time
echo > /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here."
chmod -x /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/canu.defaults
cp -pf sequence/share/ultra-long-nanopore /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/share/sequence/ultra-long-nanopore
gfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)':
gfa/alignGFA.C:151:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
151 | system(Pfile);
| ~~~~~~^~~~~~~
cp -pf sequence/share/pacbio /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/share/sequence/pacbio
cp -pf sequence/share/pacbio-hifi /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/share/sequence/pacbio-hifi
cp -pf pipelines/canu/Consensus.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/CorrectReads.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/HaplotypeReads.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Configure.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Defaults.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Execution.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/SequenceStore.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_Cloud.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_DNANexus.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_LSF.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_PBSTorque.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_SGE.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_Slurm.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Meryl.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Output.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapBasedTrimming.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapErrorAdjustment.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapInCore.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapMhap.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapMMap.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapStore.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Report.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Unitig.pm /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/site_perl/canu/
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/AS_global.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.9+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap AS_global.C
gfa/alignGFA.C:129:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=]
129 | sprintf(Pname, "plot-%s-%s", Aname, Bname);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from gfa/alignGFA.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 8199 bytes into a destination of size 4097
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gfa/alignGFA.C:130:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=]
130 | sprintf(Pfile, "plot-%s-%s.sh", Aname, Bname);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from gfa/alignGFA.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 10 and 8202 bytes into a destination of size 4097
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gfa/alignGFA.C:149:27: warning: '%s' directive writing up to 4096 bytes into a region of size 4089 [-Wformat-overflow=]
149 | sprintf(Pfile, "sh plot-%s-%s.sh", Aname, Bname);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-1.9+dfsg/src/AS_global.H:75,
from gfa/alignGFA.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 13 and 8205 bytes into a destination of size 4097
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AS_global.C: In function 'int AS_configure(int, char**)':
AS_global.C:161:29: warning: '%llu' directive output may be truncated writing between 1 and 20 bytes into a region of size between 0 and 4095 [-Wformat-truncation=]
161 | snprintf(N, FILENAME_MAX, "%s/" F_U64 "_%s_" F_U64 "_%s",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from AS_global.H:75,
from AS_global.C:38:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output 7 or more bytes (assuming 5125) into a destination of size 4096
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ar rv /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/libcanu.a /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/AS_global.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/edlib.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-buffered.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-compressed.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-memoryMapped.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/strings.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system-stackTrace.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sequence.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-reader.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-block.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-stream.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-statistics.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-exact.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/bits.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/hexDump.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/md5.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/mt19937ar.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/objectStore.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/speedCounter.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sweatShop.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/computeGlobalScore.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqCache.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqLibrary.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStore.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreConstructor.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreInfo.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreEncode.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStorePartition.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovOverlap.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStore.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreWriter.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFilter.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFile.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreHistogram.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgStore.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTig.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/gfa.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/bed.o
ar: creating /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib/libcanu.a
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/AS_global.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/edlib.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-buffered.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-compressed.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-memoryMapped.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/strings.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system-stackTrace.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sequence.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-reader.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-block.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-stream.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-statistics.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-exact.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/bits.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/hexDump.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/md5.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/mt19937ar.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/objectStore.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/speedCounter.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sweatShop.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/computeGlobalScore.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqCache.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqLibrary.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStore.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreConstructor.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreInfo.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreEncode.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStorePartition.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovOverlap.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStore.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreWriter.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFilter.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFile.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreHistogram.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgStore.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTig.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/gfa.o
a - /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/bed.o
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/dumpBlob -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/ovStoreBuild -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/ovStoreConfig -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/ovStoreBucketizer -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/ovStoreSorter -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/ovStoreIndexer -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/ovStoreDump -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/ovStoreStats -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/sqStoreCreate -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/sqStoreCreatePartition -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sqStoreCreatePartition/stores/sqStoreCreatePartition.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/sqStoreDumpFASTQ -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/sqStoreDumpMetaData -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/tgStoreCompress -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/tgStoreDump -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/tgStoreDump/stores/tgStoreDump.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/tgStoreLoad -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/tgStoreFilter -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/tgTigDisplay -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/loadCorrectedReads -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/loadTrimmedReads -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/loadErates -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/loadErates/stores/loadErates.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/meryl -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/meryl.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylCountArray.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylInput.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-count.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-countSimple.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-histogram.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-nextMer.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/meryl-import -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl-import/meryl/meryl-import.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl-import/meryl/merylCountArray.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/meryl-lookup -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/meryl-lookup/meryl/meryl-lookup.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/sequence -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-extract.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-generate.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-mutate.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-sample.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-simulate.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-summarize.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/overlapInCore -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/overlapInCorePartition -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/overlapConvert -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/overlapImport -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapImport/overlapInCore/overlapImport.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/overlapPair -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapPair/overlapInCore/overlapPair.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/edalign -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/edalign/overlapInCore/edalign.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/prefixEditDistance-matchLimitGenerate -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/mhapConvert -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/mhapConvert/mhap/mhapConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/mmapConvert -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/mmapConvert/minimap/mmapConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/wtdbgConvert -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/filterCorrectionOverlaps -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/generateCorrectionLayouts -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/filterCorrectionLayouts -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/falconsense -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/falconsense/correction/falconsense.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/falconsense/utgcns/stashContains.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/errorEstimate -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/splitHaplotype -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/trimReads -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-quality.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/splitReads -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/mergeRanges -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/overlapAlign -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/trimRead.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/findErrors -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/bogart -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/bogart.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Logging.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Outputs.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigVector.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/bogus -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogus/bogus/bogus.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/bogus/bogus/bogusUtil.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/alignGFA -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/alignGFA/gfa/alignGFA.o -lcanu
g++ -o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/utgcns -Wl,-z,relro -Wl,-z,now -D_GLIBCXX_PARALLEL -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/utgcns.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/stashContains.o /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu
Success!
canu installed in /<<BUILDDIR>>/canu-1.9+dfsg/Linux-armv7l/bin/canu
make[2]: Leaving directory '/<<BUILDDIR>>/canu-1.9+dfsg/src'
builddir=*-*/; \
find $builddir \
-name OverlapMhap.pm \
-exec sed -i 's#\(\s*my \$javaPath = \).*#\1 "/usr/lib/jvm/java-8-openjdk-armhf/bin/java";#' {} +
make[1]: Leaving directory '/<<BUILDDIR>>/canu-1.9+dfsg'
dh_auto_test -a -O--sourcedirectory=src/
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --sourcedirectory=src/
dh_testroot -a -O--sourcedirectory=src/
dh_prep -a -O--sourcedirectory=src/
dh_auto_install -a -O--sourcedirectory=src/
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/canu-1.9+dfsg'
dh_install
for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/canu-1.9+dfsg'
dh_installdocs -a -O--sourcedirectory=src/
dh_installchangelogs -a -O--sourcedirectory=src/
dh_installman -a -O--sourcedirectory=src/
dh_installinit -a -O--sourcedirectory=src/
dh_installsystemduser -a -O--sourcedirectory=src/
dh_perl -a -O--sourcedirectory=src/
dh_link -a -O--sourcedirectory=src/
dh_strip_nondeterminism -a -O--sourcedirectory=src/
dh_compress -a -O--sourcedirectory=src/
dh_fixperms -a -O--sourcedirectory=src/
dh_missing -a -O--sourcedirectory=src/
dh_dwz -a -O--sourcedirectory=src/
dh_strip -a -O--sourcedirectory=src/
dh_makeshlibs -a -O--sourcedirectory=src/
dh_shlibdeps -a -O--sourcedirectory=src/
dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/overlapInCore contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/trimReads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/bogart contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/overlapPair contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/bogus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a -O--sourcedirectory=src/
dh_gencontrol -a -O--sourcedirectory=src/
dh_md5sums -a -O--sourcedirectory=src/
dh_builddeb -a -O--sourcedirectory=src/
dpkg-deb: building package 'canu-dbgsym' in '../canu-dbgsym_1.9+dfsg-1_armhf.deb'.
dpkg-deb: building package 'canu' in '../canu_1.9+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../canu_1.9+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-12-15T11:54:07Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
canu_1.9+dfsg-1_armhf.changes:
------------------------------
Format: 1.8
Date: Sun, 10 Nov 2019 11:12:40 +0100
Source: canu
Binary: canu canu-dbgsym
Architecture: armhf
Version: 1.9+dfsg-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Steffen Moeller <moeller@debian.org>
Description:
canu - single molecule sequence assembler for genomes
Changes:
canu (1.9+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
* debhelper-compat 12
Checksums-Sha1:
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Checksums-Sha256:
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Files:
351883e05390568c76c5df6733ae1d93 13894156 debug optional canu-dbgsym_1.9+dfsg-1_armhf.deb
d8525e4ea963d2f9ae914d8e043bc0f1 6420 science optional canu_1.9+dfsg-1_armhf.buildinfo
74c72a856a0adb98022b63df1332fe40 1188492 science optional canu_1.9+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
canu-dbgsym_1.9+dfsg-1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 13894156 bytes: control archive=2912 bytes.
2416 bytes, 12 lines control
5490 bytes, 52 lines md5sums
Package: canu-dbgsym
Source: canu
Version: 1.9+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 15090
Depends: canu (= 1.9+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for canu
Build-Ids: 09fe0ae5e93c3c96d8b5bdaf0274c75c80058444 0a5ab5898ad28c9b7591ea7d1d6a1dcc938ad878 0ce0790551816475ae55433f60cb3114761396dc 3005c8eb37c8675c04050b682268f75833b1be11 30c4f5e88100dce32a0581c8db1be33af9088d9c 3550b56d6f17ced14e5cbc1818e346118d9daa30 3552637f5690b4b2a9c3e89bf910bb0bac17d7ad 3ab94fa76281e7755dd10413967e0768bc77b026 3f1733a076b77194a5a690c7b07b18c54ea30a00 48cf2f78372db6d4a013adf7638170825ea62290 52674a43b7f487c89f911a0403e3b05cec31f7a6 56f9dadd28a4dff27d252b2ce7aba7cd7a9f799f 57586efe6d2f321be1030cf0046e9784ccd427a4 5a8ca4caf941bc8b97e3be29802f19b8dfcc5444 5d88205645031927471ff24ea0e51178685b5f86 605af355583c8528cc9bc2d673d4866cb063f995 6ba756856fcbd02a653bf60f367bc92226854a24 6ed23819357986b5464265e655e34a0ce59460a7 6f6a0863829283a096b7c8400fd768f2cac8b070 71d92f5715f119902ec2a05ca67b48235c3fa356 7394443ec8d78137b010792ec9765d077013b459 796b40ff2d6308adaa8c0e9874617fa0c8bd6098 93e3a9ea48576bd0b16f32688ecdd1262b2e2ef5 94194f6744dcdc26c5ab7e13e913b7f9197d507d 957ecef6e60d0f0f3d4ab3e763dd372be62dbec3 965e93c84c92c580830efdd6d62038469ec1da78 9938e9c80093421bb93f07b90642d9c4a8a6de42 9b9c76658742b5940c80bf4715e5065a4f62c89f a79b57cd41fb4a883a8f4bb3cba1179cbef6ff93 a94eea5a869cff19d406b6d36b64e2482774ba80 b4844949cff78f3a021ae4a4eab5090b40b4d444 b748233e6bf2e2bc5ca2ee49ec75ff682c212022 b798f7a923f724ef574c2f47b500dfdc5b755f04 ba4e4e9f96ae0f6630843bd2f4d96d621f5cac4f bf5d0c5c72fc6dbb0ad292a26479f897e3444afc c15b67363b1d3f5dd87b7b915bad6e30354c2c80 c31d9708ca8829e3f3b282aff6b501f1a7a91dfa cb2845b1ce81bfabfa0cf02889c101b80716be53 ccdf833a1950abac14fed1684c50b7dde35672dd d37b8b3609f7f401ca46f40440e68b9bba4d7256 d5664e04bf8f996ad51e04c8e02435f9ea2e85f9 de515376ea65009671b64c1e5614055157637cd0 df5932cdb776489469fce109c9a1b7f4b34a3d8c e12b28b93663d965cd484b6bb84f1a622ab2bd29 e3e48edeb5b14cf27241bd9386fbc105f899c05a e680735b3f100ebd6e5d5fc9b3ea1f518f798f44 e71617165e97a795e2d2cd7145377a185ca73ef6 e9e3abf4afd1ca8a39920e926cce6a4656b0f211 f29554647fa0e98ea076972410017c7000902b80 f4bacea4076fe59315e147b922e93f80c42a258b f675c5c91efce829ceaab47ad6d9a91f8ae100ac
drwxr-xr-x root/root 0 2019-11-10 10:12 ./
drwxr-xr-x root/root 0 2019-11-10 10:12 ./usr/
drwxr-xr-x root/root 0 2019-11-10 10:12 ./usr/lib/
drwxr-xr-x root/root 0 2019-11-10 10:12 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-11-10 10:12 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-11-10 10:12 ./usr/lib/debug/.build-id/09/
-rw-r--r-- root/root 224040 2019-11-10 10:12 ./usr/lib/debug/.build-id/09/fe0ae5e93c3c96d8b5bdaf0274c75c80058444.debug
drwxr-xr-x root/root 0 2019-11-10 10:12 ./usr/lib/debug/.build-id/0a/
-rw-r--r-- root/root 197352 2019-11-10 10:12 ./usr/lib/debug/.build-id/0a/5ab5898ad28c9b7591ea7d1d6a1dcc938ad878.debug
drwxr-xr-x root/root 0 2019-11-10 10:12 ./usr/lib/debug/.build-id/0c/
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canu_1.9+dfsg-1_armhf.deb
-------------------------
new Debian package, version 2.0.
size 1188492 bytes: control archive=3088 bytes.
874 bytes, 21 lines control
5887 bytes, 85 lines md5sums
Package: canu
Version: 1.9+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8685
Depends: libc6 (>= 2.29), libgcc1 (>= 1:3.5), libgomp1 (>= 6), libstdc++6 (>= 5.2), perl:any, libfilesys-df-perl, mhap (>= 2.1.3), gnuplot
Suggests: pbgenomicconsensus, nanopolish
Section: science
Priority: optional
Homepage: http://canu.readthedocs.org/en/latest/
Description: single molecule sequence assembler for genomes
Canu is a fork of the Celera Assembler, designed for high-noise
single-molecule sequencing (such as the PacBio RS II or Oxford
Nanopore MinION).
.
Canu is a hierarchical assembly pipeline which runs in four steps:
.
* Detect overlaps in high-noise sequences using MHAP
* Generate corrected sequence consensus
* Trim corrected sequences
* Assemble trimmed corrected sequences
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-rw-r--r-- root/root 7066 2019-11-04 06:18 ./usr/lib/canu/lib/site_perl/canu/Output.pm
-rw-r--r-- root/root 10463 2019-11-04 06:18 ./usr/lib/canu/lib/site_perl/canu/OverlapBasedTrimming.pm
-rw-r--r-- root/root 24709 2019-11-04 06:18 ./usr/lib/canu/lib/site_perl/canu/OverlapErrorAdjustment.pm
-rw-r--r-- root/root 16396 2019-11-04 06:18 ./usr/lib/canu/lib/site_perl/canu/OverlapInCore.pm
-rw-r--r-- root/root 24798 2019-11-04 06:18 ./usr/lib/canu/lib/site_perl/canu/OverlapMMap.pm
-rw-r--r-- root/root 30589 2019-11-10 10:12 ./usr/lib/canu/lib/site_perl/canu/OverlapMhap.pm
-rw-r--r-- root/root 31532 2019-11-04 06:18 ./usr/lib/canu/lib/site_perl/canu/OverlapStore.pm
-rw-r--r-- root/root 5978 2019-11-04 06:18 ./usr/lib/canu/lib/site_perl/canu/Report.pm
-rw-r--r-- root/root 20706 2019-11-04 06:18 ./usr/lib/canu/lib/site_perl/canu/SequenceStore.pm
-rw-r--r-- root/root 14465 2019-11-04 06:18 ./usr/lib/canu/lib/site_perl/canu/Unitig.pm
drwxr-xr-x root/root 0 2019-11-10 10:12 ./usr/share/
drwxr-xr-x root/root 0 2019-11-10 10:12 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-11-10 10:12 ./usr/share/doc/canu/
-rw-r--r-- root/root 219 2019-11-04 06:18 ./usr/share/doc/canu/README.citation
-rw-r--r-- root/root 1968 2019-11-04 06:18 ./usr/share/doc/canu/README.md
-rw-r--r-- root/root 902 2019-11-10 10:12 ./usr/share/doc/canu/changelog.Debian.gz
-rw-r--r-- root/root 6019 2019-11-10 10:12 ./usr/share/doc/canu/copyright
drwxr-xr-x root/root 0 2019-11-10 10:12 ./usr/share/man/
drwxr-xr-x root/root 0 2019-11-10 10:12 ./usr/share/man/man1/
-rw-r--r-- root/root 325 2019-11-10 10:12 ./usr/share/man/man1/canu.1.gz
+------------------------------------------------------------------------------+
| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 217724
Build-Time: 1112
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 2318
Job: canu_1.9+dfsg-1
Machine Architecture: armhf
Package: canu
Package-Time: 3520
Source-Version: 1.9+dfsg-1
Space: 217724
Status: successful
Version: 1.9+dfsg-1
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Finished at 2019-12-15T11:54:07Z
Build needed 00:58:40, 217724k disc space