canu →
2.0+dfsg-1+b2 →
armhf → 2020-12-06 13:16:51
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| canu 2.0+dfsg-1+b2 (armhf) Sun, 06 Dec 2020 12:44:57 +0000 |
+==============================================================================+
Package: canu
Version: 2.0+dfsg-1+b2
Source Version: 2.0+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-aa3dc5af-07b4-4386-b732-98d10d60cb91' 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 [11.9 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.9 MB in 30s (821 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 1262 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main canu 2.0+dfsg-1 (dsc) [1945 B]
Get:2 http://172.17.0.1/private bullseye-staging/main canu 2.0+dfsg-1 (tar) [1254 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main canu 2.0+dfsg-1 (diff) [5976 B]
Fetched 1262 kB in 0s (3059 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/canu-rJMewE/canu-2.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/canu-rJMewE' 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-e2d51C/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-e2d51C/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-e2d51C/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-e2d51C/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-e2d51C/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-e2d51C/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-e2d51C/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-e2d51C/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2803 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:
bsdextrautils krb5-locales libpam-cap netbase sensible-utils
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 54 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-e2d51C/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 (22.1 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12762 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-e2d51C/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-e2d51C/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-e2d51C/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-e2d51C/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-e2d51C/apt_archive ./ Sources [526 B]
Get:5 copy:/<<BUILDDIR>>/resolver-e2d51C/apt_archive ./ Packages [607 B]
Fetched 2466 B in 1s (3264 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:
krb5-locales libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev binfmt-support 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 libboost1.71-dev
libbrotli1 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 libguava-java libicu67 libjpeg62-turbo
libjsr305-java liblcms2-2 libmagic-mgc libmagic1 libmeryl-dev libnspr4
libnss3 libpcsclite1 libpipeline1 libpng16-16 libsigsegv2 libssw-java
libsub-override-perl 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 ucf x11-common
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make default-jre gettext-doc
libasprintf-dev libgettextpo-dev groff libasound2-plugins alsa-utils
libatinject-jsr330-api-java-doc libboost-doc libboost1.71-doc
libboost-atomic1.71-dev libboost-chrono1.71-dev libboost-container1.71-dev
libboost-context1.71-dev libboost-contract1.71-dev
libboost-coroutine1.71-dev libboost-date-time1.71-dev
libboost-exception1.71-dev libboost-fiber1.71-dev
libboost-filesystem1.71-dev libboost-graph1.71-dev
libboost-graph-parallel1.71-dev libboost-iostreams1.71-dev
libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev
libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev
libboost-program-options1.71-dev libboost-python1.71-dev
libboost-random1.71-dev libboost-regex1.71-dev
libboost-serialization1.71-dev libboost-stacktrace1.71-dev
libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev
libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev
libboost1.71-tools-dev libmpfrc++-dev libntl-dev libxz-java cups-common
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 alsa-ucm-conf alsa-topology-conf dbus
libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev binfmt-support 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 libboost1.71-dev
libbrotli1 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 libguava-java libicu67 libjpeg62-turbo
libjsr305-java liblcms2-2 libmagic-mgc libmagic1 libmeryl-dev libnspr4
libnss3 libpcsclite1 libpipeline1 libpng16-16 libsigsegv2 libssw-java
libsub-override-perl 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 ucf x11-common
0 upgraded, 86 newly installed, 0 to remove and 54 not upgraded.
Need to get 88.0 MB of archives.
After this operation, 398 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-e2d51C/apt_archive ./ sbuild-build-depends-canu-dummy 0.invalid.0 [900 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf binfmt-support armhf 2.2.1-1 [55.0 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1h-1 [812 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20200601 [158 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf java-common all 0.72 [14.5 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libavahi-common-data armhf 0.8-3+b2 [127 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libavahi-common3 armhf 0.8-3+b2 [55.3 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libdbus-1-3 armhf 1.12.20-1+b3 [192 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libavahi-client3 armhf 0.8-3+b2 [58.0 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libcups2 armhf 2.3.3op1-2 [311 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf liblcms2-2 armhf 2.9-4 [119 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:2.0.5-1.1 [121 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2 [259 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.2+dfsg-4 [345 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libnspr4 armhf 2:4.29-1 [89.9 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libnss3 armhf 2:3.59-1 [1084 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libasound2-data all 1.2.3.2-1 [38.1 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libasound2 armhf 1.2.3.2-1 [301 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libpcsclite1 armhf 1.9.0-1 [56.7 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-2 [135 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.12-1 [311 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.12-1 [700 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libxi6 armhf 2:1.7.10-1 [77.9 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+21 [252 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libxtst6 armhf 2:1.2.3-1 [26.3 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf openjdk-11-jre-headless armhf 11.0.9.1+1-1 [33.2 MB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf default-jre-headless armhf 2:1.11-72+b4 [11.2 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates-java all 20190909 [15.7 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-1 [162 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.3-1 [1176 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf fastjar armhf 2:0.98-7 [42.7 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf jaligner all 1.0+dfsg-7 [136 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf jarwrapper all 0.77 [21.7 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libapache-pom-java all 18-1 [4676 B]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libboost1.71-dev armhf 1.71.0-7+b1 [9098 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.71.0.3+b8 [4624 B]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libcommons-parent-java all 43-1 [10.8 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libcommons-compress-java all 1.20-1 [574 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libfastutil-java all 8.4.3-1 [15.8 MB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libfilesys-df-perl armhf 0.92-6+b6 [12.9 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libjsr305-java all 0.1~+svn49-11 [26.9 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libguava-java all 29.0-6 [2419 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libmeryl-dev armhf 0~20150903+r2013-8 [65.3 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libssw-java armhf 1.1-11 [18.7 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf mhap all 2.1.3+dfsg-3 [160 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 88.0 MB in 22s (3914 kB/s)
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12762 files and directories currently installed.)
Preparing to unpack .../00-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
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Preparing to unpack .../01-groff-base_1.22.4-5_armhf.deb ...
Unpacking groff-base (1.22.4-5) ...
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Preparing to unpack .../02-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
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No schema files found: doing nothing.
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Setting up x11-common (1:7.7+21) ...
invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up gettext-base (0.19.8.1-10) ...
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Setting up libasound2-data (1.2.3.2-1) ...
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Setting up libdbus-1-3:armhf (1.12.20-1+b3) ...
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invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of start.
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Setting up libpcsclite1:armhf (1.9.0-1) ...
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Setting up ca-certificates (20200601) ...
Updating certificates in /etc/ssl/certs...
126 added, 0 removed; done.
Setting up libfreetype6:armhf (2.10.2+dfsg-4) ...
Setting up libguava-java (29.0-6) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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Setting up libcups2:armhf (2.3.3op1-2) ...
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Setting up default-jre-headless (2:1.11-72+b4) ...
Setting up openjdk-11-jre-headless:armhf (11.0.9.1+1-1) ...
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/jfr to provide /usr/bin/jfr (jfr) 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/keytool to provide /usr/bin/keytool (keytool) 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/rmid to provide /usr/bin/rmid (rmid) 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
Setting up jaligner (1.0+dfsg-7) ...
Setting up mhap (2.1.3+dfsg-3) ...
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: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:Certigna_Root_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: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:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.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:Hongkong_Post_Root_CA_3.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:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_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:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
done.
Setting up debhelper (13.2.1) ...
Setting up sbuild-build-depends-canu-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-4+rpi1) ...
Processing triggers for ca-certificates (20200601) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-16+rpi1 gcc-10_10.2.0-16+rpi1 libc6-dev_2.31-4+rpi1 libstdc++-10-dev_10.2.0-16+rpi1 libstdc++6_10.2.0-16+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.11 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc2-1 binfmt-support_2.2.1-1 binutils_2.35.1-2+rpi1 binutils-arm-linux-gnueabihf_2.35.1-2+rpi1 binutils-common_2.35.1-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 ca-certificates_20200601 ca-certificates-java_20190909 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-16+rpi1 dash_0.5.11+git20200708+dd9ef66-2 debconf_1.5.74 debhelper_13.2.1 debianutils_4.11.2 default-jre-headless_2:1.11-72+b4 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1 fastjar_2:0.98-7 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0+git20201010-2 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-16+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-16+rpi1 gcc-10-base_10.2.0-16+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 jaligner_1.0+dfsg-7 jarwrapper_0.77 java-common_0.72 krb5-locales_1.17-10 libacl1_2.2.53-8 libapache-pom-java_18-1 libapt-pkg6.0_2.1.11 libarchive-zip-perl_1.68-1 libasan6_10.2.0-16+rpi1 libasound2_1.2.3.2-1 libasound2-data_1.2.3.2-1 libassuan0_2.5.3-7.1 libatinject-jsr330-api-java_1.0+ds1-5 libatomic1_10.2.0-16+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1 libavahi-client3_0.8-3+b2 libavahi-common-data_0.8-3+b2 libavahi-common3_0.8-3+b2 libbinutils_2.35.1-2+rpi1 libblkid1_2.36-3 libboost-dev_1.71.0.3+b8 libboost-iostreams1.71.0_1.71.0-7 libboost1.71-dev_1.71.0-7+b1 libbrotli1_1.0.9-2 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-4+rpi1 libc-dev-bin_2.31-4+rpi1 libc6_2.31-4+rpi1 libc6-dev_2.31-4+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.0-16+rpi1 libcom-err2_1.45.6-1 libcommons-compress-java_1.20-1 libcommons-parent-java_43-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-2+rpi1 libctf0_2.35.1-2+rpi1 libcups2_2.3.3op1-2 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdbus-1-3_1.12.20-1+b3 libdebconfclient0_0.255 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5+rpi1 libelf1_0.182-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1 libfastutil-java_8.4.3-1 libfdisk1_2.36-3 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.9.0-1 libfilesys-df-perl_0.92-6+b6 libfontconfig1_2.13.1-4.2 libfreetype6_2.10.2+dfsg-4 libgcc-10-dev_10.2.0-16+rpi1 libgcc-s1_10.2.0-16+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.3-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-16+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libguava-java_29.0-6 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-3 libisl22_0.22.1-1 libjpeg62-turbo_1:2.0.5-1.1 libjsr305-java_0.1~+svn49-11 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 liblcms2-2_2.9-4 libldap-2.4-2_2.4.56+dfsg-1+rpi1 libldap-common_2.4.56+dfsg-1+rpi1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmeryl-dev_0~20150903+r2013-8 libmount1_2.36-3 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnspr4_2:4.29-1 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libnss3_2:3.59-1 libp11-kit0_0.23.21-2 libpam-cap_1:2.44-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libpcsclite1_1.9.0-1 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3 libreadline8_8.1~rc2-2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.0-3+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.4-2 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssl1.1_1.1.1h-1 libssw-java_1.1-11 libstdc++-10-dev_10.2.0-16+rpi1 libstdc++6_10.2.0-16+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.6-2+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-16+rpi1 libuchardet0_0.0.7-1 libudev1_246.6-2+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libx11-6_2:1.6.12-1 libx11-data_2:1.6.12-1 libxapian30_1.4.17-1 libxau6_1:1.0.8-1+b2 libxcb1_1.14-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxi6_2:1.7.10-1 libxml2_2.9.10+dfsg-6.3 libxrender1_1:0.9.10-1 libxtst6_2:1.2.3-1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mhap_2.1.3+dfsg-3 mount_2.36-3 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.2 openjdk-11-jre-headless_11.0.9.1+1-1 openssl_1.1.1h-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.32_5.32.0-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.1~rc2-2 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_2.96-5 tar_1.30+dfsg-7 tzdata_2020d-1 ucf_3.0043 util-linux_2.36-3 x11-common_1:7.7+21 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.lES34z2d/trustedkeys.kbx': General error
gpgv: Signature made Fri Mar 27 23:47:02 2020 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_2.0+dfsg-1.dsc
dpkg-source: info: extracting canu in /<<BUILDDIR>>/canu-2.0+dfsg
dpkg-source: info: unpacking canu_2.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking canu_2.0+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 canu_version.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2.0+dfsg-1+b2
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-aa3dc5af-07b4-4386-b732-98d10d60cb91
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package canu
dpkg-buildpackage: info: source version 2.0+dfsg-1+b2
dpkg-buildpackage: info: source distribution bullseye-staging
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-2.0+dfsg'
rm -rf Linux-*
rm -f src/canu_version.H
make[1]: Leaving directory '/<<BUILDDIR>>/canu-2.0+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-2.0+dfsg'
dh_auto_build
cd src && make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<BUILDDIR>>/canu-2.0+dfsg/src'
WARNING:
WARNING: g++ 10 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher.
WARNING:
Building for 'Linux' '4.9.0-0.bpo.4-armmp' as 'armv7l' into '/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/{bin,obj}'.
Using '/usr/bin/g++' version '10'.
Using user-supplied CXXFLAGS '-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security'.
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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 v2.0
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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}
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C
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:678:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
678 | fgets(line, FILENAME_MAX, F);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
utility/files.C:684:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
684 | fgets(line, FILENAME_MAX, F);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/logging.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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system.C
In file included from utility/system.C:46:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
utility/logging.C: In member function 'void logFileInstance::rotate()':
utility/logging.C:160:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
160 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name);
| ^
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from utility/logging.H:29,
from utility/logging.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utility/logging.C:161:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
161 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name);
| ^
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from utility/logging.H:29,
from utility/logging.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utility/logging.C:157:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
157 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name);
| ^
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from utility/logging.H:29,
from utility/logging.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utility/logging.C:158:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID);
| ^
utility/logging.C:158:43: note: using the range [-2147483648, 2147483647] for directive argument
158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from utility/logging.H:29,
from utility/logging.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 13 and 8220 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 function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'void logFileInstance::rotateMessage()' at utility/logging.C:173:15:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: warning: 'int __builtin___snprintf_chk(char*, unsigned int, int, unsigned int, const char*, ...)' specified bound 1024 exceeds destination size 256 [-Wstringop-overflow=]
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-reader.C
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-reader.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | 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
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}
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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.H:32,
from utility/kmers-writer.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | 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
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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
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-2.0+dfsg/src/AS_global.H:67,
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-writer-block.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | 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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | 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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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-statistics.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | 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:178:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
178 | 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:192:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
192 | 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:192:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
192 | 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:195:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
195 | 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:195:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
195 | 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:198:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
198 | 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:198:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
198 | 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:205:52: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
205 | 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:210:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
210 | 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:212:55: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
212 | 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:213:55: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
213 | 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:214:55: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
214 | 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:349:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
349 | 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
350 | _nSuffix, _suffixBits, arraySize, bitsToGB(arraySize), bitsToMB(arrayBlockMin));
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-exact.C:349:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
349 | 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
350 | _nSuffix, _suffixBits, arraySize, bitsToGB(arraySize), bitsToMB(arrayBlockMin));
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-exact.C:361:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
361 | fprintf(stderr, " %lu values of %u bits each -> %lu bits (%.3f GB) in blocks of %.3f MB\n",
| ~~^
| |
| long unsigned int
| %llu
362 | _nSuffix, _valueBits, arraySize, bitsToGB(arraySize), bitsToMB(arrayBlockMin));
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-exact.C:361:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
361 | fprintf(stderr, " %lu values of %u bits each -> %lu bits (%.3f GB) in blocks of %.3f MB\n",
| ~~^
| |
| long unsigned int
| %llu
362 | _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:419:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
419 | fprintf(stderr, "minValue " F_U32 " maxValue " F_U32 " value " F_U64 " bits " F_U32 "\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
420 | _minValue, _maxValue, value, _valueBits);
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-exact.C:419:29: 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:508:41: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
508 | fprintf(stderr, "FAILED kmer 0x%016lx\n", kmer);
| ~~~~~^ ~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
utility/kmers-exact.C:509:41: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
509 | fprintf(stderr, "FAILED prefix 0x%016lx\n", prefix);
| ~~~~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
utility/kmers-exact.C:510:41: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
510 | fprintf(stderr, "FAILED suffix 0x%016lx\n", suffix);
| ~~~~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
utility/kmers-exact.C:512:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
512 | 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:512:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
512 | 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:513:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
513 | fprintf(stderr, "final %9lu %9lu\n", bgn, end);
| ~~~^ ~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %9llu
utility/kmers-exact.C:513:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
513 | fprintf(stderr, "final %9lu %9lu\n", bgn, end);
| ~~~^ ~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %9llu
utility/kmers-exact.C:524:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
524 | 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:524:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
524 | 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:524:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
524 | 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:524:59: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
524 | 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:524:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
524 | 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:539:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
539 | 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:539:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
539 | 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:539:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
539 | 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:539:59: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
539 | 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:539:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
539 | 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
In file included from utility/kmers-statistics.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-alignTag.C:73:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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 correction/falconConsensus.H:75,
from correction/falconConsensus.C:73:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C
stores/sqCache.C: In constructor 'sqCache::sqCache(sqStore*, sqRead_which, uint64)':
stores/sqCache.C:108:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
108 | fprintf(stderr, "sqCache: found %u %s reads with %lu bases.\n", nReads, toString(_which), nBases);
| ~~^ ~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
stores/sqCache.C: In member function 'void sqCache::sqCache_loadReads(uint32, uint32, bool)':
stores/sqCache.C:356:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
356 | fprintf(stderr, "Loading %u reads and %lu bases from range %u-%u inclusive.\n",
| ~~^
| |
| long unsigned int
| %llu
357 | nReads, nBases, bgnID, endID);
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C
stores/sqReadDataWriter.C: In member function 'void sqReadDataWriter::sqReadDataWriter_writeBlob(writeBuffer*)':
stores/sqReadDataWriter.C:109:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
109 | buffer->writeIFFchunk("BLOB");
| ^~~~~~
stores/sqReadDataWriter.C:110:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
110 | buffer->writeIFFchunk("NAME", _name, _nameLen);
| ^~~~~~
stores/sqReadDataWriter.C:115:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
115 | buffer->writeIFFchunk("2SQR", rseq, rseq2Len); // Two-bit encoded sequence (ACGT only)
| ^~~~~~
stores/sqReadDataWriter.C:117:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
117 | buffer->writeIFFchunk("3SQR", rseq, rseq3Len); // Three-bit encoded sequence (ACGTN)
| ^~~~~~
stores/sqReadDataWriter.C:119:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
119 | buffer->writeIFFchunk("USQR", rseq, rseqULen); // Unencoded sequence
| ^~~~~~
stores/sqReadDataWriter.C:124:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
124 | buffer->writeIFFchunk("2SQC", cseq, cseq2Len); // Two-bit encoded sequence (ACGT only)
| ^~~~~~
stores/sqReadDataWriter.C:126:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
126 | buffer->writeIFFchunk("3SQC", cseq, cseq3Len); // Three-bit encoded sequence (ACGTN)
| ^~~~~~
stores/sqReadDataWriter.C:128:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
128 | buffer->writeIFFchunk("USQC", cseq, cseqULen); // Unencoded sequence
| ^~~~~~
stores/sqReadDataWriter.C:132:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
132 | buffer->closeIFFchunk("BLOB");
| ^~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C
In file included from stores/sqStoreBlob.C:26:
stores/sqStore.H: In constructor 'sqStoreBlobWriter::sqStoreBlobWriter(const char*, sqStoreInfo*)':
stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber);
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreBlob.C:26:
/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/sqStoreBlob.C:26:
stores/sqStore.H: In member function 'void sqStoreBlobWriter::writeData(sqReadDataWriter*)':
stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber);
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreBlob.C:26:
/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/sqStoreBlob.C:26:
stores/sqStore.H: In member function 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)':
stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber);
stores/sqStore.H:126:36: note: directive argument in the range [0, 65535]
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreBlob.C:26:
/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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.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
| ^~~~~~~
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/sqStoreInfo.C: In member function 'bool sqStoreInfo::readInfo8(char*)':
stores/sqStoreInfo.C:229:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
229 | fprintf(stderr, "sqStore_loadInfo()-- Error: Unsupported historical version %lu detected.\n", _sqVersion);
| ~~^ ~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
stores/sqStoreInfo.C: In member function 'void sqStoreInfo::writeInfo(char*)':
stores/sqStoreInfo.C:333:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
333 | B->writeIFFobject("MAGC", _sqMagic);
| ^~~~~~
stores/sqStoreInfo.C:334:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
334 | B->writeIFFobject("VERS", _sqVersion);
| ^~~~~~
stores/sqStoreInfo.C:336:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
336 | B->writeIFFobject("LSIZ", _sqLibrarySize);
| ^~~~~~
stores/sqStoreInfo.C:337:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
337 | B->writeIFFobject("RSIZ", _sqReadSize);
| ^~~~~~
stores/sqStoreInfo.C:338:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
338 | B->writeIFFobject("MLB ", _sqMaxLibrariesBits);
| ^~~~~~
stores/sqStoreInfo.C:339:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
339 | B->writeIFFobject("LNS ", _sqLibraryNameSize);
| ^~~~~~
stores/sqStoreInfo.C:340:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
340 | B->writeIFFobject("MRB ", _sqMaxReadBits);
| ^~~~~~
stores/sqStoreInfo.C:341:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
341 | B->writeIFFobject("MRLB", _sqMaxReadLenBits);
| ^~~~~~
stores/sqStoreInfo.C:343:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
343 | B->writeIFFobject("NLIB", _numLibraries);
| ^~~~~~
stores/sqStoreInfo.C:344:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
344 | B->writeIFFobject("NREA", _numReads);
| ^~~~~~
stores/sqStoreInfo.C:345:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
345 | B->writeIFFobject("NBLO", _numBlobs);
| ^~~~~~
stores/sqStoreInfo.C:347:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
347 | B->writeIFFarray("READ", _reads, sqRead_largest);
| ^~~~~~
stores/sqStoreInfo.C:348:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
348 | B->writeIFFarray("BASE", _bases, sqRead_largest);
| ^~~~~~
stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()':
stores/sqStoreConstructor.C:204:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
204 | snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, _storePath, V);
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:212:35: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
212 | snprintf(No, FILENAME_MAX, "%s/libraries", _storePath);
| ^~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:213:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
213 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/libraries", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:216:35: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
216 | snprintf(No, FILENAME_MAX, "%s/reads", _storePath);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:217:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
217 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:220:35: warning: '/reads-rawu' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
220 | snprintf(No, FILENAME_MAX, "%s/reads-rawu", _storePath);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:221:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
221 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-rawu", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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 24 and 4127 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:224:35: warning: '/reads-rawc' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
224 | snprintf(No, FILENAME_MAX, "%s/reads-rawc", _storePath);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:225:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
225 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-rawc", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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 24 and 4127 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:228:35: warning: '/reads-coru' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
228 | snprintf(No, FILENAME_MAX, "%s/reads-coru", _storePath);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:229:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
229 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-coru", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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 24 and 4127 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:232:35: warning: '/reads-corc' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
232 | snprintf(No, FILENAME_MAX, "%s/reads-corc", _storePath);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:233:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
233 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-corc", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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 24 and 4127 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:236:35: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
236 | snprintf(No, FILENAME_MAX, "%s/info", _storePath);
| ^~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:237:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
237 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/info", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:240:35: warning: '/info.txt' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
240 | snprintf(No, FILENAME_MAX, "%s/info.txt", _storePath);
| ^~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:241:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
241 | 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-2.0+dfsg/src/AS_global.H:67,
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:207:34: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
207 | snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, _storePath, V);
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C
stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_delete()':
stores/sqStoreConstructor.C:289:35: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
289 | snprintf(path, FILENAME_MAX, "%s/info", _storePath); AS_UTL_unlink(path);
| ^~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:290:35: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
290 | snprintf(path, FILENAME_MAX, "%s/libraries", _storePath); AS_UTL_unlink(path);
| ^~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:291:35: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
291 | snprintf(path, FILENAME_MAX, "%s/reads", _storePath); AS_UTL_unlink(path);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:292:35: warning: '/reads-rawu' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
292 | snprintf(path, FILENAME_MAX, "%s/reads-rawu", _storePath); AS_UTL_unlink(path);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:293:35: warning: '/reads-rawc' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
293 | snprintf(path, FILENAME_MAX, "%s/reads-rawc", _storePath); AS_UTL_unlink(path);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:294:35: warning: '/reads-coru' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
294 | snprintf(path, FILENAME_MAX, "%s/reads-coru", _storePath); AS_UTL_unlink(path);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:295:35: warning: '/reads-corc' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
295 | snprintf(path, FILENAME_MAX, "%s/reads-corc", _storePath); AS_UTL_unlink(path);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:296:35: warning: '/blobs' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
296 | snprintf(path, FILENAME_MAX, "%s/blobs", _storePath); AS_UTL_unlink(path);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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/ovOverlap.C: In member function 'char* ovOverlap::toString(char*, ovOverlapDisplayType, bool)':
stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=]
71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
75 | dat.ovl.ahg5, dat.ovl.ahg3,
| ~~~~~~~~~~~~
| |
| int
stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=]
stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=]
stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=]
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C
stores/ovStore.C: In member function 'void ovStore::testStore(bool)':
stores/ovStore.C:182:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
182 | fprintf(stderr, "Success! Found %u reads with %lu overlaps out of %u reads total.\n",
| ~~^
| |
| long unsigned int
| %llu
183 | nrds, novl, lid);
| ~~~~
| |
| uint64 {aka long long unsigned int}
stores/ovStore.C: In member function 'void ovStore::dumpMetaData(uint32, uint32)':
stores/ovStore.C:493:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
493 | fprintf(stdout, "%9u %5u %5u %9u %9u %9lu\n", ii,
| ~~~^
| |
| long unsigned int
| %9llu
......
498 | _index[ii]._overlapID);
| ~~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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::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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-2.0+dfsg/src/AS_global.H:67,
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);
| ^
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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: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-2.0+dfsg/src/AS_global.H:67,
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
stores/ovStoreHistogram.C: In member function 'void ovErateLengthHistogram::addOverlap(ovOverlap*)':
stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'int' [-Wformat=]
359 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
360 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3,
| ~~~~~~~~~~~~~~~~~~~~~
| |
| int
stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'int' [-Wformat=]
stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=]
stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=]
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-2.0+dfsg/src/AS_global.H:67,
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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/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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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/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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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/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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C
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-2.0+dfsg/src/AS_global.H:67,
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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/tgTig.C:34:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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
In file included from stores/tgTig.H:36,
from stores/tgTigSizeAnalysis.H:41,
from stores/tgTigSizeAnalysis.C:42:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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*, bool)':
stores/tgTig.C:547:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
547 | 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:806:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
806 | ">tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgTig.C: In member function 'void tgTig::dumpFASTQ(FILE*)':
stores/tgTig.C:826:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
826 | "@tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)':
stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
140 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat);
| ^~~~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C:141:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
141 | printSummary(out, "lenSuggestCircular", lenSuggestCircular);
| ^~~~~~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C:143:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
143 | printSummary(out, "lenUnassembled", lenUnassembled);
| ^~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C:144:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
144 | printSummary(out, "lenBubble", lenBubble);
| ^~~~~~~~~~~
stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
145 | 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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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 'bool tgTig::loadLayout(FILE*)':
stores/tgTig.C:565:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fgets(LINE, LINEmax, F); LINEnum++;
| ~~~~~^~~~~~~~~~~~~~~~~~
stores/tgTig.C:690:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
690 | fgets(LINE, LINEmax, F); LINEnum++;
| ~~~~~^~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/liboverlap/prefixEditDistance-extend.C:69:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | 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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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
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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C
In file included from /usr/include/c++/10/set:60,
from utility/strings.H:37,
from stores/ovOverlap.H:45,
from stores/ovStore.H:42,
from utgcns/libNDalign/NDalign.H:39,
from utgcns/libNDalign/NDalign.C:34:
/usr/include/c++/10/bits/stl_tree.h: In 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++/10/bits/stl_tree.h:2458:7: 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' changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~
In file included from /usr/include/c++/10/map:61,
from utgcns/libNDalign/NDalign.H:45,
from utgcns/libNDalign/NDalign.C:34:
/usr/include/c++/10/bits/stl_map.h: In member function 'bool NDalign::findHits()':
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h: In member function 'void NDalign::fastFindMersA(bool)':
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h: In member function 'void NDalign::fastFindMersB(bool)':
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/dumpBlob.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreBuild.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreConfig.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreBucketizer.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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreSorter.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreIndexer.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreDump.C
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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/ovStoreDump.C:56:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
stores/ovStoreDump.C: In function 'int main(int, char**)':
stores/ovStoreDump.C:832:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
832 | err.push_back("ERROR: no input seqStore (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreDump.C:835:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
835 | err.push_back("ERROR: no input ovlStore (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreDump.C:838:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
838 | err.push_back("ERROR: -prefix is necessary for -binary output.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreStats.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Isequence stores/sqStoreDumpMetaData.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Isequence sequence/sequence-summarize.C
stores/sqStoreDumpFASTQ.C: In function 'int main(int, char**)':
stores/sqStoreDumpFASTQ.C:459:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
459 | AS_UTL_writeFastQ(out[outid]->getFASTQ(), seq, seqLen, qlt, seqLen, "@%s\n", readName);
| ^~~~~~~
stores/sqStoreDumpFASTQ.C:461:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
461 | AS_UTL_writeFastA(out[outid]->getFASTA(), seq, seqLen, 0, ">%s\n", readName);
| ^~~~~~~
stores/sqStoreDumpMetaData.C: In function 'void dumpReads(sqStore*, uint32, uint32, sqRead_which)':
stores/sqStoreDumpMetaData.C:226:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
226 | fprintf(stdout, "%10" F_U32P " %10" F_U32P "%s %s %4lu %12lu\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
231 | seqs->sqStore_getReadSegm(rid),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
stores/sqStoreDumpMetaData.C:226:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
stores/sqStoreDumpMetaData.C: In function 'void dumpHistogram(sqStore*, uint32, uint32, sqRead_which, bool)':
stores/sqStoreDumpMetaData.C:277:26: 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=]
277 | fprintf(stdout, "%lu\n", lengths[ii]);
| ~~^
| |
| long unsigned int
| %llu
sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogramSimple(std::vector<long long unsigned int>)':
sequence/sequence-summarize.C:106:24: 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=]
106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn);
| ~~^
| |
| long unsigned int
| %llu
sequence/sequence-summarize.C:106:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn);
| ~~^ ~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
sequence/sequence-summarize.C: In function 'void doSummarize_dumpLengths(std::vector<long long unsigned int>)':
sequence/sequence-summarize.C:120:24: 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=]
120 | fprintf(stdout, "%lu\n", lengths[ii]);
| ~~^
| |
| long unsigned int
| %llu
sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogram(std::vector<long long unsigned int>, uint64, bool)':
sequence/sequence-summarize.C:290:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector<long long unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
290 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", 0.0, lengths.size(), lSum, histPlot[hp++]); // Occurs if only empty sequences in the input!
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| std::vector<long long unsigned int>::size_type {aka unsigned int}
sequence/sequence-summarize.C:292:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector<long long unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
292 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", (double)lSum / genomeSize, lengths.size(), lSum, histPlot[hp++]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| std::vector<long long unsigned int>::size_type {aka unsigned int}
sequence/sequence-summarize.C:294:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector<long long unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
294 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " ||\n", (double)lSum / genomeSize, lengths.size(), lSum);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| std::vector<long long unsigned int>::size_type {aka unsigned int}
stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTQ()':
stores/sqStoreDumpFASTQ.C:137:36: warning: '.fastq' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
137 | snprintf(N, FILENAME_MAX, "%s.fastq%s", _p, _s);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:135:37: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size between 0 and 4095 [-Wformat-truncation=]
135 | snprintf(N, FILENAME_MAX, "%s.%s.fastq%s", _p, _n, _s);
| ^~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:167:36: warning: '.fasta' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
167 | snprintf(N, FILENAME_MAX, "%s.fasta%s", _p, _s);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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:165:37: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size between 0 and 4095 [-Wformat-truncation=]
165 | snprintf(N, FILENAME_MAX, "%s.%s.fasta%s", _p, _n, _s);
| ^~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from stores/sqStoreDumpMetaData.C:34:
/usr/include/c++/10/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::less<long long unsigned int> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: 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
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from stores/sqStoreDumpMetaData.C:34:
/usr/include/c++/10/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::less<long long unsigned int> >]':
/usr/include/c++/10/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++/10/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
/usr/include/c++/10/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++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: 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
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/tgStoreCompress.C
/usr/include/c++/10/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::less<long long unsigned int> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: 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++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/10/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::less<long long unsigned int> >]':
/usr/include/c++/10/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++/10/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
/usr/include/c++/10/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
/usr/include/c++/10/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++/10/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
/usr/include/c++/10/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
/usr/include/c++/10/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
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_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::less<long long unsigned int> >]':
/usr/include/c++/10/bits/stl_algo.h:1881:5: 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
1881 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1881:5: 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++/10/bits/stl_algo.h:1881:5: 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++/10/bits/stl_algo.h:1886:25: 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
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: 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
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from utility/strings.H:38,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:32,
from sequence/sequence-summarize.C:30:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/10/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::less<long long unsigned int> >]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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++/10/bits/stl_algo.h:1959:25: 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
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void doSummarize_lengthHistogramSimple(std::vector<long long unsigned int>)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: 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
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: 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
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void doSummarize_dumpLengths(std::vector<long long unsigned int>)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: 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
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: 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
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from utility/files.H:36,
from stores/sqStore.H:38,
from stores/sqStoreDumpMetaData.C:35:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: 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
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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++/10/bits/stl_algo.h:1959:25: 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
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from stores/sqStoreDumpMetaData.C:34:
/usr/include/c++/10/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::less<long long unsigned int> >]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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++/10/bits/stl_algo.h:1959:25: 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
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
/usr/include/c++/10/bits/stl_algo.h: In function 'void doSummarize_lengthHistogram(std::vector<long long unsigned int>, uint64, bool)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: 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
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: 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
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: 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
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from utility/files.H:36,
from stores/sqStore.H:38,
from stores/sqStoreDumpMetaData.C:35:
/usr/include/c++/10/bits/vector.tcc: In function 'void dumpHistogram(sqStore*, uint32, uint32, sqRead_which, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from stores/sqStoreDumpMetaData.C:34:
/usr/include/c++/10/bits/stl_algo.h:1974:25: 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
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: 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
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: 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
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreDumpMetaData.C:279:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
279 | }
| ^
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/tgStoreDump.C
In file included from /usr/include/c++/10/vector:67,
from utility/strings.H:38,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:32,
from sequence/sequence-summarize.C:30:
/usr/include/c++/10/bits/stl_vector.h: In function 'void doSummarize(std::vector<char*>&, summarizeParameters&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from utility/strings.H:38,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:32,
from sequence/sequence-summarize.C:30:
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:675:2: warning: #warning replace this with genericStatistics [-Wcpp]
675 | #warning replace this with genericStatistics
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/tgTigSizeAnalysis.C
sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
474 | }
| ^
sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/tgStoreLoad.C
In file included from stores/tgTig.H:36,
from stores/tgTigSizeAnalysis.H:41,
from stores/tgTigSizeAnalysis.C:42:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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/tgStoreDump.C:55:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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:1166:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1166 | err.push_back("No sequence store (-S option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:1169:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1169 | err.push_back("No tig store (-T option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:1172:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1172 | err.push_back("No tig store version (-T option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:1175:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1175 | err.push_back("-coverage needs and output prefix (-o option).\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:1178:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1178 | err.push_back("No DUMP TYPE supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)':
stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
140 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat);
| ^~~~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C:141:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
141 | printSummary(out, "lenSuggestCircular", lenSuggestCircular);
| ^~~~~~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C:143:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
143 | printSummary(out, "lenUnassembled", lenUnassembled);
| ^~~~~~~~~~~~~~~~
stores/tgTigSizeAnalysis.C:144:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
144 | printSummary(out, "lenBubble", lenBubble);
| ^~~~~~~~~~~
stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
145 | printSummary(out, "lenContig", lenContig);
| ^~~~~~~~~~~
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/tgStoreFilter.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/tgTigDisplay.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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/loadCorrectedReads.C:29:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C
stores/loadCorrectedReads.C: In function 'int main(int, char**)':
stores/loadCorrectedReads.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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadCorrectedReads.C:78:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
78 | err.push_back("ERROR: no tig store (-T) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 input tigs supplied on command line and no -L file supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadCorrectedReads.C:185:19: 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=]
185 | 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-2.0+dfsg/Linux-armv7l/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/loadErates.C
stores/loadTrimmedReads.C: In function 'int main(int, char**)':
stores/loadTrimmedReads.C:180:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
180 | err.push_back("ERROR: no sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl.C
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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp]
261 | #warning HARD CODED NUMBER OF FILES!
| ^~~~~~~
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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 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:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | 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");
| ^
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+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/merylCountArray.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-count.C
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:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | 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 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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:89,
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:205:23: required from 'swv<VALUE>* merylCountArray<VALUE>::unpackSuffixesAndValues(uint64) [with VALUE = unsigned int; uint64 = long long unsigned int]'
meryl/merylCountArray.C:396:16: 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:205:23: required from 'swv<VALUE>* merylCountArray<VALUE>::unpackSuffixesAndValues(uint64) [with VALUE = long long unsigned int; uint64 = long long unsigned int]'
meryl/merylCountArray.C:397:16: 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 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:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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.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");
| ^
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:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
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");
| ^
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:385:19: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
385 | fprintf(stderr, "Counting %lu (estimated)%s %s%s%s " F_U32 "-mers from " F_SIZE_T " input file%s:\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
386 | 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:603:69: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
603 | fprintf(stderr, "Used %3.3f GB out of %3.3f GB to store %12lu kmers.\n",
| ~~~~^
| |
| long unsigned int
| %12llu
......
606 | kmersAdded);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-countSimple.C
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+dfsg/src/AS_global.H:67,
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 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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | 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");
| ^
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
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-histogram.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.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-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+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-histogram.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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-histogram.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | 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");
| ^
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | 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");
| ^
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 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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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 meryl/meryl-import.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+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:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| 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:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | 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");
| ^
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");
| ^
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
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | 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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-lookup.C
In file included from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:89,
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:205:23: required from 'swv<VALUE>* merylCountArray<VALUE>::unpackSuffixesAndValues(uint64) [with VALUE = unsigned int; uint64 = long long unsigned int]'
meryl/merylCountArray.C:396:16: 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:205:23: required from 'swv<VALUE>* merylCountArray<VALUE>::unpackSuffixesAndValues(uint64) [with VALUE = long long unsigned int; uint64 = long long unsigned int]'
meryl/merylCountArray.C:397:16: 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);
| ^~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-extract.C
In file included from utility/kmers.H:32,
from meryl/meryl-lookup.C:28:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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:28:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C: In function 'void dumpExistence(dnaSeqFile*, compressedFileWriter*, std::vector<kmerCountExactLookup*>&, std::vector<const char*>&)':
meryl/meryl-lookup.C:83:43: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
83 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\n",
| ~~^
| |
| long unsigned int
| %llu
......
86 | kiter.position(),
| ~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C:97:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
97 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\t%s\t%lu\t%s\t%lu\t%s\n",
| ~~^
| |
| long unsigned int
| %llu
......
100 | kiter.position(),
| ~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C:97:58: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
97 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\t%s\t%lu\t%s\t%lu\t%s\n",
| ~~^
| |
| long unsigned int
| %llu
......
102 | kiter.fmer().toString(fString), fValue,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C:97:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
97 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\t%s\t%lu\t%s\t%lu\t%s\n",
| ~~^
| |
| long unsigned int
| %llu
......
103 | kiter.rmer().toString(rString), rValue,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C: In function 'void reportExistence(dnaSeqFile*, compressedFileWriter*, std::vector<kmerCountExactLookup*>&, std::vector<const char*>&)':
meryl/meryl-lookup.C:134:35: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
134 | fprintf(ofile->file(), "%s\t%lu\t%lu\t%lu\n", seq.name(), nKmer, klookup[0]->nKmers(), nKmerFound);
| ~~^ ~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C:134:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
134 | fprintf(ofile->file(), "%s\t%lu\t%lu\t%lu\n", seq.name(), nKmer, klookup[0]->nKmers(), nKmerFound);
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C:134:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
134 | fprintf(ofile->file(), "%s\t%lu\t%lu\t%lu\n", seq.name(), nKmer, klookup[0]->nKmers(), nKmerFound);
| ~~^ ~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C: In function 'void filter(dnaSeqFile*, dnaSeqFile*, compressedFileWriter*, compressedFileWriter*, std::vector<kmerCountExactLookup*>&, bool)':
meryl/meryl-lookup.C:204:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
204 | fprintf(stderr, "\nIncluding %lu reads (or read pairs) out of %lu.\n", nReadsFound, nReads);
| ~~^ ~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C:204:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
204 | fprintf(stderr, "\nIncluding %lu reads (or read pairs) out of %lu.\n", nReadsFound, nReads);
| ~~^ ~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C: In function 'int main(int, char**)':
meryl/meryl-lookup.C:285:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
285 | err.push_back("No input sequences (-sequence) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-lookup.C:287:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
287 | err.push_back("No query meryl database (-mers) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-lookup.C:289:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
289 | err.push_back("No report-type (-existence, etc) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C: In function 'int main(int, char**)':
sequence/sequence.C:414:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
414 | err.push_back("ERROR: No mode (summarize, extract, generate or simulate) specified.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:418:21: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
418 | err.push_back("ERROR: No input sequence files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:422:21: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
422 | err.push_back("ERROR: No input sequence files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:428:21: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
428 | err.push_back("ERROR: No reference genome sequence (-genome) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:432:21: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
432 | err.push_back("ERROR: No input sequence files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from utility/strings.H:38,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:32,
from sequence/sequence.C:26:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void extractParameters::finalize()':
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/bits/vector.tcc:121:21: 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++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-generate.C
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/bits/vector.tcc:121:21: 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++/10/bits/vector.tcc:121:21: 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from utility/strings.H:38,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:32,
from sequence/sequence.C:26:
/usr/include/c++/10/bits/stl_vector.h: In function 'void decodeRange(char*, std::vector<T>&, std::vector<T>&) [with T = long long unsigned int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-mutate.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-sample.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister.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:272:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
272 | AS_UTL_writeFastA(outFile1, seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name());
| ^~~~~~~
sequence/sequence-sample.C:273:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
273 | 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:417:73: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
417 | AS_UTL_writeFastA(outFiles[of], seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name());
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-emit-fast.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-fast.C
In file included from sequence/sequence-shiftregister.C:31:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-slow.C
In file included from /usr/include/c++/10/vector:72,
from utility/strings.H:38,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:32,
from sequence/sequence-sample.C:30:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqEntry>::iterator' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const seqEntry&, const seqEntry&)>]':
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/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++/10/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
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_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++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1881 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from sequence/sequence-shiftregister-emit-fast.C:29:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
sequence/sequence-shiftregister-emit-fast.C: In function 'void emitShiftRegisterFast(shiftRegisterParameters&)':
sequence/sequence-shiftregister-emit-fast.C:52:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
52 | fprintf(stderr, "Emitting %lu bases, plus an extra %u.\n", srPar.length - srPar.order - 1 - 1, srPar.order - 1);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
sequence/sequence-shiftregister-emit-fast.C:53:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
53 | fprintf(stderr, " sr %0*lo\n", srPar.order, expandTo3(sr));
| ~~~~^ ~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %0*llo
sequence/sequence-shiftregister-emit-fast.C:54:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
54 | fprintf(stderr, " cyclen %lu\n", cyclen);
| ~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
sequence/sequence-shiftregister-emit-fast.C:55:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
55 | fprintf(stderr, " cycmax %lu\n", cycmax);
| ~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
sequence/sequence-shiftregister-emit-fast.C:56:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
56 | fprintf(stderr, " sv %0*lo\n", srPar.order, expandTo3(sv));
| ~~~~^ ~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %0*llo
sequence/sequence-shiftregister-emit-fast.C:57:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
57 | fprintf(stderr, " svmax %0*lo\n", srPar.order, expandTo3(svmax));
| ~~~~^ ~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %0*llo
sequence/sequence-shiftregister-emit-fast.C:58:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
58 | fprintf(stderr, " svmask %0*lo\n", srPar.order, expandTo3(svmask));
| ~~~~^ ~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %0*llo
In file included from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _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++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1662 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1925 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1937 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from sequence/sequence-shiftregister-search-fast.C:29:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
sequence/sequence-shiftregister-search-fast.C: In function 'void searchShiftRegisterFast(shiftRegisterParameters&)':
sequence/sequence-shiftregister-search-fast.C:47:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
47 | fprintf(stderr, " sr %0*lo\n", srPar.order, expandTo3(sr));
| ~~~~^ ~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %0*llo
sequence/sequence-shiftregister-search-fast.C:48:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
48 | fprintf(stderr, " cyclen %lu\n", cyclen);
| ~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
sequence/sequence-shiftregister-search-fast.C:49:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
49 | fprintf(stderr, " cycmax %lu\n", cycmax);
| ~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
sequence/sequence-shiftregister-search-fast.C:50:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
50 | fprintf(stderr, " sv %0*lo\n", srPar.order, expandTo3(sv));
| ~~~~^ ~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %0*llo
sequence/sequence-shiftregister-search-fast.C:51:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
51 | fprintf(stderr, " svmax %0*lo\n", srPar.order, expandTo3(svmax));
| ~~~~^ ~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %0*llo
sequence/sequence-shiftregister-search-fast.C:52:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
52 | fprintf(stderr, " svmask %0*lo\n", srPar.order, expandTo3(svmask));
| ~~~~^ ~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %0*llo
sequence/sequence-shiftregister-search-fast.C:131:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
131 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %0*lo\n",
| ~~~~^
| |
| long unsigned int
| %14llu
132 | cyclen,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
sequence/sequence-shiftregister-search-fast.C:131:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
131 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %0*lo\n",
| ~~~~^
| |
| long unsigned int
| %14llu
132 | cyclen,
133 | cycmax,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
sequence/sequence-shiftregister-search-fast.C:131:59: warning: format '%lo' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
131 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %0*lo\n",
| ~~~~^
| |
| long unsigned int
| %0*llo
......
136 | expandTo3(sv));
| ~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
/usr/include/c++/10/bits/stl_algo.h: In function 'void doSample_sample(sampleParameters&, uint64, uint64, std::vector<seqEntry>&)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from utility/strings.H:38,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:32,
from sequence/sequence-sample.C:30:
/usr/include/c++/10/bits/stl_vector.h: In function 'void doSample_paired(std::vector<char*>&, sampleParameters&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from sequence/sequence-shiftregister-search-slow.C:29:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
sequence/sequence-shiftregister-search-slow.C: In function 'void searchShiftRegisterSlow(shiftRegisterParameters&)':
sequence/sequence-shiftregister-search-slow.C:154:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
154 | fprintf(stderr, " cyclen %lu\n", cyclen);
| ~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
sequence/sequence-shiftregister-search-slow.C:155:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
155 | fprintf(stderr, " cycmax %lu\n", cycmax);
| ~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
sequence/sequence-shiftregister-search-slow.C:209:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
209 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %s\n",
| ~~~~^
| |
| long unsigned int
| %14llu
210 | cyclen,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
sequence/sequence-shiftregister-search-slow.C:209:34: 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, "%14lu/%14lu %7.3f%% for vector %s\n",
| ~~~~^
| |
| long unsigned int
| %14llu
210 | cyclen,
211 | cycmax,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-simulate.C
/usr/include/c++/10/bits/stl_vector.h: In function 'void doSample_single(std::vector<char*>&, sampleParameters&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-summarize.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C
sequence/sequence-simulate.C: In member function 'void simulateParameters::finalize()':
sequence/sequence-simulate.C:44:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
44 | char *path = findSharedFile("share/sequence", distribName);
| ^~~~~~~~~~~~~~~~
sequence/sequence-simulate.C: In function 'void doSimulate_loadSequences(simulateParameters&, std::vector<dnaSeq*>&, uint64&)':
sequence/sequence-simulate.C:89:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<dnaSeq*>::size_type' {aka 'unsigned int'} [-Wformat=]
89 | 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:194:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
194 | fprintf(stdout, ">read=%lu,%s,position=%lu,length=%u,%s\n",
| ~~^
| |
| long unsigned int
| %llu
195 | nReads+1,
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
sequence/sequence-simulate.C:194:48: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
194 | fprintf(stdout, ">read=%lu,%s,position=%lu,length=%u,%s\n",
| ~~^
| |
| long unsigned int
| %llu
......
197 | position,
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogramSimple(std::vector<long long unsigned int>)':
sequence/sequence-summarize.C:106:24: 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=]
106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn);
| ~~^
| |
| long unsigned int
| %llu
sequence/sequence-summarize.C:106:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn);
| ~~^ ~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
sequence/sequence-summarize.C: In function 'void doSummarize_dumpLengths(std::vector<long long unsigned int>)':
sequence/sequence-summarize.C:120:24: 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=]
120 | fprintf(stdout, "%lu\n", lengths[ii]);
| ~~^
| |
| long unsigned int
| %llu
sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogram(std::vector<long long unsigned int>, uint64, bool)':
sequence/sequence-summarize.C:290:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector<long long unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
290 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", 0.0, lengths.size(), lSum, histPlot[hp++]); // Occurs if only empty sequences in the input!
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| std::vector<long long unsigned int>::size_type {aka unsigned int}
sequence/sequence-summarize.C:292:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector<long long unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
292 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", (double)lSum / genomeSize, lengths.size(), lSum, histPlot[hp++]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| std::vector<long long unsigned int>::size_type {aka unsigned int}
sequence/sequence-summarize.C:294:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector<long long unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
294 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " ||\n", (double)lSum / genomeSize, lengths.size(), lSum);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| std::vector<long long unsigned int>::size_type {aka unsigned int}
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/overlapInCore-Build_Hash_Index.C:67:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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 overlapInCore/overlapInCore.H:66,
from overlapInCore/overlapInCore.C:51:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
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);
| ~~~~~^~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: 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
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/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::less<long long unsigned int> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: 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++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/10/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::less<long long unsigned int> >]':
/usr/include/c++/10/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++/10/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
/usr/include/c++/10/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
/usr/include/c++/10/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++/10/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
/usr/include/c++/10/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
/usr/include/c++/10/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
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_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::less<long long unsigned int> >]':
/usr/include/c++/10/bits/stl_algo.h:1881:5: 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
1881 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1881:5: 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++/10/bits/stl_algo.h:1881:5: 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++/10/bits/stl_algo.h:1886:25: 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
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: 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
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from utility/strings.H:38,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:32,
from sequence/sequence-summarize.C:30:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/10/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::less<long long unsigned int> >]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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++/10/bits/stl_algo.h:1959:25: 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
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void doSummarize_lengthHistogramSimple(std::vector<long long unsigned int>)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: 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
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: 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
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void doSummarize_dumpLengths(std::vector<long long unsigned int>)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: 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
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: 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
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/overlapInCore-Find_Overlaps.C:71:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
/usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: 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
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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++/10/bits/stl_algo.h:1959:25: 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
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C
/usr/include/c++/10/bits/stl_algo.h: In function 'void doSummarize_lengthHistogram(std::vector<long long unsigned int>, uint64, bool)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: 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
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: 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
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: 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
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C
In file included from /usr/include/c++/10/vector:67,
from utility/strings.H:38,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:32,
from sequence/sequence-summarize.C:30:
/usr/include/c++/10/bits/stl_vector.h: In function 'void doSummarize(std::vector<char*>&, summarizeParameters&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from utility/strings.H:38,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:32,
from sequence/sequence-summarize.C:30:
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/overlapInCore-Output.C:67:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
474 | }
| ^
sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/overlapInCore-Process_Overlaps.C:71:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/overlapInCore-Process_String_Overlaps.C:72:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C
overlapInCore/overlapInCorePartition.C: In function 'int main(int, char**)':
overlapInCore/overlapInCorePartition.C:430:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
430 | FILE *BAT = openOutput(outputPrefix, "ovlbat");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:431:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
431 | FILE *JOB = openOutput(outputPrefix, "ovljob");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:432:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
432 | FILE *OPT = openOutput(outputPrefix, "ovlopt");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:445:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
445 | renameToFinal(outputPrefix, "ovlbat");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:446:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
446 | renameToFinal(outputPrefix, "ovljob");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:447:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
447 | renameToFinal(outputPrefix, "ovlopt");
| ^~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/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-2.0+dfsg/Linux-armv7l/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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/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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C
minimap/mmapConvert.C: In function 'int main(int, char**)':
minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=]
139 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
142 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3,
| ~~~~~~~~~~~~~~~
| |
| int
minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=]
minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=]
minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=]
mhap/mhapConvert.C: In function 'int main(int, char**)':
mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=]
158 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
162 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3,
| ~~~~~~~~~~~~~~~
| |
| int
mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=]
mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=]
mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 11 has type 'int' [-Wformat=]
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionOverlaps.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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 utgcns/stashContains.H:35,
from utgcns/stashContains.C:30:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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 correction/generateCorrectionLayouts.C:37:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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}
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionLayouts.C
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C
correction/falconsense.C: In function 'void generateFalconConsensus(falconConsensus*, tgTig*, sqCache*, std::map<unsigned int, sqRead*>&, bool, uint32)':
correction/falconsense.C:207:41: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
207 | 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:207:51: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
207 | 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:359:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
359 | err.push_back("ERROR: no seqStore input (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
correction/falconsense.C:362:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
362 | err.push_back("ERROR: no corStore input (-C) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/set:60,
from utility/strings.H:37,
from stores/ovOverlap.H:45,
from stores/ovStore.H:42,
from wtdbg/wtdbgConvert.C:31:
/usr/include/c++/10/bits/stl_tree.h: In 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++/10/bits/stl_tree.h:2458:7: 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' changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-2.0+dfsg/Linux-armv7l/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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++/10/map:61,
from stores/tgTig.H:38,
from stores/tgStore.H:43,
from wtdbg/wtdbgConvert.C:33:
/usr/include/c++/10/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++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from correction/errorEstimate.C:34:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
/usr/include/c++/10/bits/stl_map.h: In function 'int main(int, char**)':
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C
In file included from utility/kmers.H:32,
from haplotyping/splitHaplotype.C:34:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
overlapBasedTrimming/trimReads.C: In function 'int main(int, char**)':
overlapBasedTrimming/trimReads.C:480:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
480 | readsIn .generatePlots(outputPrefix, "inputReads", 250);
| ^~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:481:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
481 | deletedIn.generatePlots(outputPrefix, "inputDeletedReads", 250);
| ^~~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:482:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
482 | noTrimIn .generatePlots(outputPrefix, "inputNoTrimReads", 250);
| ^~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:492:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
492 | readsOut .generatePlots(outputPrefix, "outputTrimmedReads", 250);
| ^~~~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:493:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
493 | noOvlOut .generatePlots(outputPrefix, "outputNoOvlReads", 250);
| ^~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:494:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
494 | deletedOut .generatePlots(outputPrefix, "outputDeletedReads", 250);
| ^~~~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:495:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
495 | noChangeOut.generatePlots(outputPrefix, "outputUnchangedReads", 250);
| ^~~~~~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:503:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
503 | trim5.generatePlots(outputPrefix, "trim5", 25);
| ^~~~~~~
overlapBasedTrimming/trimReads.C:504:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
504 | 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:74:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
74 | system(N);
| ~~~~~~^~~
In file included from haplotyping/splitHaplotype.C:34:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | 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:443:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
443 | 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:707:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
707 | ">%s\n", s->_names[ii].string());
| ^~~~~~~
haplotyping/splitHaplotype.C: In function 'int main(int, char**)':
haplotyping/splitHaplotype.C:771:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
771 | err.push_back("No input sequences supplied with either (-S) or (-R).\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplotyping/splitHaplotype.C:773:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
773 | err.push_back("Only one type of input reads (-S or -R) supported.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplotyping/splitHaplotype.C:775:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
775 | err.push_back("Not enough haplotypes (-H) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplotyping/splitHaplotype.C:854:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
854 | 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:855:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
855 | 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:857:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
857 | 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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustFlipped.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/mergeRanges.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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 overlapAlign/trimRead.C:33:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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 overlapAlign/computeOverlapAlignment.C:32:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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:581:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
581 | if (computeAlignment(_bRead, bbgn, bend, blen, "B", _bID, // Align all of sequence B into
| ^~~
overlapAlign/computeOverlapAlignment.C:582:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
582 | _aRead, abgn, aend, alen, "A", _aID, // sequence A with free ends.
| ^~~
overlapAlign/computeOverlapAlignment.C:626:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
626 | if (computeAlignment(_aRead, abgn, aend, alen, "A", _aID, // Align all of sequence A into
| ^~~
overlapAlign/computeOverlapAlignment.C:627:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
627 | _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends.
| ^~~
overlapAlign/computeOverlapAlignment.C:674:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
674 | if (computeAlignment(_bRead, bbgn, bend, blen, "B", _bID, // Align all of sequence B into
| ^~~
overlapAlign/computeOverlapAlignment.C:675:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
675 | _aRead, abgn, aend, alen, "A", _aID, // sequence A with free ends.
| ^~~
overlapAlign/computeOverlapAlignment.C:719:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
719 | if (computeAlignment(_aRead, abgn, aend, alen, "A", _aID, // Align all of sequence A into
| ^~~
overlapAlign/computeOverlapAlignment.C:720:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
720 | _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends.
| ^~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from overlapErrorAdjustment/findErrors.H:34,
from overlapErrorAdjustment/findErrors.C:30:
/usr/include/c++/10/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_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type 'Olap_Info_t' changed in GCC 9.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = Olap_Info_t*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:355:22: note: parameter passing for argument of type '_ValueType' {aka 'Olap_Info_t'} changed in GCC 9.1
355 | std::__adjust_heap(__first, __parent, __len, _GLIBCXX_MOVE(__value),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
356 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:263:25: note: parameter passing for argument of type '_ValueType' {aka 'Olap_Info_t'} changed in GCC 9.1
263 | std::__adjust_heap(__first, _DistanceType(0),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
264 | _DistanceType(__last - __first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
265 | _GLIBCXX_MOVE(__value), __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:263:25: note: parameter passing for argument of type '_ValueType' {aka 'Olap_Info_t'} changed in GCC 9.1
263 | std::__adjust_heap(__first, _DistanceType(0),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
264 | _DistanceType(__last - __first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
265 | _GLIBCXX_MOVE(__value), __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C
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",
| ^~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C
overlapErrorAdjustment/correctOverlaps-Correct_Frags.C: In function 'void Correct_Frags(coParameters*, sqStore*, FILE*)':
overlapErrorAdjustment/correctOverlaps-Correct_Frags.C:281:74: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
281 | AS_UTL_writeFastA(correctedReads, read.bases, read.basesLen, 60, ">%d\n", curID);
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/bogart.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/bogart.C:46:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | 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:338:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
338 | if (erateGraph < 0.0) err.push_back("Invalid overlap error threshold (-eg option); must be at least 0.0.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:339:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
339 | if (erateMax < 0.0) err.push_back("Invalid overlap error threshold (-eM option); must be at least 0.0.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:340:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
340 | if (prefix == NULL) err.push_back("No output prefix name (-o option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:341:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
341 | if (seqStorePath == NULL) err.push_back("No sequence store (-S option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:342:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
342 | if (ovlStorePath == NULL) err.push_back("No overlap store (-O option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:736:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
736 | writeTigsToStore(contigs, prefix, "ctg", true);
| ^~~~~
bogart/bogart.C:756:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
756 | writeTigsToStore(unitigs, prefix, "utg", true);
| ^~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C
In file included from bogart/AS_BAT_Unitig.H:49,
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:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_BestOverlapGraph.C:46:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from /usr/include/c++/10/vector:72,
from utility/files.H:36,
from stores/ovStore.H:38,
from bogart/AS_BAT_ReadInfo.H:30,
from bogart/AS_BAT_AssemblyGraph.C:26:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BestPlacement>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from utility/files.H:36,
from stores/ovStore.H:38,
from bogart/AS_BAT_ReadInfo.H:30,
from bogart/AS_BAT_AssemblyGraph.C:26:
/usr/include/c++/10/bits/stl_vector.h: In function '_ZN13AssemblyGraph10buildGraphEPKcdR9TigVector._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BestPlacement*, std::vector<BestPlacement> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
bogart/AS_BAT_AssemblyGraph.C:164:9: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
164 | #pragma omp parallel for schedule(dynamic, blockSize)
| ^~~
bogart/AS_BAT_ChunkGraph.C: In function 'ReadEnd followOverlap(ReadEnd)':
bogart/AS_BAT_ChunkGraph.C:120:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
120 | followOverlap(ReadEnd end) {
| ^~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+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
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DetectSpurs.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
bogart/AS_BAT_BestOverlapGraph.C: In function 'double _ZL12overlapScorejj.part.0(uint32, uint32)':
bogart/AS_BAT_BestOverlapGraph.C:457:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
457 | overlapScore(uint32 aid, uint32 bid) {
| ^~~~~~~~~~~~
bogart/AS_BAT_BestOverlapGraph.C:457:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
bogart/AS_BAT_BestOverlapGraph.C:457:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
In file included from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1881 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bogart/AS_BAT_Unitig.H:49,
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:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | 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:49,
from bogart/AS_BAT_DetectSpurs.C:31:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
bogart/AS_BAT_BestOverlapGraph.C: In member function 'void BestOverlapGraph::removeContainedDovetails()':
bogart/AS_BAT_BestOverlapGraph.C:942:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
942 | BestOverlapGraph::removeContainedDovetails(void) {
| ^~~~~~~~~~~~~~~~
In file included from bogart/AS_BAT_Unitig.H:49,
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:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Instrumentation.C
In file included from /usr/include/c++/10/vector:72,
from utility/files.H:36,
from stores/ovStore.H:38,
from bogart/AS_BAT_ReadInfo.H:30,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void BestOverlapGraph::findErrorRateThreshold()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from utility/files.H:36,
from stores/ovStore.H:38,
from bogart/AS_BAT_ReadInfo.H:30,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from utility/files.H:36,
from stores/ovStore.H:38,
from bogart/AS_BAT_ReadInfo.H:30,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C
bogart/AS_BAT_BestOverlapGraph.C:156:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
156 | BestOverlapGraph::findErrorRateThreshold(void) {
| ^~~~~~~~~~~~~~~~
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_Instrumentation.C:43:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
bogart/AS_BAT_Instrumentation.C: In function 'void reportTigs(TigVector&, const char*, const char*, uint64)':
bogart/AS_BAT_Instrumentation.C:421:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
421 | writeTigsToStore(tigs, getLogFilePrefix(), "tig", false);
| ^~~~~
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-2.0+dfsg/src/AS_global.H:67,
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-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C
bogart/AS_BAT_CreateUnitigs.C: In function 'uint32 checkRead(Unitig*, ufNode*, std::vector<overlapPlacement>&, TigVector&, std::vector<breakPointEnd>&, uint32, uint32, bool)':
bogart/AS_BAT_CreateUnitigs.C:319:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
319 | checkRead(Unitig *tgA,
| ^~~~~~~~~
bogart/AS_BAT_BestOverlapGraph.C: In member function 'void BestOverlapGraph::removeSpannedSpurs(const char*, uint32)':
bogart/AS_BAT_BestOverlapGraph.C:489:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
489 | BestOverlapGraph::removeSpannedSpurs(const char *prefix, uint32 spurDepth) {
| ^~~~~~~~~~~~~~~~
In file included from bogart/AS_BAT_Unitig.H:49,
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:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C
bogart/AS_BAT_MarkRepeatReads.C: In function 'uint32 splitTig(TigVector&, Unitig*, std::vector<breakPointCoords>&, Unitig**, int32*, uint32*, uint32*, bool)':
bogart/AS_BAT_MarkRepeatReads.C:170:64: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'std::vector<breakPointCoords>::size_type' {aka 'unsigned int'} [-Wformat=]
170 | fprintf(stderr, "Failed to place read %u at %d-%d with %lu BPs:\n", frg.ident, frgbgn, frgend, BP.size());
| ~~^ ~~~~~~~~~
| | |
| long unsigned int std::vector<breakPointCoords>::size_type {aka unsigned int}
| %u
bogart/AS_BAT_Instrumentation.C: In function 'void reportOverlaps(TigVector&, const char*, const char*)':
bogart/AS_BAT_Instrumentation.C:474:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
474 | reportOverlaps(TigVector &tigs, const char *UNUSED(prefix), const char *UNUSED(name)) {
| ^~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OptimizePositions.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_MergeOrphans.C:35:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
bogart/AS_BAT_MergeOrphans.C: In function 'void findPotentialOrphans(TigVector&, BubTargetList&)':
bogart/AS_BAT_MergeOrphans.C:196:69: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'int' [-Wformat=]
196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n",
| ~~^
| |
| long int
| %d
197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end,
198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang,
| ~~~~~~~~~~~~~~
| |
| int
bogart/AS_BAT_MergeOrphans.C:196:73: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'int' [-Wformat=]
196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n",
| ~~^
| |
| long int
| %d
197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end,
198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang,
| ~~~~~~~~~~~~~~
| |
| int
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_OptimizePositions.C:44:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Outputs.C
bogart/AS_BAT_MarkRepeatReads.C: In function 'bestSco scoreBestOverlap(TigVector&, ufNode*, ufNode*, bool, bool)':
bogart/AS_BAT_MarkRepeatReads.C:774:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
774 | scoreBestOverlap(TigVector &tigs, ufNode *rdA, ufNode *rdB, bool is3p, bool internal) {
| ^~~~~~~~~~~~~~~~
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_Outputs.C:47:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | 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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C
bogart/AS_BAT_OptimizePositions.C: In member function 'void Unitig::optimize_initPlace(uint32, optPos*, optPos*, bool, std::set<unsigned int>&, bool)':
bogart/AS_BAT_OptimizePositions.C:232:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
232 | Unitig::optimize_initPlace(uint32 ii,
| ^~~~~~
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_OverlapCache.C:49:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from /usr/include/c++/10/vector:72,
from utility/files.H:36,
from stores/ovStore.H:38,
from bogart/AS_BAT_ReadInfo.H:30,
from bogart/AS_BAT_MergeOrphans.C:30:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<overlapPlacement>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from utility/files.H:36,
from stores/ovStore.H:38,
from bogart/AS_BAT_ReadInfo.H:30,
from bogart/AS_BAT_MergeOrphans.C:30:
/usr/include/c++/10/bits/stl_vector.h: In function 'void assignReadsToTargets(Unitig*, std::vector<overlapPlacement>*, std::vector<candidatePop*>)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<overlapPlacement*, std::vector<overlapPlacement> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C
/usr/include/c++/10/bits/stl_vector.h: In function '_Z24findOrphanReadPlacementsR9TigVectorRSt3mapIjSt6vectorIjSaIjEESt4lessIjESaISt4pairIKjS4_EEEdd._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<overlapPlacement*, std::vector<overlapPlacement> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_PlaceContains.C:43:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | 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:49,
from bogart/AS_BAT_PlaceReadUsingOverlaps.C:43:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
bogart/AS_BAT_MergeOrphans.C: In function 'void findPotentialOrphans(TigVector&, BubTargetList&)':
bogart/AS_BAT_MergeOrphans.C:126:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
126 | findPotentialOrphans(TigVector &tigs,
| ^~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PromoteToSingleton.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_PopulateUnitig.C:42:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ReadInfo.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_PromoteToSingleton.C:40:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from /usr/include/c++/10/vector:72,
from utility/files.H:36,
from stores/ovStore.H:38,
from bogart/AS_BAT_ReadInfo.H:30,
from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<overlapPlacement>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<overlapPlacement>::iterator' changed in GCC 7.1
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SetParentAndHang.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SplitDiscontinuous.C
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigGraph.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_SetParentAndHang.C:41:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from /usr/include/c++/10/vector:67,
from utility/files.H:36,
from stores/ovStore.H:38,
from bogart/AS_BAT_ReadInfo.H:30,
from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'bool placeReadUsingOverlaps(TigVector&, Unitig*, uint32, std::vector<overlapPlacement>&, uint32)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<overlapPlacement*, std::vector<overlapPlacement> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigVector.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_SplitDiscontinuous.C:41:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
bogart/AS_BAT_PlaceReadUsingOverlaps.C:532:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
532 | placeReadUsingOverlaps(TigVector &tigs,
| ^~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig.C
In file included from bogart/AS_BAT_Unitig.H:49,
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:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | 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:49,
from bogart/AS_BAT_TigVector.C:28:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_AddRead.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_Unitig.C:39:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogus/bogus/bogus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogus/bogus.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_Unitig_AddRead.C:43:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogus/bogus/bogusUtil.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogus/bogusUtil.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C:43:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | 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:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utgcns/utgcns.C: In function 'uint32 createPartitions_greedilyPartition(cnsParameters&, tigInfo*, uint32)':
utgcns/utgcns.C:294:35: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
294 | fprintf(stderr, "%9u %9lu %9lu %12lu %9.3f %9u\n",
| ~~~^
| |
| long unsigned int
| %9llu
295 | tigs[ti].tigID,
296 | tigs[ti].tigChildren,
| ~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utgcns/utgcns.C:294:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
294 | fprintf(stderr, "%9u %9lu %9lu %12lu %9.3f %9u\n",
| ~~~^
| |
| long unsigned int
| %9llu
......
297 | tigs[ti].tigLength,
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utgcns/utgcns.C:294:46: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
294 | fprintf(stderr, "%9u %9lu %9lu %12lu %9.3f %9u\n",
| ~~~~^
| |
| long unsigned int
| %12llu
......
298 | tigs[ti].consensusArea,
| ~~~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utgcns/utgcns.C: In function 'uint64* createPartitions_outputPartitions(cnsParameters&, tigInfo*, uint32, uint32)':
utgcns/utgcns.C:363:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
363 | parts[pi]->writeIFFobject("MAGC", magc);
| ^~~~~~
utgcns/utgcns.C:364:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
364 | parts[pi]->writeIFFobject("VERS", vers);
| ^~~~~~
utgcns/utgcns.C:365:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
365 | parts[pi]->writeIFFobject("DEFV", defv);
| ^~~~~~
utgcns/utgcns.C: In function 'void createPartitions(cnsParameters&)':
utgcns/utgcns.C:419:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
419 | fprintf(partFile, "%9u %9lu %9lu %12lu %9.3f %9u %9.3f\n",
| ~~~^
| |
| long unsigned int
| %9llu
420 | tigs[ti].tigID,
421 | tigs[ti].tigChildren,
| ~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utgcns/utgcns.C:419:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
419 | fprintf(partFile, "%9u %9lu %9lu %12lu %9.3f %9u %9.3f\n",
| ~~~^
| |
| long unsigned int
| %9llu
......
422 | tigs[ti].tigLength,
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utgcns/utgcns.C:419:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
419 | fprintf(partFile, "%9u %9lu %9lu %12lu %9.3f %9u %9.3f\n",
| ~~~~^
| |
| long unsigned int
| %12llu
......
423 | tigs[ti].consensusArea,
| ~~~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utgcns/utgcns.C: In function 'std::map<unsigned int, sqRead*>* loadPartitionedReads(char*)':
utgcns/utgcns.C:582:75: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
582 | fprintf(stderr, "File '%s' isn't a utgcns seqFile: found magic 0x%016lx.\n", seqFile, magc), exit(1);
| ~~~~~^ ~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
utgcns/utgcns.C:588:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
588 | fprintf(stderr, "File '%s' is a utgcns seqFile, but an unsupported version %lu.\n", seqFile, vers), exit(1);
| ~~^ ~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utgcns/utgcns.C: In function 'int main(int, char**)':
utgcns/utgcns.C:887:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
887 | err.push_back("ERROR: No sequence data! Need one of seqStore (-S), read file (-R) or package (-p).\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/utgcns.C:890:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
890 | err.push_back("ERROR: No tigStore (-T) OR no test tig (-t) OR no package (-p) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C
In file included from /usr/include/c++/10/vector:72,
from utility/files.H:36,
from bogus/bogusUtil.H:44,
from bogus/bogusUtil.C:43:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<genomeAlignment>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from utility/files.H:36,
from bogus/bogusUtil.H:44,
from bogus/bogusUtil.C:43:
/usr/include/c++/10/bits/stl_vector.h: In function 'void addAlignment(std::vector<genomeAlignment>&, int32, int32, int32, bool, int32, int32, double, int32, int32, int32)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const genomeAlignment&, const genomeAlignment&)>]':
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/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++/10/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++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _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++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1662 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1925 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1937 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__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++/10/bits/stl_algo.h:1969:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1969 | __sort(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~
/usr/include/c++/10/bits/stl_algo.h:1969:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
/usr/include/c++/10/bits/stl_algo.h: In function 'int main(int, char**)':
/usr/include/c++/10/bits/stl_algo.h:4894:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
4894 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__comp));
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:4894:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
4894 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__comp));
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C
/usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C
cp -pf pipelines/canu.pl /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/canu
chmod +x /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/canu
cp -pf pipelines/canu-time.pl /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/canu-time
chmod +x /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/canu-time
echo > /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here."
chmod -x /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/canu.defaults
cp -pf sequence/share/ultra-long-nanopore /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/share/sequence/ultra-long-nanopore
cp -pf sequence/share/pacbio /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/share/sequence/pacbio
cp -pf sequence/share/pacbio-hifi /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/share/sequence/pacbio-hifi
cp -pf pipelines/canu/Consensus.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/CorrectReads.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/HaplotypeReads.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Configure.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Defaults.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Execution.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/SequenceStore.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_Cloud.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_DNANexus.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_LSF.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_PBSTorque.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_SGE.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_Slurm.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Meryl.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Output.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapBasedTrimming.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapErrorAdjustment.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapInCore.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapMhap.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapMMap.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapStore.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Report.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Unitig.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/
g++ -o /<<BUILDDIR>>/canu-2.0+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-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap AS_global.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from gfa/alignGFA.C:32:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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 utgcns/unitigConsensus.H:67,
from utgcns/unitigConsensus.C:74:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | 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&, sequences&, bool, bool)':
gfa/alignGFA.C:507:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
507 | success &= checkRecord_align("ALL",
| ^~~~~
gfa/alignGFA.C:535:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
535 | success &= checkRecord_align("LEFT",
| ^~~~~~
gfa/alignGFA.C:541:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
541 | success &= checkRecord_align("RIGHT",
| ^~~~~~~
gfa/alignGFA.C: In function 'void processBEDtoGFA(char*, uint32, char*, char*, double, uint32)':
gfa/alignGFA.C:782:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
782 | gfaFile *gfa = new gfaFile("H\tVN:Z:1.0");
| ^~~~~~~~~~~~~
gfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)':
gfa/alignGFA.C:162:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
162 | system(Pfile);
| ~~~~~~^~~~~~~
gfa/alignGFA.C:140:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=]
140 | sprintf(Pname, "plot-%s-%s", Aname, Bname);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from gfa/alignGFA.C:30:
/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:141:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=]
141 | sprintf(Pfile, "plot-%s-%s.sh", Aname, Bname);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from gfa/alignGFA.C:30:
/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:160:27: warning: '%s' directive writing up to 4096 bytes into a region of size 4089 [-Wformat-overflow=]
160 | sprintf(Pfile, "sh plot-%s-%s.sh", Aname, Bname);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from gfa/alignGFA.C:30:
/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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ar rv /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/libcanu.a /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/AS_global.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/edlib.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-buffered.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-compressed.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-memoryMapped.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/logging.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/strings.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system-stackTrace.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sequence.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-reader.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-block.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-stream.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-statistics.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-exact.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/bits.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/hexDump.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/md5.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/mt19937ar.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/objectStore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/speedCounter.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sweatShop.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/computeGlobalScore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqCache.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqLibrary.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadData.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadDataWriter.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreBlob.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreConstructor.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreInfo.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovOverlap.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreWriter.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFilter.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFile.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreHistogram.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgStore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTig.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/gfa.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/bed.o
ar: creating /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib/libcanu.a
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/AS_global.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/edlib.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-buffered.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-compressed.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-memoryMapped.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/logging.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/strings.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system-stackTrace.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sequence.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-reader.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-block.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-stream.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-statistics.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-exact.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/bits.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/hexDump.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/md5.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/mt19937ar.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/objectStore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/speedCounter.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sweatShop.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/computeGlobalScore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqCache.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqLibrary.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadData.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadDataWriter.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreBlob.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreConstructor.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreInfo.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovOverlap.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreWriter.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFilter.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFile.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreHistogram.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgStore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTig.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/gfa.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/bed.o
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/dumpBlob -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreBuild -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreConfig -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreBucketizer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreSorter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreIndexer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreStats -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/sqStoreCreate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/sqStoreDumpFASTQ -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/sqStoreDumpMetaData -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/tgStoreCompress -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/tgStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreDump/stores/tgStoreDump.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/tgStoreLoad -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/tgStoreFilter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/tgTigDisplay -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/loadCorrectedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/loadTrimmedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/loadErates -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/loadErates/stores/loadErates.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/meryl -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/meryl.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylCountArray.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylInput.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-count.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-countSimple.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-histogram.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-nextMer.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/meryl-import -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl-import/meryl/meryl-import.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl-import/meryl/merylCountArray.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/meryl-lookup -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl-lookup/meryl/meryl-lookup.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/sequence -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-extract.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-generate.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-mutate.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-sample.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-simulate.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-summarize.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/overlapInCore -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/overlapInCorePartition -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/overlapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/overlapImport -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapImport/overlapInCore/overlapImport.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/overlapPair -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapPair/overlapInCore/overlapPair.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/edalign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/edalign/overlapInCore/edalign.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/prefixEditDistance-matchLimitGenerate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/mhapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/mhapConvert/mhap/mhapConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/mmapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/mmapConvert/minimap/mmapConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/wtdbgConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/filterCorrectionOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/generateCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/filterCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/falconsense -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/falconsense/correction/falconsense.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/falconsense/utgcns/stashContains.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/errorEstimate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/splitHaplotype -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/trimReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/splitReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/mergeRanges -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/overlapAlign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/trimRead.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/findErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/bogart -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/bogart.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Logging.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Outputs.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigVector.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/bogus -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogus/bogus/bogus.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogus/bogus/bogusUtil.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/alignGFA/gfa/alignGFA.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/utgcns.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/stashContains.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu
Success!
canu installed in /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv7l/bin/canu
make[2]: Leaving directory '/<<BUILDDIR>>/canu-2.0+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-2.0+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-2.0+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-2.0+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/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/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/bogus 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/overlapInCore 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' in '../canu_2.0+dfsg-1+b2_armhf.deb'.
dpkg-deb: building package 'canu-dbgsym' in '../canu-dbgsym_2.0+dfsg-1+b2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../canu_2.0+dfsg-1+b2_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 2020-12-06T13:16:34Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
canu_2.0+dfsg-1+b2_armhf.changes:
---------------------------------
Format: 1.8
Date: Sat, 28 Mar 2020 00:42:06 +0100
Source: canu (2.0+dfsg-1)
Binary: canu canu-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 2.0+dfsg-1+b2
Distribution: bullseye-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
canu - single molecule sequence assembler for genomes
Changes:
canu (2.0+dfsg-1+b2) bullseye-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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96f0d12b0e9eaf3140fcf73b98b5f965795858b3 1039844 canu_2.0+dfsg-1+b2_armhf.deb
Checksums-Sha256:
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740ba29d89b5395e9caad1f263f939dab74004d19fe302b4d4a20737e8a398e0 7050 canu_2.0+dfsg-1+b2_armhf.buildinfo
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Files:
cd0073f57a456a40966b0cfa5b597220 11761780 debug optional canu-dbgsym_2.0+dfsg-1+b2_armhf.deb
b0d4d58ba6c2609e786073d0ed9d17e9 7050 science optional canu_2.0+dfsg-1+b2_armhf.buildinfo
2c3201745c38e2c3bc4f94590dffa9ba 1039844 science optional canu_2.0+dfsg-1+b2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
canu-dbgsym_2.0+dfsg-1+b2_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 11761780 bytes: control archive=2868 bytes.
2394 bytes, 12 lines control
5384 bytes, 51 lines md5sums
Package: canu-dbgsym
Source: canu (2.0+dfsg-1)
Version: 2.0+dfsg-1+b2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 12979
Depends: canu (= 2.0+dfsg-1+b2)
Section: debug
Priority: optional
Description: debug symbols for canu
Build-Ids: 0a9f5b651e323fc8589442e7cd8bc9ecafd62873 0b5b4fe24cfab1944c3e29df030783ed5208ab65 0c609158dbd803de94eb3ff401af07004a9fac82 0e4c9daac0b69e6ee2a25bccf74f8f44c441b816 0e80476664e011967ed50abb961569aa74962db7 0f3255489b7aa90ccf4b04902a9dc479ea86cfe5 1cc813e6fe5d70409c6d21516c682e9c7be4a033 27ec9dcc32ecbca75ebea79d18a55dc76cd9b208 314479b323b2ee7f1d1363875123fcacf749f597 360d00889a37566a54fe32e58c35180bbf13dd73 384417dbd1c0725ae9ee9ba39c8425b816c684ca 3e8b32746977a6409d046ab97cdb3320ce3afee5 471d86867d5cd2b9d2ed85bf110728b456f51347 517858ac2ae87e971229a327b09a5572a5f7d1cc 55b1336e40f09bad841054d6ab1d046efe342127 58326320c2eeb897b8ec92292851e2e0b0cb2cfc 58f52db97a114ab5b15715e68e3fceb823774e70 5a6de05ef6409bef24d25efbcba1834201535d0d 60c9fb5be350825e0cd61b3f591c713acf92ef2c 6af9593b4ce93855e90c90c5c0f008f4e581b150 81f073f470ba68a90670c640076a4db6deaa239a 8683d39b9cf1bb8eb86ef6cd490d03e222dbd185 88ea53b62c3d8bfef4ce284446d15f6c33e62613 8f5a50ddb0a3d576fbd71e8f7cac3b6194d9205f 90ba7e9bdbdfb1e4261ad9d47f239bec7991a7a1 93a264714c53953f61918f3825fd60eabea20230 9bb137eac3f62cb526458896adcf65c958a9b3e0 a000da9ef62852d0143300c9b52ceec60024f2db b81b10b3b9b93cb6906a49f672ccadc59a9c4637 be596447534ebb2ef5fa26477f7b818d14a4353b c93e69f6da98aaa2b8b1dc11df9e749f604bb626 cc590b27d3d699f09173d7c8ba5410a99a20d9e9 ce8fda4ce16861ca39290e592661bf01c6202f79 cf3305234001b1c5c88523e4a2841194f14dd7c9 d063b89b01222534fc48be4af3faf8923c452b8f d7ce2a765d74f75bb7ccccdd35acedfe915aaac9 d86cab1bbff36998f5d163ffa64bafda45aeb918 dc25bfbec425d8612e86b98ed33a6f60419605b5 dc367597be546abaa413a2d1105111a6ae138575 ddbb6b9b903b700bb84b3d7550a397f0832b5281 e4866c855b1c91fa798558d43efcfbfb115d083e e8c8471034e84971f3b509bc38af71c3b0a59e5b e8f68653a473637ca86d8282a2c3faa1d95cca48 ec18d377c91dae153eaa9118af976465d1cdd58d f36d770daa7911480278c54cfa990cee4e60595d f384548481d46287488cfa60ab73d7c6391c1140 f4f35d380c252dc10453a5c8b8942a594eb87408 fa72288b2582203c6cb762b49141daeede18da8e fb6d526fb6555a5fc25b9403d529dbaab9f7e836 fda42de6ce56ad86a23aa9818908e13074344d3d
drwxr-xr-x root/root 0 2020-03-27 23:42 ./
drwxr-xr-x root/root 0 2020-03-27 23:42 ./usr/
drwxr-xr-x root/root 0 2020-03-27 23:42 ./usr/lib/
drwxr-xr-x root/root 0 2020-03-27 23:42 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-03-27 23:42 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-03-27 23:42 ./usr/lib/debug/.build-id/0a/
-rw-r--r-- root/root 294140 2020-03-27 23:42 ./usr/lib/debug/.build-id/0a/9f5b651e323fc8589442e7cd8bc9ecafd62873.debug
drwxr-xr-x root/root 0 2020-03-27 23:42 ./usr/lib/debug/.build-id/0b/
-rw-r--r-- root/root 342024 2020-03-27 23:42 ./usr/lib/debug/.build-id/0b/5b4fe24cfab1944c3e29df030783ed5208ab65.debug
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-rw-r--r-- root/root 164776 2020-03-27 23:42 ./usr/lib/debug/.build-id/0c/609158dbd803de94eb3ff401af07004a9fac82.debug
drwxr-xr-x root/root 0 2020-03-27 23:42 ./usr/lib/debug/.build-id/0e/
-rw-r--r-- root/root 398396 2020-03-27 23:42 ./usr/lib/debug/.build-id/0e/4c9daac0b69e6ee2a25bccf74f8f44c441b816.debug
-rw-r--r-- root/root 246720 2020-03-27 23:42 ./usr/lib/debug/.build-id/0e/80476664e011967ed50abb961569aa74962db7.debug
drwxr-xr-x root/root 0 2020-03-27 23:42 ./usr/lib/debug/.build-id/0f/
-rw-r--r-- root/root 284968 2020-03-27 23:42 ./usr/lib/debug/.build-id/0f/3255489b7aa90ccf4b04902a9dc479ea86cfe5.debug
drwxr-xr-x root/root 0 2020-03-27 23:42 ./usr/lib/debug/.build-id/1c/
-rw-r--r-- root/root 149888 2020-03-27 23:42 ./usr/lib/debug/.build-id/1c/c813e6fe5d70409c6d21516c682e9c7be4a033.debug
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canu_2.0+dfsg-1+b2_armhf.deb
----------------------------
new Debian package, version 2.0.
size 1039844 bytes: control archive=3116 bytes.
903 bytes, 22 lines control
5892 bytes, 85 lines md5sums
Package: canu
Source: canu (2.0+dfsg-1)
Version: 2.0+dfsg-1+b2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8053
Depends: libc6 (>= 2.29), libgcc-s1 (>= 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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-rwxr-xr-x root/root 91732 2020-03-27 23:42 ./usr/lib/canu/bin/meryl-import
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-rwxr-xr-x root/root 120460 2020-03-27 23:42 ./usr/lib/canu/bin/mhapConvert
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 160480
Build-Time: 1146
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 695
Job: canu_2.0+dfsg-1
Machine Architecture: armhf
Package: canu
Package-Time: 1897
Source-Version: 2.0+dfsg-1
Space: 160480
Status: successful
Version: 2.0+dfsg-1+b2
--------------------------------------------------------------------------------
Finished at 2020-12-06T13:16:34Z
Build needed 00:31:37, 160480k disc space