canu →
2.0+dfsg-1+b1 →
armhf → 2020-09-28 11:04:41
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| canu 2.0+dfsg-1+b1 (armhf) Mon, 28 Sep 2020 10:55:57 +0000 |
+==============================================================================+
Package: canu
Version: 2.0+dfsg-1+b1
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-17c366f7-239e-4a02-a9a5-99e8d9a7b2e1' 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 [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.3 MB in 10s (2376 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 (3868 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/canu-9d8R7Z/canu-2.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/canu-9d8R7Z' 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-VmUEcr/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-VmUEcr/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-VmUEcr/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-VmUEcr/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-VmUEcr/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-VmUEcr/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-VmUEcr/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-VmUEcr/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (3048 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 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 34 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-VmUEcr/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (47.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12498 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-VmUEcr/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-VmUEcr/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-VmUEcr/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-VmUEcr/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-VmUEcr/apt_archive ./ Sources [526 B]
Get:5 copy:/<<BUILDDIR>>/resolver-VmUEcr/apt_archive ./ Packages [609 B]
Fetched 2468 B in 1s (3872 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install canu build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev binfmt-support 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 libgssapi-krb5-2 libguava-java libicu67
libjpeg62-turbo libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblcms2-2 libmagic-mgc libmagic1 libmeryl-dev libnspr4
libnss3 libpcsclite1 libpipeline1 libpng16-16 libsigsegv2 libssl1.1
libssw-java libsub-override-perl 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
krb5-doc krb5-user libjsr305-java-doc liblcms2-utils pcscd libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho
fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl
Recommended packages:
curl | wget | lynx alsa-ucm-conf alsa-topology-conf dbus
libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs
krb5-locales libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev binfmt-support 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 libgssapi-krb5-2 libguava-java libicu67
libjpeg62-turbo libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblcms2-2 libmagic-mgc libmagic1 libmeryl-dev libnspr4
libnss3 libpcsclite1 libpipeline1 libpng16-16 libsigsegv2 libssl1.1
libssw-java libsub-override-perl 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, 92 newly installed, 0 to remove and 34 not upgraded.
Need to get 88.3 MB/89.5 MB of archives.
After this operation, 402 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-VmUEcr/apt_archive ./ sbuild-build-depends-canu-dummy 0.invalid.0 [892 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 1.1.1g-1 [811 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 libkrb5support0 armhf 1.17-10+b3 [62.0 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-10+b3 [112 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-10+b3 [318 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-10+b3 [135 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libcups2 armhf 2.3.3-3+rpi1 [310 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf liblcms2-2 armhf 2.9-4 [119 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:2.0.5-1.1 [121 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2 [259 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.2+dfsg-3 [347 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libnspr4 armhf 2:4.28-1 [89.9 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libnss3 armhf 2:3.56-1 [1084 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libasound2-data all 1.2.3.2-1 [38.1 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libasound2 armhf 1.2.3.2-1 [301 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libpcsclite1 armhf 1.9.0-1 [56.7 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-2 [135 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.12-1 [311 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.12-1 [700 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libxi6 armhf 2:1.7.10-1 [77.9 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+20 [252 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libxtst6 armhf 2:1.2.3-1 [26.3 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf openjdk-11-jre-headless armhf 11.0.8+10-1 [33.1 MB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf default-jre-headless armhf 2:1.11-72+b4 [11.2 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates-java all 20190909 [15.7 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.181-1 [161 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.0-2 [1173 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6 [578 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf fastjar armhf 2:0.98-7 [42.7 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf jaligner all 1.0+dfsg-7 [136 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf jarwrapper all 0.77 [21.7 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libapache-pom-java all 18-1 [4676 B]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libboost1.71-dev armhf 1.71.0-6+b1 [9099 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.71.0.3+b3 [4620 B]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libcommons-parent-java all 43-1 [10.8 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libcommons-compress-java all 1.20-1 [574 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libfastutil-java all 8.3.1-1 [15.4 MB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libfilesys-df-perl armhf 0.92-6+b5 [12.8 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libjsr305-java all 0.1~+svn49-11 [26.9 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libguava-java all 29.0-5 [2419 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libmeryl-dev armhf 0~20150903+r2013-8 [65.3 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libssw-java armhf 1.1-11 [18.7 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf mhap all 2.1.3+dfsg-2 [160 kB]
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Setting up libxtst6:armhf (2:1.2.3-1) ...
Setting up po-debconf (1.0.21) ...
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 default-jre-headless (2:1.11-72+b4) ...
Setting up debhelper (13.2.1) ...
Setting up jaligner (1.0+dfsg-7) ...
Setting up mhap (2.1.3+dfsg-2) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-canu-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-3+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.
Setting up openjdk-11-jre-headless:armhf (11.0.8+10-1) ...
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-5+rpi1 gcc-10_10.2.0-5+rpi1 libc6-dev_2.31-3+rpi1 libstdc++-10-dev_10.2.0-5+rpi1 libstdc++6_10.2.0-5+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 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_3.5.47 bash_5.0-7 binfmt-support_2.2.1-1 binutils_2.35-2+rpi1 binutils-arm-linux-gnueabihf_2.35-2+rpi1 binutils-common_2.35-2+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_8.30-3 cpp_4:10.1.0-1+rpi1 cpp-10_10.2.0-5+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debianutils_4.9.1 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_1.24-1 fastjar_2:0.98-7 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 g++_4:10.1.0-1+rpi1 g++-10_10.2.0-5+rpi1 gcc_4:10.1.0-1+rpi1 gcc-10_10.2.0-5+rpi1 gcc-10-base_10.2.0-5+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_3.4-1 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 libacl1_2.2.53-8 libapache-pom-java_18-1 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.2.0-5+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_10.2.0-5+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libavahi-client3_0.8-3+b2 libavahi-common-data_0.8-3+b2 libavahi-common3_0.8-3+b2 libbinutils_2.35-2+rpi1 libblkid1_2.36-3 libboost-dev_1.71.0.3+b3 libboost-iostreams1.71.0_1.71.0-6+b1 libboost1.71-dev_1.71.0-6+b1 libbrotli1_1.0.9-2 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-3+rpi1 libc-dev-bin_2.31-3+rpi1 libc6_2.31-3+rpi1 libc6-dev_2.31-3+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.43-1 libcap2-bin_1:2.43-1 libcc1-0_10.2.0-5+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_2.35-2+rpi1 libctf0_2.35-2+rpi1 libcups2_2.3.3-3+rpi1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdbus-1-3_1.12.20-1+b3 libdebconfclient0_0.253 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5+rpi1 libelf1_0.181-1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfastutil-java_8.3.1-1 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libfilesys-df-perl_0.92-6+b5 libfontconfig1_2.13.1-4.2 libfreetype6_2.10.2+dfsg-3 libgcc-10-dev_10.2.0-5+rpi1 libgcc-s1_10.2.0-5+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.0-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.2.0-5+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libguava-java_29.0-5 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-1 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_2.4.51+dfsg-1 libldap-common_2.4.51+dfsg-1 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~rc1-1 libmpfr6_4.1.0-3 libncursesw6_6.2-1 libnettle8_3.6-2 libnpth0_1.6-2 libnspr4_2:4.28-1 libnss3_2:3.56-1 libp11-kit0_0.23.21-2 libpam-cap_1:2.43-1 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 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.2-1 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libssw-java_1.1-11 libstdc++-10-dev_10.2.0-5+rpi1 libstdc++6_10.2.0-5+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.2-1+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.2.0-5+rpi1 libuchardet0_0.0.7-1 libudev1_246.2-1+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 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-2 mount_2.36-3 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 openjdk-11-jre-headless_11.0.8+10-1 openssl_1.1.1g-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 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_2.96-4 tar_1.30+dfsg-7 tzdata_2020a-1 ucf_3.0043 util-linux_2.36-3 x11-common_1:7.7+20 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.tZMIoKEJ/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 disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2.0+dfsg-1+b1
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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-17c366f7-239e-4a02-a9a5-99e8d9a7b2e1
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package canu
dpkg-buildpackage: info: source version 2.0+dfsg-1+b1
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' '4.15.0-76-generic' as 'armv8l' into '/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/{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-armv8l/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-armv8l/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-armv8l/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-armv8l/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}
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-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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
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.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
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
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
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}
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-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
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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.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.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-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-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}
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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-armv8l/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-armv8l/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-armv8l/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.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-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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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
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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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/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/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/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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
| ^~~~~~~
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-armv8l/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-armv8l/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
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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 '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/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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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/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/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/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/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-armv8l/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
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
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",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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
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++;
| ~~~~~^~~~~~~~~~~~~~~~~~
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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
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-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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
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>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-armv8l/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
gfa/gfa.C: In member function 'void gfaSequence::load(char*)':
gfa/gfa.C:123:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
123 | findGFAtokenI(_features, "LN:i:", _length);
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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
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);
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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}
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 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
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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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: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 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/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:675:2: warning: #warning replace this with genericStatistics [-Wcpp]
675 | #warning replace this with genericStatistics
| ^~~~~~~
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 | }
| ^
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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-armv8l/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
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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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-armv8l/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-armv8l/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
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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-armv8l/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/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-armv8l/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/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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp]
261 | #warning HARD CODED NUMBER OF FILES!
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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 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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
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}
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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 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");
| ^
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 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-armv8l/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 /<<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 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 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 meryl/meryl.H:51,
from meryl/merylInput.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
meryl/meryl.C: In 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-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/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");
| ^
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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/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-armv8l/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
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-armv8l/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
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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!"
| ^~~~~~~
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");
| ^
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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 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 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");
| ^
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 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
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
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/merylOp-nextMer.C: In member function 'bool merylOperation::nextMer()':
meryl/merylOp-nextMer.C:612:46: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n",
| ~~^
| |
| long unsigned int
| %llu
613 | _kmer.toString(str), _actCount[0], _actCount[1]);
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-nextMer.C:612:70: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n",
| ~~^
| |
| long unsigned int
| %llu
613 | _kmer.toString(str), _actCount[0], _actCount[1]);
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/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/meryl.H:51,
from meryl/merylCountArray.H:29,
from meryl/meryl-import.C:31:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
meryl/meryl-import.C: In function 'int main(int, char**)':
meryl/meryl-import.C:92:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
92 | err.push_back("No input kmer file (-kmers) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-import.C:94:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
94 | err.push_back("No output database name (-output) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-import.C:96:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
96 | err.push_back("No kmer size (-k) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-import.C:233:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
233 | fprintf(stderr, "Found %lu kmers in the input.\n", nKmers);
| ~~^ ~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
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");
| ^
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-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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
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 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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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
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-armv8l/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-armv8l/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-armv8l/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
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
/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 /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
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
/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);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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 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}
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/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-armv8l/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
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-armv8l/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-armv8l/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-armv8l/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}
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
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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);
| ~~~~~^~~~~~~~~~~~~~~
/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);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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-armv8l/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
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
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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-armv8l/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
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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
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-armv8l/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-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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-armv8l/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
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);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
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,
| ^~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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,
| ^~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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=]
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=]
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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 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-armv8l/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-armv8l/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 /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>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<>());
| ~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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
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 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_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<>());
| ~~~~~~~~~~~~~~~
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-armv8l/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 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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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
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
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
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);
| ~~~~~~^~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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
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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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
/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);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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::__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-armv8l/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-armv8l/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-armv8l/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-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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-armv8l/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-armv8l/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-armv8l/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-armv8l/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-armv8l/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
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
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-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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 /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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp]
486 | #warning deviationGraph hard coded
| ^~~~~~~
In file included from /usr/include/c++/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,
| ^~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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/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
/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
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
/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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>::
| ^~~~~~~~~~~~~~~~~~~
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
/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);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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_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-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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_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
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
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-armv8l/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
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-armv8l/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
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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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-armv8l/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 /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-armv8l/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_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
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: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-armv8l/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-armv8l/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-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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_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 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
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
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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-armv8l/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
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-armv8l/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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 /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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'int main(int, char**)':
/usr/include/c++/10/bits/stl_algo.h:4892:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
4892 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__comp));
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:4892:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >' changed in GCC 7.1
4892 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__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_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-armv8l/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-armv8l/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-armv8l/bin/canu
chmod +x /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/canu
cp -pf pipelines/canu-time.pl /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/canu-time
chmod +x /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/canu-time
echo > /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here."
chmod -x /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/canu.defaults
cp -pf sequence/share/ultra-long-nanopore /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/share/sequence/ultra-long-nanopore
cp -pf sequence/share/pacbio /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/share/sequence/pacbio
cp -pf sequence/share/pacbio-hifi /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/share/sequence/pacbio-hifi
cp -pf pipelines/canu/Consensus.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/CorrectReads.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/HaplotypeReads.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Configure.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Defaults.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Execution.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/SequenceStore.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_Cloud.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_DNANexus.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_LSF.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_PBSTorque.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_SGE.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_Slurm.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Meryl.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Output.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapBasedTrimming.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapErrorAdjustment.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapInCore.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapMhap.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapMMap.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapStore.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Report.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Unitig.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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
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-armv8l/lib/libcanu.a /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/AS_global.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/edlib.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-buffered.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-compressed.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-memoryMapped.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/logging.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/strings.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/system.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/system-stackTrace.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/sequence.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-reader.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer-block.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer-stream.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-statistics.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-exact.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/bits.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/hexDump.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/md5.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/mt19937ar.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/objectStore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/speedCounter.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/sweatShop.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/computeGlobalScore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/falconConsensus.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqCache.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqLibrary.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqReadData.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqReadDataWriter.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreBlob.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreConstructor.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreInfo.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovOverlap.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreWriter.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreFilter.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreFile.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreHistogram.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgStore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTig.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/gfa/gfa.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/gfa/bed.o
ar: creating /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/libcanu.a
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/AS_global.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/edlib.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-buffered.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-compressed.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-memoryMapped.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/logging.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/strings.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/system.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/system-stackTrace.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/sequence.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-reader.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer-block.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer-stream.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-statistics.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-exact.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/bits.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/hexDump.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/md5.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/mt19937ar.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/objectStore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/speedCounter.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/sweatShop.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/computeGlobalScore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/falconConsensus.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqCache.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqLibrary.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqReadData.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqReadDataWriter.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreBlob.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreConstructor.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreInfo.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovOverlap.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreWriter.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreFilter.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreFile.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreHistogram.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgStore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTig.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/gfa/gfa.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/gfa/bed.o
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/dumpBlob -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreBuild -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -lcanu
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreConfig -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreBucketizer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreSorter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreIndexer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreStats -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/sqStoreCreate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/sqStoreDumpFASTQ -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/sqStoreDumpMetaData -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/tgStoreCompress -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/tgStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreDump/stores/tgStoreDump.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/tgStoreLoad -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/tgStoreFilter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/tgTigDisplay -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/loadCorrectedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/loadTrimmedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/loadErates -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/loadErates/stores/loadErates.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/meryl -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/meryl.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylCountArray.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylInput.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp-count.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp-countSimple.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp-histogram.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp-nextMer.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/meryl-import -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl-import/meryl/meryl-import.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl-import/meryl/merylCountArray.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/meryl-lookup -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl-lookup/meryl/meryl-lookup.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/sequence -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-extract.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-generate.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-mutate.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-sample.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-shiftregister.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-simulate.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-summarize.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/overlapInCore -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/overlapInCorePartition -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/overlapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/overlapImport -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapImport/overlapInCore/overlapImport.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/overlapPair -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapPair/overlapInCore/overlapPair.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/edalign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/edalign/overlapInCore/edalign.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/prefixEditDistance-matchLimitGenerate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/mhapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/mhapConvert/mhap/mhapConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/mmapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/mmapConvert/minimap/mmapConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/wtdbgConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/filterCorrectionOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/generateCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/filterCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/falconsense -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/falconsense/correction/falconsense.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/falconsense/utgcns/stashContains.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/errorEstimate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/splitHaplotype -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/trimReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/splitReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/mergeRanges -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/overlapAlign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/trimRead.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/findErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/bogart -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/bogart.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Logging.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Outputs.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_TigVector.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Unitig.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/bogus -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogus/bogus/bogus.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogus/bogus/bogusUtil.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/alignGFA/gfa/alignGFA.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/utgcns/utgcns/utgcns.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/utgcns/utgcns/stashContains.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu
Success!
canu installed in /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/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/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/overlapInCore contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/overlapPair contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/bogus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a -O--sourcedirectory=src/
dh_gencontrol -a -O--sourcedirectory=src/
dh_md5sums -a -O--sourcedirectory=src/
dh_builddeb -a -O--sourcedirectory=src/
dpkg-deb: building package 'canu' in '../canu_2.0+dfsg-1+b1_armhf.deb'.
dpkg-deb: building package 'canu-dbgsym' in '../canu-dbgsym_2.0+dfsg-1+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../canu_2.0+dfsg-1+b1_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 2020-09-28T11:04:33Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
canu_2.0+dfsg-1+b1_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+b1
Distribution: bullseye-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
canu - single molecule sequence assembler for genomes
Changes:
canu (2.0+dfsg-1+b1) 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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71c5741efc19c25b8e5bad691537fe7a4f273678 6784 canu_2.0+dfsg-1+b1_armhf.buildinfo
c2281b1b530acbe1ad82f0f985f18d5192e6d2f1 1040336 canu_2.0+dfsg-1+b1_armhf.deb
Checksums-Sha256:
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547a10e82085364a53a9eb7fa1bf9a796c02afdcdda43ae42710a4ac6ca5bee0 6784 canu_2.0+dfsg-1+b1_armhf.buildinfo
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Files:
91846638ccabe6b88eb70a0a708be301 11767324 debug optional canu-dbgsym_2.0+dfsg-1+b1_armhf.deb
428a612c4ca9c2dc48bfab2baaced260 6784 science optional canu_2.0+dfsg-1+b1_armhf.buildinfo
0d1e683ec56dba2ebfa03a8813a0b2bf 1040336 science optional canu_2.0+dfsg-1+b1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
canu-dbgsym_2.0+dfsg-1+b1_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 11767324 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+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 12972
Depends: canu (= 2.0+dfsg-1+b1)
Section: debug
Priority: optional
Description: debug symbols for canu
Build-Ids: 04a072f1a2d40a932123e8603856825a2880c49b 193d3e48114e26d9367bd82793d6d975f19b4c1f 195edc0100840ce86ab11041aac47e61a34b1222 19df195cae021e4882763b06fcf444e3188d6dbd 1f98cf95499f5f4e1b2f2bf9b10de445987a4245 2185940a8ecf2f8105e0f5fcafbd2bfc866c5942 2534d22ec649794681404816bbe8a5f777bec50e 2540b0a74c95f363aac04f38e24b7315cff0c4d2 277600fd48db1b589e9cfab140282522c5db1107 2876ad22fb03b39b8a0335207cedae7eea7eea6a 2bd02de404ffe0050a7d0c907e6a02e5f385df38 322ef09f0df8ca114bee98277334332298a6d54b 3321aa71c668892162413bf2456be1fecde4b3b3 33f93fc385ca20f01ecd5ae48d94002d1d353350 36e9f6211442c9dd99e934b87b32235b8425acd0 445f279a6a222b1f761b7128b671a2721b91aea5 51d8248e448620f2f39efcb6f435e7312ec902d3 5315a3eb8d297683b10bdb15f527300bc3ade5a3 5f44f6ac193e1b4974af1d03a0da87745f6c20f6 64c55d7a318386eda69b7f5172967b57f512a134 6576b606a364b426d6c810e6d44ad66533f1e927 669ec8f50629c0e92671c1cea53abcdf49d40eba 6a0e7e12fba2eed1c3c6883f6516e95962338fdf 6a9318582b808aca617a4209983cc20ead94731b 74a7baa27818913ce12b0a5626cb1d92224d454b 75aeac0ef68f6be2a124eb00d894441a3710a86a 793fea616ea42b742324417f85d391e641ece05e 7b4b5e4b9cabdd82c136e7396a1d1607bf585d46 7da398e966ebed00b6127c321eff9996919000a0 7dc739fa801d86ce2989fe33350524cc078708b5 808309abc124f0dc7f8c857fb081ced15b9c4c27 81568dd6496db92d6fb652f887bd791f4f36467b 827016130938e9bc07b7aa4dbd90c191ea574871 861d470ec0f62f7b9756ffb21cf4f05f65ac5074 93b6ae8277b3666960de847f7e1025e30942a9f8 9526a6fb07d5d023e009da2881211bba781ceeda b8e282725ab917e01ab9b7b90e1cac356cec232d b9a920bd8521d6af0be66dccd3cc56f705568797 c01e27cb1507c3f997b876b1fddbfc4bc16bdec3 d1b8a35c1f52600108e61a644258111e3ef12efe d3d848487ac4555e6874ab7ca818d755a50d8f38 d96119180fca1e6a36afdaf68aaae2d39aa055c4 dd6293739f5822bf1a37cece407a4301c3c04165 e09b56c7b775563aaceab121714014f99165fe89 e42de8c2c65f2c6df3b3ca18334dc6662904210f eb431139a2e6df6086212783f0f2194da4d81640 ed726bf2f8c10c554907605b027ccb27b80c7cf2 efe70d81f4270dd07a735709150f560df974f26b fd05cb11c6b2da0f58cd9dcd9db7c4a4623330ed ffb02f40e06198ae29747ab74fc5a74f2c3f25dd
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/04/
-rw-r--r-- root/root 228748 2020-03-27 23:42 ./usr/lib/debug/.build-id/04/a072f1a2d40a932123e8603856825a2880c49b.debug
drwxr-xr-x root/root 0 2020-03-27 23:42 ./usr/lib/debug/.build-id/19/
-rw-r--r-- root/root 365636 2020-03-27 23:42 ./usr/lib/debug/.build-id/19/3d3e48114e26d9367bd82793d6d975f19b4c1f.debug
-rw-r--r-- root/root 330992 2020-03-27 23:42 ./usr/lib/debug/.build-id/19/5edc0100840ce86ab11041aac47e61a34b1222.debug
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drwxr-xr-x root/root 0 2020-03-27 23:42 ./usr/lib/debug/.build-id/25/
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canu_2.0+dfsg-1+b1_armhf.deb
----------------------------
new Debian package, version 2.0.
size 1040336 bytes: control archive=3112 bytes.
903 bytes, 22 lines control
5892 bytes, 85 lines md5sums
Package: canu
Source: canu (2.0+dfsg-1)
Version: 2.0+dfsg-1+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8049
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 95828 2020-03-27 23:42 ./usr/lib/canu/bin/mergeRanges
-rwxr-xr-x root/root 202328 2020-03-27 23:42 ./usr/lib/canu/bin/meryl
-rwxr-xr-x root/root 91732 2020-03-27 23:42 ./usr/lib/canu/bin/meryl-import
-rwxr-xr-x root/root 104020 2020-03-27 23:42 ./usr/lib/canu/bin/meryl-lookup
-rwxr-xr-x root/root 120460 2020-03-27 23:42 ./usr/lib/canu/bin/mhapConvert
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-rwxr-xr-x root/root 132748 2020-03-27 23:42 ./usr/lib/canu/bin/ovStoreConfig
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-rwxr-xr-x root/root 145036 2020-03-27 23:42 ./usr/lib/canu/bin/ovStoreSorter
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 160492
Build-Time: 237
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 259
Job: canu_2.0+dfsg-1
Machine Architecture: armhf
Package: canu
Package-Time: 516
Source-Version: 2.0+dfsg-1
Space: 160492
Status: successful
Version: 2.0+dfsg-1+b1
--------------------------------------------------------------------------------
Finished at 2020-09-28T11:04:33Z
Build needed 00:08:36, 160492k disk space