canu →
2.0+dfsg-2+b4 →
armhf → 2022-03-17 04:52:17
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| canu 2.0+dfsg-2+b4 (armhf) Thu, 17 Mar 2022 04:36:51 +0000 |
+==============================================================================+
Package: canu
Version: 2.0+dfsg-2+b4
Source Version: 2.0+dfsg-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-cd9fb370-cc00-4b18-ba55-054614a28e76' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/canu-G9pBtJ/resolver-aaNAMp' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [12.9 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [13.8 MB]
Fetched 26.7 MB in 11s (2530 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| 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://172.17.4.1/private bookworm-staging/main canu 2.0+dfsg-2 (dsc) [1930 B]
Get:2 http://172.17.4.1/private bookworm-staging/main canu 2.0+dfsg-2 (tar) [1254 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main canu 2.0+dfsg-2 (diff) [6244 B]
Fetched 1262 kB in 0s (5286 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/canu-G9pBtJ/canu-2.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/canu-G9pBtJ' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [398 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [481 B]
Fetched 1836 B in 0s (47.2 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev binfmt-support bsdextrautils
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 libboost1.74-dev
libbrotli1 libcommons-compress-java libcommons-parent-java libcups2
libdbus-1-3 libdebhelper-perl libelf1 libexpat1 libfastutil-java
libfile-stripnondeterminism-perl libfilesys-df-perl libfontconfig1
libfreetype6 libglib2.0-0 libgraphite2-3 libguava-java libharfbuzz0b
libicu67 libjpeg62-turbo libjsr305-java liblcms2-2 libmagic-mgc libmagic1
libmeryl-dev libnspr4 libnss3 libpcsclite1 libpipeline1 libpng16-16
libsigsegv2 libssw-java libsub-override-perl libtool libuchardet0 libxml2 m4
man-db mhap openjdk-11-jre-headless openssl po-debconf ucf
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 libboost1.74-doc
libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev
libboost-context1.74-dev libboost-contract1.74-dev
libboost-coroutine1.74-dev libboost-date-time1.74-dev
libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
libboost-program-options1.74-dev libboost-python1.74-dev
libboost-random1.74-dev libboost-regex1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libxz-java cups-common libjsr305-java-doc liblcms2-utils pcscd libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho
fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl
Recommended packages:
curl | wget | lynx alsa-ucm-conf alsa-topology-conf dbus
libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev binfmt-support bsdextrautils
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 libboost1.74-dev
libbrotli1 libcommons-compress-java libcommons-parent-java libcups2
libdbus-1-3 libdebhelper-perl libelf1 libexpat1 libfastutil-java
libfile-stripnondeterminism-perl libfilesys-df-perl libfontconfig1
libfreetype6 libglib2.0-0 libgraphite2-3 libguava-java libharfbuzz0b
libicu67 libjpeg62-turbo libjsr305-java liblcms2-2 libmagic-mgc libmagic1
libmeryl-dev libnspr4 libnss3 libpcsclite1 libpipeline1 libpng16-16
libsigsegv2 libssw-java libsub-override-perl libtool libuchardet0 libxml2 m4
man-db mhap openjdk-11-jre-headless openssl po-debconf
sbuild-build-depends-main-dummy ucf
0 upgraded, 77 newly installed, 0 to remove and 30 not upgraded.
Need to get 91.9 MB of archives.
After this operation, 404 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [900 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.3-1 [136 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.5-1 [32.9 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.1-1 [1358 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 1.1.1m-1 [815 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates all 20211016 [156 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-2 [295 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-2 [119 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-2 [65.8 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf binfmt-support armhf 2.2.1-2 [55.0 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf java-common all 0.72 [14.5 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libavahi-common-data armhf 0.8-5 [123 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libavahi-common3 armhf 0.8-5 [55.3 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libdbus-1-3 armhf 1.14.0-1 [210 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libavahi-client3 armhf 0.8-5 [57.9 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libcups2 armhf 2.4.1op1-2 [310 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf liblcms2-2 armhf 2.12~rc1-2 [121 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.4-1 [82.4 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.11.1+dfsg-1 [334 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config all 2.13.1-4.4 [281 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.4 [331 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libnspr4 armhf 2:4.32-3 [90.8 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libnss3 armhf 2:3.75-1 [1096 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libasound2-data all 1.2.6.1-2 [38.8 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libasound2 armhf 1.2.6.1-2 [317 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.4-1 [1209 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libharfbuzz0b armhf 2.7.4-1 [1422 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libpcsclite1 armhf 1.9.5-3 [57.4 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf openjdk-11-jre-headless armhf 11.0.14+9-1 [32.8 MB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf default-jre-headless armhf 2:1.11-72+b4 [11.2 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates-java all 20190909 [15.7 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.6 [193 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.186-1 [174 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.13+dfsg-1 [593 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.6 [1054 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf fastjar armhf 2:0.98-7 [42.7 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf jaligner all 1.0+dfsg-8 [136 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf jarwrapper all 0.78 [21.8 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libapache-pom-java all 18-1 [4676 B]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-14+b1 [9533 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libboost-dev armhf 1.74.0.3+b4 [4824 B]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libcommons-parent-java all 43-1 [10.8 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libcommons-compress-java all 1.21-1 [600 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libfastutil-java all 8.5.8+dfsg-1 [19.4 MB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libfilesys-df-perl armhf 0.92-6+b7 [12.9 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libjsr305-java all 0.1~+svn49-11 [26.9 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libguava-java all 29.0-6 [2419 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libmeryl-dev armhf 0~20150903+r2013-8+b1 [59.6 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libssw-java armhf 1.1-13 [19.2 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf mhap all 2.1.3+dfsg-3 [160 kB]
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Unpacking fontconfig-config (2.13.1-4.4) ...
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Unpacking default-jre-headless (2:1.11-72+b4) ...
Selecting previously unselected package ca-certificates-java.
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Unpacking ca-certificates-java (20190909) ...
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Unpacking dwz (0.14-1) ...
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Unpacking libicu67:armhf (67.1-7) ...
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Unpacking gettext (0.21-4) ...
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Setting up libexpat1:armhf (2.4.4-1) ...
Setting up libpipeline1:armhf (1.5.5-1) ...
Setting up fastjar (2:0.98-7) ...
Setting up libgraphite2-3:armhf (1.3.14-1) ...
Setting up liblcms2-2:armhf (2.12~rc1-2) ...
Setting up libfastutil-java (8.5.8+dfsg-1) ...
Setting up libboost1.74-dev:armhf (1.74.0-14+b1) ...
Setting up libjsr305-java (0.1~+svn49-11) ...
Setting up bsdextrautils (2.37.3-1) ...
Setting up java-common (0.72) ...
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.41-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.70.4-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.6) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libfilesys-df-perl (0.92-6+b7) ...
Setting up libmagic1:armhf (1:5.41-2) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.41-2) ...
Setting up libssw-java (1.1-13) ...
Setting up libasound2-data (1.2.6.1-2) ...
Setting up autotools-dev (20220109.1) ...
Setting up libjpeg62-turbo:armhf (1:2.1.2-1) ...
Setting up libnspr4:armhf (2:4.32-3) ...
Setting up libapache-pom-java (18-1) ...
Setting up libavahi-common-data:armhf (0.8-5) ...
Setting up libatinject-jsr330-api-java (1.0+ds1-5) ...
Setting up libdbus-1-3:armhf (1.14.0-1) ...
Setting up libsigsegv2:armhf (2.14-1) ...
Setting up libpng16-16:armhf (1.6.37-3) ...
Setting up libmeryl-dev (0~20150903+r2013-8+b1) ...
Setting up autopoint (0.21-4) ...
Setting up binfmt-support (2.2.1-2) ...
invoke-rc.d: could not determine current runlevel
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of restart.
Setting up fonts-dejavu-core (2.37-2) ...
Setting up libpcsclite1:armhf (1.9.5-3) ...
Setting up ucf (3.0043) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libasound2:armhf (1.2.6.1-2) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libboost-dev:armhf (1.74.0.3+b4) ...
Setting up openssl (1.1.1m-1) ...
Setting up libelf1:armhf (0.186-1) ...
Setting up libxml2:armhf (2.9.13+dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up gettext (0.21-4) ...
Setting up jarwrapper (0.78) ...
Setting up libtool (2.4.6-15) ...
Setting up fontconfig-config (2.13.1-4.4) ...
Setting up libcommons-parent-java (43-1) ...
Setting up libavahi-common3:armhf (0.8-5) ...
Setting up m4 (1.4.18-5) ...
Setting up libnss3:armhf (2:3.75-1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
127 added, 0 removed; done.
Setting up libfreetype6:armhf (2.11.1+dfsg-1) ...
Setting up libguava-java (29.0-6) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-8) ...
Setting up libharfbuzz0b:armhf (2.7.4-1) ...
Setting up libfontconfig1:armhf (2.13.1-4.4) ...
Setting up libavahi-client3:armhf (0.8-5) ...
Setting up automake (1:1.16.5-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libcommons-compress-java (1.21-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.10.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up libcups2:armhf (2.4.1op1-2) ...
Setting up debhelper (13.6) ...
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:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.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_EC-384_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Certum_Trusted_Root_CA.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: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: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:GLOBALTRUST_2020.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: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:GlobalSign_Root_E46.pem
Adding debian:GlobalSign_Root_R46.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:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Warning: there was a problem reading the certificate file /etc/ssl/certs/NetLock_Arany_=Class_Gold=_F?tan?s?tv?ny.pem. Message:
/etc/ssl/certs/NetLock_Arany_=Class_Gold=_F?tan?s?tv?ny.pem (No such file or directory)
Adding debian:Network_Solutions_Certificate_Authority.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_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:Staat_der_Nederlanden_EV_Root_CA.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: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:Trustwave_Global_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.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:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.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 jaligner (1.0+dfsg-8) ...
Setting up mhap (2.1.3+dfsg-3) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.33-5+rpi1) ...
Processing triggers for ca-certificates (20211016) ...
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 (11.0.14+9-1) ...
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.37.90.20220207-1+rpi1 dpkg-dev_1.21.1+rpi1 g++-11_11.2.0-16+rpi1 gcc-11_11.2.0-16+rpi1 libc6-dev_2.33-5+rpi1 libstdc++-11-dev_11.2.0-16+rpi1 libstdc++6_11.2.0-16+rpi1 linux-libc-dev_5.15.15-2+rpi1
Package versions: adduser_3.118 apt_2.3.15 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.5.52 bash_5.1-6 binfmt-support_2.2.1-2 binutils_2.37.90.20220207-1+rpi1 binutils-arm-linux-gnueabihf_2.37.90.20220207-1+rpi1 binutils-common_2.37.90.20220207-1+rpi1 bsdextrautils_2.37.3-1 bsdutils_1:2.37.3-1 build-essential_12.9 bzip2_1.0.8-5 ca-certificates_20211016 ca-certificates-java_20190909 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-16+rpi1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.6 debianutils_4.11.2 default-jre-headless_2:1.11-72+b4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-3 dpkg_1.21.1+rpi1 dpkg-dev_1.21.1+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.27-1 fastjar_2:0.98-7 file_1:5.41-2 findutils_4.8.0-1 fontconfig-config_2.13.1-4.4 fonts-dejavu-core_2.37-2 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-16+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-16+rpi1 gcc-11-base_11.2.0-16+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-3 gnupg-l10n_2.2.27-3 gnupg-utils_2.2.27-3 gpg_2.2.27-3 gpg-agent_2.2.27-3 gpg-wks-client_2.2.27-3 gpg-wks-server_2.2.27-3 gpgconf_2.2.27-3 gpgsm_2.2.27-3 gpgv_2.2.27-3 grep_3.7-1 groff-base_1.22.4-8 gzip_1.10-4 hostname_3.23 init-system-helpers_1.61 intltool-debian_0.35.0+20060710.5 jaligner_1.0+dfsg-8 jarwrapper_0.78 java-common_0.72 libacl1_2.3.1-1 libapache-pom-java_18-1 libapt-pkg6.0_2.3.15 libarchive-zip-perl_1.68-1 libasan6_11.2.0-16+rpi1 libasound2_1.2.6.1-2 libasound2-data_1.2.6.1-2 libassuan0_2.5.5-1 libatinject-jsr330-api-java_1.0+ds1-5 libatomic1_11.2.0-16+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1 libavahi-client3_0.8-5 libavahi-common-data_0.8-5 libavahi-common3_0.8-5 libbinutils_2.37.90.20220207-1+rpi1 libblkid1_2.37.3-1 libboost-dev_1.74.0.3+b4 libboost1.74-dev_1.74.0-14+b1 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-5 libc-bin_2.33-5+rpi1 libc-dev-bin_2.33-5+rpi1 libc6_2.33-5+rpi1 libc6-dev_2.33-5+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-16+rpi1 libcom-err2_1.46.5-2 libcommons-compress-java_1.21-1 libcommons-parent-java_43-1 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.37.90.20220207-1+rpi1 libctf0_2.37.90.20220207-1+rpi1 libcups2_2.4.1op1-2 libdb5.3_5.3.28+dfsg1-0.8 libdbus-1-3_1.14.0-1 libdebconfclient0_0.261 libdebhelper-perl_13.6 libdpkg-perl_1.21.1+rpi1 libelf1_0.186-1 libexpat1_2.4.4-1 libext2fs2_1.46.5-2 libfakeroot_1.27-1 libfastutil-java_8.5.8+dfsg-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libfilesys-df-perl_0.92-6+b7 libfontconfig1_2.13.1-4.4 libfreetype6_2.11.1+dfsg-1 libgcc-11-dev_11.2.0-16+rpi1 libgcc-s1_11.2.0-16+rpi1 libgcrypt20_1.9.4-5 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libglib2.0-0_2.70.4-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.3-4 libgomp1_11.2.0-16+rpi1 libgpg-error0_1.43-3 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.18.3-7 libguava-java_29.0-6 libharfbuzz0b_2.7.4-1 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libjpeg62-turbo_1:2.1.2-1 libjsr305-java_0.1~+svn49-11 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 liblcms2-2_2.12~rc1-2 libldap-2.4-2_2.4.59+dfsg-1+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmeryl-dev_0~20150903+r2013-8+b1 libmount1_2.37.3-1 libmpc3_1.2.1-1 libmpfr6_4.1.0-3 libncursesw6_6.3-2 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnspr4_2:4.32-3 libnss3_2:3.75-1 libp11-kit0_0.24.0-6 libpam-modules_1.4.0-11 libpam-modules-bin_1.4.0-11 libpam-runtime_1.4.0-11 libpam0g_1.4.0-11 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libpcsclite1_1.9.5-3 libperl5.32_5.32.1-6 libperl5.34_5.34.0-3 libpipeline1_1.5.5-1 libpng16-16_1.6.37-3 libreadline8_8.1.2-1 libsasl2-2_2.1.27+dfsg2-3 libsasl2-modules-db_2.1.27+dfsg2-3 libseccomp2_2.5.3-2+rpi1 libselinux1_3.3-1 libsemanage-common_3.3-1 libsemanage2_3.3-1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.14-1 libsmartcols1_2.37.3-1 libsqlite3-0_3.37.2-2 libss2_1.46.5-2 libssl1.1_1.1.1m-1 libssw-java_1.1-13 libstdc++-11-dev_11.2.0-16+rpi1 libstdc++6_11.2.0-16+rpi1 libsub-override-perl_0.09-2 libsystemd0_250.3-2+rpi1 libtasn1-6_4.18.0-4 libtinfo6_6.3-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-16+rpi1 libuchardet0_0.0.7-1 libudev1_250.3-2+rpi1 libunistring2_1.0-1 libuuid1_2.37.3-1 libxml2_2.9.13+dfsg-1 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.15.15-2+rpi1 login_1:4.11.1+dfsg1-1 logsave_1.46.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.1-1 mawk_1.3.4.20200120-3 mhap_2.1.3+dfsg-3 mount_2.37.3-1 ncurses-base_6.3-2 ncurses-bin_6.3-2 openjdk-11-jre-headless_11.0.14+9-1 openssl_1.1.1m-1 passwd_1:4.11.1+dfsg1-1 patch_2.7.6-7 perl_5.34.0-3 perl-base_5.34.0-3 perl-modules-5.32_5.32.1-6 perl-modules-5.34_5.34.0-3 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.01-1 tar_1.34+dfsg-1 tzdata_2021e-1 ucf_3.0043 util-linux_2.37.3-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: canu
Binary: canu
Architecture: any
Version: 2.0+dfsg-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Homepage: http://canu.readthedocs.org/en/latest/
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/canu
Vcs-Git: https://salsa.debian.org/med-team/canu.git
Build-Depends: debhelper-compat (= 13), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap
Package-List:
canu deb science optional arch=any
Checksums-Sha1:
7108de84ccb133607108da7f61eeed1dfca6158d 1254040 canu_2.0+dfsg.orig.tar.xz
11bb2c3381a2e827590c17323d1b1278d0c745ec 6244 canu_2.0+dfsg-2.debian.tar.xz
Checksums-Sha256:
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94fee5350c965f474b520ad9863258f5cd7120c53e96817a4d1e6a454bae608d 6244 canu_2.0+dfsg-2.debian.tar.xz
Files:
0edc678cd6a5f954e72d12c116292cdb 1254040 canu_2.0+dfsg.orig.tar.xz
bcc0ea4d5098aebe0646824e1bd66e06 6244 canu_2.0+dfsg-2.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.wlSVysQv/trustedkeys.kbx': General error
gpgv: Signature made Thu Oct 28 20:38:47 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./canu_2.0+dfsg-2.dsc
dpkg-source: info: extracting canu in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking canu_2.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking canu_2.0+dfsg-2.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
dpkg-source: info: applying remove-deprecated-sysctl.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2.0+dfsg-2+b4
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=12b0d11b34b646c0abd5fc586dfab6e4
JOURNAL_STREAM=8:22125
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-cd9fb370-cc00-4b18-ba55-054614a28e76
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c70427
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package canu
dpkg-buildpackage: info: source version 2.0+dfsg-2+b4
dpkg-buildpackage: info: source distribution bookworm-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 '/<<PKGBUILDDIR>>'
rm -rf Linux-*
rm -f src/canu_version.H
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
dh_auto_build
cd src && make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
WARNING:
WARNING: g++ 11 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher.
WARNING:
Building for 'Linux' '4.19.20-v7+' as 'armv7l' into '/<<PKGBUILDDIR>>/Linux-armv7l/{bin,obj}'.
Using '/usr/bin/g++' version '11'.
Using user-supplied CXXFLAGS '-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security'.
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/edlib.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-compressed.C
utility/files.C: In function ‘void writeToFile(void*, const char*, uint64, uint64, FILE*)’:
utility/files.C:89:56: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
90 | nWritten, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:89:67: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
90 | nWritten, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:89:85: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
90 | nWritten, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:94:54: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
94 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): Short write\n",
| ~~^
| |
| long unsigned int
| %llu
95 | nWritten, nObjects, description, objectSize), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:94:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
94 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): Short write\n",
| ~~^
| |
| long unsigned int
| %llu
95 | nWritten, nObjects, description, objectSize), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:94:83: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
94 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): Short write\n",
| ~~^
| |
| long unsigned int
| %llu
95 | nWritten, nObjects, description, objectSize), exit(1);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C: In function ‘uint64 loadFromFile(void*, const char*, uint64, uint64, FILE*, bool)’:
utility/files.C:134:59: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
134 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): End of file\n",
| ~~^
| |
| long unsigned int
| %llu
135 | nLoaded, nObjects, description, objectSize);
| ~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:134:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
134 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): End of file\n",
| ~~^
| |
| long unsigned int
| %llu
135 | nLoaded, nObjects, description, objectSize);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:134:88: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
134 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): End of file\n",
| ~~^
| |
| long unsigned int
| %llu
135 | nLoaded, nObjects, description, objectSize);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:150:57: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
150 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
151 | nLoaded, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:150:68: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
150 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
151 | nLoaded, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:150:86: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
150 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
151 | nLoaded, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C
utility/files.C: In function ‘void AS_UTL_symlink(const char*, const char*)’:
utility/files.C:311:10: warning: ignoring return value of ‘int symlink(const char*, const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
311 | symlink(pathToFile, pathToLink);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
utility/files.C: In function ‘void AS_UTL_loadFileList(char*, std::vector<char*>&)’:
utility/files.C:678:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
678 | fgets(line, FILENAME_MAX, F);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
utility/files.C:684:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
684 | fgets(line, FILENAME_MAX, F);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/logging.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/strings.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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system.C
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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from utility/logging.H:29,
from utility/logging.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 6 and 8205 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from utility/logging.H:29,
from utility/logging.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 6 and 8205 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from utility/logging.H:29,
from utility/logging.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 6 and 8205 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from utility/logging.H:29,
from utility/logging.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 13 and 8220 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:71:35: warning: ‘int __builtin___snprintf_chk(char*, unsigned int, int, unsigned int, const char*, ...)’ specified bound 1024 exceeds destination size 256 [-Wstringop-overflow=]
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sequence.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-reader.C
In file included from utility/kmers.H:32,
from utility/kmers.C:26:
utility/bits.H: In member function ‘void stuffedBits::updateBlk(uint64)’:
utility/bits.H:791:44: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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.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:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp]
58 | #warning how to set prefix size for streaming operations?
| ^~~~~~~
In file included from utility/kmers.H:32,
from utility/kmers-reader.C:26:
utility/bits.H: In member function ‘void stuffedBits::updateBlk(uint64)’:
utility/bits.H: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
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}
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-block.C
utility/kmers-reader.C:342:77: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2);
| ~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-reader.C: In member function ‘void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)’:
utility/kmers-reader.C:143:32: warning: ‘/merylIndex’ directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
143 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _inName);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from utility/kmers.H:29,
from utility/kmers-reader.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
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
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-stream.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
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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
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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from utility/kmers.H:29,
from utility/kmers-writer.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /usr/include/c++/11/map:60,
from utility/kmers.H:34,
from utility/kmers-writer-block.C:26:
/usr/include/c++/11/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, long long unsigned int>; _KeyOfValue = std::_Select1st<std::pair<const long long unsigned int, long long unsigned int> >; _Compare = std::less<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, long long unsigned int> >]’:
/usr/include/c++/11/bits/stl_tree.h:2428:7: note: parameter passing for argument of type ‘std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, long long unsigned int>, std::_Select1st<std::pair<const long long unsigned int, long long unsigned int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, long long unsigned int> > >::const_iterator’ changed in GCC 7.1
2428 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 /usr/include/c++/11/map:61,
from utility/kmers.H:34,
from utility/kmers-writer-block.C:26:
/usr/include/c++/11/bits/stl_map.h: In member function ‘void kmerCountBlockWriter::addBlock(uint64, uint64, uint64*, uint64*)’:
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, long long unsigned int>, std::_Select1st<std::pair<const long long unsigned int, long long unsigned int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, long long unsigned 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<>());
| ~~~~~~~~~~~~~~~
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}
/usr/include/c++/11/bits/stl_map.h: In member function ‘void kmerCountBlockWriter::mergeBatches(uint32)’:
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, long long unsigned int>, std::_Select1st<std::pair<const long long unsigned int, long long unsigned int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, long long unsigned 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<>());
| ~~~~~~~~~~~~~~~
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-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}
/usr/include/c++/11/bits/stl_map.h: In member function ‘void kmerCountBlockWriter::addBlock(uint64, uint64, uint64*, uint32*)’:
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, long long unsigned int>, std::_Select1st<std::pair<const long long unsigned int, long long unsigned int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, long long unsigned 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<>());
| ~~~~~~~~~~~~~~~
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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/bits.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/hexDump.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=]
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: 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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/objectStore.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C
utility/objectStore.C: In function ‘bool fetchFromObjectStore(char*)’:
utility/objectStore.C:257:13: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
257 | args[1] = "download";
| ^~~~~~~~~~
utility/objectStore.C:258:13: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
258 | args[2] = "--overwrite";
| ^~~~~~~~~~~~~
utility/objectStore.C:259:13: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
259 | args[3] = "--no-progress";
| ^~~~~~~~~~~~~~~
utility/objectStore.C:260:13: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
260 | args[4] = "--output";
| ^~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreBlob.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4114 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreBlob.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4114 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreBlob.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4109 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C
stores/ovOverlap.C:217:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp]
217 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING
| ^~~~~~~
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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 13 and 4109 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 11 and 4107 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 23 and 4126 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 7 and 4103 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 19 and 4122 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 24 and 4127 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 24 and 4127 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:229:32: warning: ‘/version.’ directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
229 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-coru", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 24 and 4127 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 24 and 4127 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 6 and 4102 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 18 and 4121 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 10 and 4106 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 22 and 4125 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 13 and 4116 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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);
| ^~~~~~
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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 6 and 4102 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 11 and 4107 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 7 and 4103 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 7 and 4103 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.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=]
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 9 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",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
76 | dat.ovl.bhg5, dat.ovl.bhg3,
| ~~~~~~~~~~~~
| |
| int
stores/ovOverlap.C:71:20: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 10 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",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
76 | dat.ovl.bhg5, dat.ovl.bhg3,
| ~~~~~~~~~~~~
| |
| int
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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStore.C:59:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 6 and 4102 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStore.C:59:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4105 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C
stores/ovStoreWriter.C: In member function ‘uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)’:
stores/ovStoreWriter.C:228:37: warning: ‘/bucket’ directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
228 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum);
| ^~~~~~~
stores/ovStoreWriter.C:228:34: note: directive argument in the range [0, 536870910]
228 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 22 and 4129 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 23 and 4124 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 22 and 4130 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4114 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 11 and 4113 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 11 and 4112 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4114 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 6 and 4102 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C: In member function ‘void ovStoreSliceWriter::removeOverlapSlice()’:
stores/ovStoreWriter.C:486:37: warning: ‘/bucket’ directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
486 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, _sliceNum);
| ^~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 22 and 4130 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 11 and 4113 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4114 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4114 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 11 and 4113 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 23 and 4125 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 22 and 4130 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4114 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C
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=]
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 9 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,
361 | overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3,
| ~~~~~~~~~~~~~~~~~~~~~
| |
| int
stores/ovStoreHistogram.C:359:21: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 10 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,
361 | overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3,
| ~~~~~~~~~~~~~~~~~~~~~
| |
| int
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
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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreFile.C:47:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 4 and 4100 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
stores/tgStore.C: In member function ‘void tgStore::purgeVersion(uint32)’:
stores/tgStore.C:191:36: warning: ‘/seqDB.v’ directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
191 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name);
| ^~~~~~~~
stores/tgStore.C:191:33: note: using the range [-2147483648, 2147483647] for directive argument
191 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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);
| ^~~~~~~~
stores/tgStore.C:626:37: note: directive argument in the range [-2147483645, 2147483647]
626 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, i);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
stores/tgStore.C: In member function ‘FILE* tgStore::openDB(uint32)’:
stores/tgStore.C:695:36: warning: ‘/seqDB.v’ directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
695 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version);
| ^~~~~~~~
stores/tgStore.C:695:33: note: using the range [-2147483648, 2147483647] for directive argument
695 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C
In file included from stores/tgTig.H:36,
from stores/tgTig.C:34:
utility/bits.H: In member function ‘void stuffedBits::updateBlk(uint64)’:
utility/bits.H:791:44: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C
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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc
stores/tgTig.C: In member function ‘bool tgTig::loadLayout(FILE*)’:
stores/tgTig.C: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
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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/liboverlap/prefixEditDistance-extend.C:69:
utility/bits.H: In member function ‘void stuffedBits::updateBlk(uint64)’:
utility/bits.H:791:44: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C
In file included from /usr/include/c++/11/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++/11/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++/11/bits/stl_tree.h:2428:7: 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
2428 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from utgcns/libNDalign/NDalign.H:45,
from utgcns/libNDalign/NDalign.C:34:
/usr/include/c++/11/bits/stl_map.h: In member function ‘bool NDalign::findHits()’:
/usr/include/c++/11/bits/stl_map.h:501:44: 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++/11/bits/stl_map.h: In member function ‘void NDalign::fastFindMersA(bool)’:
/usr/include/c++/11/bits/stl_map.h:501:44: 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++/11/bits/stl_map.h:501:44: 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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C
/usr/include/c++/11/bits/stl_map.h: In member function ‘void NDalign::fastFindMersB(bool)’:
/usr/include/c++/11/bits/stl_map.h:501:44: 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++/11/bits/stl_map.h:501:44: 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++/11/bits/stl_map.h:501:44: 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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility stores/dumpBlob.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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility stores/ovStoreBuild.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility stores/ovStoreConfig.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility stores/ovStoreSorter.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility stores/ovStoreIndexer.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility stores/ovStoreStats.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C
In file included from /usr/include/c++/11/map:60,
from utgcns/libpbutgcns/AlnGraphBoost.C:68:
/usr/include/c++/11/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, long long int>; _KeyOfValue = std::_Select1st<std::pair<const unsigned int, long long int> >; _Compare = std::less<unsigned int>; _Alloc = std::allocator<std::pair<const unsigned int, long long int> >]’:
/usr/include/c++/11/bits/stl_tree.h:2428:7: note: parameter passing for argument of type ‘std::_Rb_tree<unsigned int, std::pair<const unsigned int, long long int>, std::_Select1st<std::pair<const unsigned int, long long int> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, long long int> > >::const_iterator’ changed in GCC 7.1
2428 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from utgcns/libpbutgcns/AlnGraphBoost.C:68:
/usr/include/c++/11/bits/stl_map.h: In member function ‘const std::vector<AlnNode> AlnGraphBoost::bestPath()’:
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<unsigned int, std::pair<const unsigned int, long long int>, std::_Select1st<std::pair<const unsigned int, long long int> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, long long 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++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<unsigned int, std::pair<const unsigned int, long long int>, std::_Select1st<std::pair<const unsigned int, long long int> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, long long 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++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<unsigned int, std::pair<const unsigned int, long long int>, std::_Select1st<std::pair<const unsigned int, long long int> >, std::less<unsigned int>, std::allocator<std::pair<const unsigned int, long long 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<>());
| ~~~~~~~~~~~~~~~
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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStoreDumpFASTQ.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 7 and 8197 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStoreDumpFASTQ.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 8 and 12293 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStoreDumpFASTQ.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 7 and 8197 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/sqStoreDumpFASTQ.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 8 and 12293 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Isequence sequence/sequence-summarize.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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=]
226 | fprintf(stdout, "%10" F_U32P " %10" F_U32P "%s %s %4lu %12lu\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
232 | seqs->sqStore_getReadByte(rid));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
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++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from stores/sqStoreDumpMetaData.C:34:
/usr/include/c++/11/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++/11/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++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from stores/sqStoreDumpMetaData.C:34:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: 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
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: 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++/11/bits/stl_algo.h:1819:5: 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++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/11/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++/11/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++/11/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++/11/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++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: 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
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: 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++/11/bits/stl_algo.h:1819:5: 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++/11/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++/11/bits/stl_algo.h:1819:5: 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++/11/bits/stl_algo.h:1819:5: 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++/11/bits/stl_algo.h:1819:5: 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++/11/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++/11/bits/stl_algo.h:1861:5: 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
1861 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1861:5: 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++/11/bits/stl_algo.h:1861:5: 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++/11/bits/stl_algo.h:1866:32: 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
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: 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
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility stores/tgStoreDump.C
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from stores/sqStoreDumpMetaData.C:34:
/usr/include/c++/11/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++/11/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++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/11/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++/11/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++/11/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++/11/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++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from stores/sqStoreDumpMetaData.C:34:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: 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
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: 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++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: 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
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: 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++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility stores/tgTigSizeAnalysis.C
stores/tgStoreDump.C:675:2: warning: #warning replace this with genericStatistics [-Wcpp]
675 | #warning replace this with genericStatistics
| ^~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void doSummarize_lengthHistogramSimple(std::vector<long long unsigned int>)’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: 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
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1957:38: 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
1957 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void doSummarize_dumpLengths(std::vector<long long unsigned int>)’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: 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
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1957:38: 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
1957 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from stores/sqStoreDumpMetaData.C:34:
/usr/include/c++/11/bits/vector.tcc: In function ‘void dumpHistogram(sqStore*, uint32, uint32, sqRead_which, bool)’:
/usr/include/c++/11/bits/vector.tcc:121:28: 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++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from stores/sqStoreDumpMetaData.C:34:
/usr/include/c++/11/bits/stl_algo.h:1954:32: 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
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: 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
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: 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
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: 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
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: 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++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void doSummarize_lengthHistogram(std::vector<long long unsigned int>, uint64, bool)’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: 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
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: 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
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: 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
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility stores/tgStoreLoad.C
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void doSummarize(std::vector<char*>&, summarizeParameters&)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: 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++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/11/bits/vector.tcc:121:28: 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
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
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility stores/tgStoreFilter.C
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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility stores/loadCorrectedReads.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility stores/loadErates.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
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}
stores/loadTrimmedReads.C: In function ‘int main(int, char**)’:
stores/loadTrimmedReads.C:180:19: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
180 | err.push_back("ERROR: no sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<PKGBUILDDIR>>/src -Iutility -Istores meryl/meryl.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<PKGBUILDDIR>>/src -Iutility -Istores meryl/merylCountArray.C
meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp]
261 | #warning HARD CODED NUMBER OF FILES!
| ^~~~~~~
stores/loadErates.C: In function ‘int main(int, char**)’:
stores/loadErates.C:214:19: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
214 | err.push_back("ERROR: No overlap store (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadErates.C:217:19: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
217 | err.push_back("ERROR: No sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadErates.C:220:19: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
220 | err.push_back("ERROR: No input erate files (-L or last on the command line) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<PKGBUILDDIR>>/src -Iutility -Istores meryl/merylInput.C
stores/loadErates.C: In member function ‘void ovStore::addEvalues(std::vector<char*>&)’:
stores/loadErates.C:86:41: warning: ‘/evalues.WORKING’ directive output may be truncated writing 16 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
86 | snprintf(evalueTemp, FILENAME_MAX, "%s/evalues.WORKING", _storePath);
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/loadErates.C:43:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 17 and 4113 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from stores/loadErates.C:43:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4105 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
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}
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/meryl.H:51,
from meryl/meryl.C:46:
meryl/merylInput.H: In member function ‘char* merylInput::inputType()’:
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
58 | return("invalid-input");
| ^
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<PKGBUILDDIR>>/src -Iutility -Istores meryl/merylOp-count.C
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
utility/kmers.H: In member function ‘void kmerCountFileIndex::set(uint64, FILE*, uint64)’:
utility/kmers.H:594:42: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
meryl/merylInput.H: In member function ‘char* merylInput::inputType()’:
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
58 | return("invalid-input");
| ^
In file included from /<<PKGBUILDDIR>>/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");
| ^
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");
| ^
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);
| ^~~~~~~~~~~
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
In file included from /usr/include/stdio.h:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from meryl/meryl.H:49,
from meryl/meryl.C:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from meryl/meryl.H:49,
from meryl/meryl.C:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 6 and 4102 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from meryl/meryl.H:49,
from meryl/meryl.C:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 7 and 4103 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from meryl/meryl.H:49,
from meryl/meryl.C:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 31 and 4127 bytes into a destination of size 1024
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<PKGBUILDDIR>>/src -Iutility -Istores meryl/merylOp-countSimple.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<PKGBUILDDIR>>/src -Iutility -Istores meryl/merylOp-histogram.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<PKGBUILDDIR>>/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-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-nextMer.C:98:2: warning: #warning "need to decide whic direction we're going?" [-Wcpp]
98 | #warning "need to decide whic direction we're going?"
| ^~~~~~~
meryl/merylOp-nextMer.C:116:2: warning: #warning "rounding issues in word-frequency!" [-Wcpp]
116 | #warning "rounding issues in word-frequency!"
| ^~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<PKGBUILDDIR>>/src -Iutility -Istores meryl/merylOp.C
meryl/merylOp-countSimple.C: In member function ‘void merylOperation::countSimple()’:
meryl/merylOp-countSimple.C:107:76: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
107 | fprintf(stderr, "Increasing to %u-bit storage (for kmer 0x%016lx).\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
108 | lowBitsSize + hib + 1, kidx);
| ~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-countSimple.C:150:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
150 | fprintf(stderr, " nPrefix %lu\n", nPrefix);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
meryl/merylOp-countSimple.C:151:33: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
151 | fprintf(stderr, " nSuffix %lu\n", nSuffix);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
meryl/merylOp-countSimple.C:152:38: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
152 | fprintf(stderr, " sMask 0x%016lx\n", sMask);
| ~~~~~^ ~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
In file included from 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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl-import/meryl/meryl-import.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<PKGBUILDDIR>>/src -Iutility -Istores meryl/meryl-import.C
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-histogram.C:26:
utility/kmers.H: In member function ‘void kmerCountFileIndex::set(uint64, FILE*, uint64)’:
utility/kmers.H:594:42: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylOp-histogram.C:26:
meryl/merylInput.H: In member function ‘char* merylInput::inputType()’:
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
58 | return("invalid-input");
| ^
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-nextMer.C:26:
utility/bits.H: In member function ‘void stuffedBits::updateBlk(uint64)’:
utility/bits.H:791:44: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-nextMer.C:26:
utility/kmers.H: In member function ‘void kmerCountFileIndex::set(uint64, FILE*, uint64)’:
utility/kmers.H:594:42: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylOp-nextMer.C:26:
meryl/merylInput.H: In member function ‘char* merylInput::inputType()’:
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
58 | return("invalid-input");
| ^
meryl/merylOp-nextMer.C: In member function ‘void merylOperation::initializeThreshold()’:
meryl/merylOp-nextMer.C:113:66: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
113 | fprintf(stderr, "For fraction-distinct %f, found threshold %lu\n", _fracDist, _threshold);
| ~~^ ~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
meryl/merylOp-nextMer.C:121:63: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
121 | fprintf(stderr, "For word-frequency %f, found threshold %lu\n", _wordFreq, _threshold);
| ~~^ ~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
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
meryl/merylOp-nextMer.C: In member function ‘bool merylOperation::nextMer()’:
meryl/merylOp-nextMer.C:612:46: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n",
| ~~^
| |
| long unsigned int
| %llu
613 | _kmer.toString(str), _actCount[0], _actCount[1]);
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-nextMer.C:612:70: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n",
| ~~^
| |
| long unsigned int
| %llu
613 | _kmer.toString(str), _actCount[0], _actCount[1]);
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp.C:26:
utility/kmers.H: In member function ‘void kmerCountFileIndex::set(uint64, FILE*, uint64)’:
utility/kmers.H: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.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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl-import/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<PKGBUILDDIR>>/src -Iutility -Istores meryl/merylCountArray.C
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
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}
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl-lookup/meryl/meryl-lookup.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<PKGBUILDDIR>>/src -Iutility -Istores meryl/meryl-lookup.C
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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<PKGBUILDDIR>>/src -Iutility sequence/sequence.C
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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-extract.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<PKGBUILDDIR>>/src -Iutility sequence/sequence-extract.C
In file included from utility/kmers.H:32,
from meryl/meryl-lookup.C:28:
utility/bits.H: In member function ‘void stuffedBits::updateBlk(uint64)’:
utility/bits.H:791:44: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/meryl-lookup.C:28:
utility/kmers.H: In member function ‘void kmerCountFileIndex::set(uint64, FILE*, uint64)’:
utility/kmers.H:594:42: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C: In function ‘void dumpExistence(dnaSeqFile*, compressedFileWriter*, std::vector<kmerCountExactLookup*>&, std::vector<const char*>&)’:
meryl/meryl-lookup.C:83:43: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
83 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\n",
| ~~^
| |
| long unsigned int
| %llu
......
86 | kiter.position(),
| ~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C:97:45: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
97 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\t%s\t%lu\t%s\t%lu\t%s\n",
| ~~^
| |
| long unsigned int
| %llu
......
100 | kiter.position(),
| ~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C:97:58: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
97 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\t%s\t%lu\t%s\t%lu\t%s\n",
| ~~^
| |
| long unsigned int
| %llu
......
102 | kiter.fmer().toString(fString), fValue,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C:97:67: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 10 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
97 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\t%s\t%lu\t%s\t%lu\t%s\n",
| ~~^
| |
| long unsigned int
| %llu
......
103 | kiter.rmer().toString(rString), rValue,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C: In function ‘void reportExistence(dnaSeqFile*, compressedFileWriter*, std::vector<kmerCountExactLookup*>&, std::vector<const char*>&)’:
meryl/meryl-lookup.C:134:35: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
134 | fprintf(ofile->file(), "%s\t%lu\t%lu\t%lu\n", seq.name(), nKmer, klookup[0]->nKmers(), nKmerFound);
| ~~^ ~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C:134:40: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
134 | fprintf(ofile->file(), "%s\t%lu\t%lu\t%lu\n", seq.name(), nKmer, klookup[0]->nKmers(), nKmerFound);
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C:134:45: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
134 | fprintf(ofile->file(), "%s\t%lu\t%lu\t%lu\n", seq.name(), nKmer, klookup[0]->nKmers(), nKmerFound);
| ~~^ ~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C: In function ‘void filter(dnaSeqFile*, dnaSeqFile*, compressedFileWriter*, compressedFileWriter*, std::vector<kmerCountExactLookup*>&, bool)’:
meryl/meryl-lookup.C:204:34: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
204 | fprintf(stderr, "\nIncluding %lu reads (or read pairs) out of %lu.\n", nReadsFound, nReads);
| ~~^ ~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C:204:67: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
204 | fprintf(stderr, "\nIncluding %lu reads (or read pairs) out of %lu.\n", nReadsFound, nReads);
| ~~^ ~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C: In function ‘int main(int, char**)’:
meryl/meryl-lookup.C:285:19: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
285 | err.push_back("No input sequences (-sequence) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-lookup.C:287:19: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
287 | err.push_back("No query meryl database (-mers) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-lookup.C:289:19: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
289 | err.push_back("No report-type (-existence, etc) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C: In function ‘int main(int, char**)’:
sequence/sequence.C:414:19: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
414 | err.push_back("ERROR: No mode (summarize, extract, generate or simulate) specified.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:418:21: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
418 | err.push_back("ERROR: No input sequence files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:422:21: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
422 | err.push_back("ERROR: No input sequence files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:428:21: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
428 | err.push_back("ERROR: No reference genome sequence (-genome) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:432:21: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
432 | err.push_back("ERROR: No input sequence files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence.C:26:
/usr/include/c++/11/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++/11/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++/11/bits/vector.tcc: In member function ‘void extractParameters::finalize()’:
/usr/include/c++/11/bits/vector.tcc:121:28: 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++/11/bits/vector.tcc:121:28: 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++/11/bits/vector.tcc:121:28: 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++/11/bits/vector.tcc:121:28: 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++/11/bits/vector.tcc:121:28: 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++/11/bits/vector.tcc:121:28: 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++/11/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++/11/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++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence.C:26:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void decodeRange(char*, std::vector<T>&, std::vector<T>&) [with T = long long unsigned int]’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: 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++/11/bits/stl_vector.h:1198:28: 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 /<<PKGBUILDDIR>>/src/sequence/sequence.H:32,
from sequence/sequence.C:26:
utility/strings.H:112:1: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ changed in GCC 7.1
112 | }
| ^
utility/strings.H:112:1: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ changed in GCC 7.1
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-generate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<PKGBUILDDIR>>/src -Iutility sequence/sequence-generate.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-mutate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<PKGBUILDDIR>>/src -Iutility sequence/sequence-mutate.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-sample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<PKGBUILDDIR>>/src -Iutility sequence/sequence-sample.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<PKGBUILDDIR>>/src -Iutility sequence/sequence-shiftregister.C
sequence/sequence-generate.C: In function ‘void doGenerate(generateParameters&)’:
sequence/sequence-generate.C:92:23: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
92 | ">random%08 " F_U64P "\n", nSeqs);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<PKGBUILDDIR>>/src -Iutility sequence/sequence-shiftregister-emit-fast.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<PKGBUILDDIR>>/src -Iutility sequence/sequence-shiftregister-search-fast.C
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/11/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++/11/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++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<seqEntry>::iterator’ changed in GCC 7.1
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
/usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {seqEntry}; _Tp = seqEntry; _Alloc = std::allocator<seqEntry>]’:
/usr/include/c++/11/bits/vector.tcc:121:28: 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++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/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 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/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
/usr/include/c++/11/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++/11/bits/stl_algo.h:1861:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
1861 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1861:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1861:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/11/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++/11/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++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void doSample_sample(sampleParameters&, uint64, uint64, std::vector<seqEntry>&)’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1957:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
1957 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1957:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<seqEntry*, std::vector<seqEntry> >’ changed in GCC 7.1
1957 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<PKGBUILDDIR>>/src -Iutility sequence/sequence-shiftregister-search-slow.C
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void doSample_paired(std::vector<char*>&, sampleParameters&)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: 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++/11/bits/stl_vector.h: In function ‘void doSample_single(std::vector<char*>&, sampleParameters&)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from sequence/sequence-shiftregister-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
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-simulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<PKGBUILDDIR>>/src -Iutility sequence/sequence-simulate.C
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}
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<PKGBUILDDIR>>/src -Iutility sequence/sequence-summarize.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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.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}
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C
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}
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_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.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
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/11/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++/11/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++/11/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++/11/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++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: 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
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: 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++/11/bits/stl_algo.h:1819:5: 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++/11/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++/11/bits/stl_algo.h:1819:5: 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++/11/bits/stl_algo.h:1819:5: 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++/11/bits/stl_algo.h:1819:5: 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++/11/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++/11/bits/stl_algo.h:1861:5: 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
1861 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1861:5: 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++/11/bits/stl_algo.h:1861:5: 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++/11/bits/stl_algo.h:1866:32: 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
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: 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
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/11/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++/11/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++/11/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++/11/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++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: 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
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: 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++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/overlapInCore-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
/usr/include/c++/11/bits/stl_algo.h: In function ‘void doSummarize_lengthHistogramSimple(std::vector<long long unsigned int>)’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: 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
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1957:38: 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
1957 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void doSummarize_dumpLengths(std::vector<long long unsigned int>)’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: 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
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1957:38: 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
1957 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: 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
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: 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++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++/11/bits/stl_algo.h: In function ‘void doSummarize_lengthHistogram(std::vector<long long unsigned int>, uint64, bool)’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: 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
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: 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
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: 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
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void doSummarize(std::vector<char*>&, summarizeParameters&)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: 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++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from /<<PKGBUILDDIR>>/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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
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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/overlapInCore-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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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
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");
| ^~~~~~~~
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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C
overlapInCore/overlapPair.C:479:2: warning: #warning do we need to check for contained too? [-Wcpp]
479 | #warning do we need to check for contained too?
| ^~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C
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());
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
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
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C
overlapInCore/overlapPair.C: In function ‘void* recomputeOverlaps(void*)’:
overlapInCore/overlapPair.C:429:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
429 | if (extendAlignment(bRead, bbgn, bend, blen, "B", bID,
| ^~~
overlapInCore/overlapPair.C:430:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
430 | aRead, abgn, aend, alen, "A", aID,
| ^~~
overlapInCore/overlapPair.C:437:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
437 | if (extendAlignment(aRead, abgn, aend, alen, "A", aID,
| ^~~
overlapInCore/overlapPair.C:438:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
438 | bRead, bbgn, bend, blen, "B", bID,
| ^~~
overlapInCore/overlapPair.C:506:56: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
506 | if (extendAlignment(bRead, bbgn, bend, blen, "Bb5", bID,
| ^~~~~
overlapInCore/overlapPair.C:507:56: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
507 | aRead, abgn, aend, alen, "Ab5", aID,
| ^~~~~
overlapInCore/overlapPair.C:532:56: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
532 | if (extendAlignment(aRead, abgn, aend, alen, "Aa5", aID,
| ^~~~~
overlapInCore/overlapPair.C:533:56: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
533 | bRead, bbgn, bend, blen, "Ba5", bID,
| ^~~~~
overlapInCore/overlapPair.C:560:56: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
560 | if (extendAlignment(aRead, abgn, aend, alen, "Aa3", aID,
| ^~~~~
overlapInCore/overlapPair.C:561:56: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
561 | bRead, bbgn, bend, blen, "Ba3", bID,
| ^~~~~
overlapInCore/overlapPair.C:586:56: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
586 | if (extendAlignment(bRead, bbgn, bend, blen, "Bb3", bID,
| ^~~~~
overlapInCore/overlapPair.C:587:56: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
587 | aRead, abgn, aend, alen, "Ab3", aID,
| ^~~~~
overlapInCore/edalign.C: In function ‘bool readLine(FILE*, char*, int32, int32&, splitToWords&)’:
overlapInCore/edalign.C:38:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
38 | fgets(line, lineMax, file);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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=]
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 10 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",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
163 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3,
| ~~~~~~~~~~~~~~~
| |
| int
mhap/mhapConvert.C:158:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 11 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",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
163 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3,
| ~~~~~~~~~~~~~~~
| |
| int
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores correction/filterCorrectionOverlaps.C
minimap/mmapConvert.C: In function ‘int main(int, char**)’:
minimap/mmapConvert.C:139:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 7 has type ‘int’ [-Wformat=]
139 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
142 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3,
| ~~~~~~~~~~~~~~~
| |
| int
minimap/mmapConvert.C:139:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 8 has type ‘int’ [-Wformat=]
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 9 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",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
143 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3,
| ~~~~~~~~~~~~~~~
| |
| int
minimap/mmapConvert.C:139:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 10 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",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
143 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3,
| ~~~~~~~~~~~~~~~
| |
| int
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from wtdbg/wtdbgConvert.C:33:
utility/bits.H: In member function ‘void stuffedBits::updateBlk(uint64)’:
utility/bits.H: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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Iutgcns utgcns/stashContains.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores correction/filterCorrectionLayouts.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from correction/generateCorrectionLayouts.C:37:
utility/bits.H: In member function ‘void stuffedBits::updateBlk(uint64)’:
utility/bits.H: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}
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from utgcns/stashContains.H:35,
from utgcns/stashContains.C:30:
utility/bits.H: In member function ‘void stuffedBits::updateBlk(uint64)’:
utility/bits.H:791:44: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from /usr/include/c++/11/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++/11/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++/11/bits/stl_tree.h:2428:7: 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
2428 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Iutgcns correction/falconsense.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
In file included from /usr/include/c++/11/map:61,
from stores/tgTig.H:38,
from stores/tgStore.H:43,
from wtdbg/wtdbgConvert.C:33:
/usr/include/c++/11/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++/11/bits/stl_map.h:501:44: 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++/11/bits/stl_map.h: In function ‘int main(int, char**)’:
/usr/include/c++/11/bits/stl_map.h:501:44: 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++/11/bits/stl_map.h:501:44: 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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.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
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)) {
| ~~~~~^~~~~~~~~~~~
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 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
In file included from haplotyping/splitHaplotype.C:34:
utility/kmers.H: In member function ‘void kmerCountFileIndex::set(uint64, FILE*, uint64)’:
utility/kmers.H:594:42: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
haplotyping/splitHaplotype.C: In member function ‘void hapData::initializeKmerTable(uint32)’:
haplotyping/splitHaplotype.C:443:34: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
443 | fprintf(stderr, "-- loaded %lu kmers.\n", nKmers);
| ~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
haplotyping/splitHaplotype.C: In function ‘void outputReadBatch(void*, void*)’:
haplotyping/splitHaplotype.C:707:23: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
707 | ">%s\n", s->_names[ii].string());
| ^~~~~~~
haplotyping/splitHaplotype.C: In function ‘int main(int, char**)’:
haplotyping/splitHaplotype.C:771:19: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
771 | err.push_back("No input sequences supplied with either (-S) or (-R).\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplotyping/splitHaplotype.C:773:19: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
773 | err.push_back("Only one type of input reads (-S or -R) supported.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplotyping/splitHaplotype.C:775:19: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
775 | err.push_back("Not enough haplotypes (-H) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplotyping/splitHaplotype.C:854:39: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
854 | fprintf(stdout, "-- %8u reads %12lu bases written to haplotype file %s.\n", G->_haps[ii]->nReads, G->_haps[ii]->nBases, G->_haps[ii]->outputName);
| ~~~~^
| |
| long unsigned int
| %12llu
haplotyping/splitHaplotype.C:855:37: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
855 | fprintf(stdout, "-- %8u reads %12lu bases written to haplotype file %s.\n", G->_ambiguousReads, G->_ambiguousBases, G->_ambiguousName);
| ~~~~^ ~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %12llu
haplotyping/splitHaplotype.C:857:37: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
857 | fprintf(stdout, "-- %8u reads %12lu bases filtered for being too short.\n", G->_filteredReads, G->_filteredBases);
| ~~~~^ ~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %12llu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores overlapBasedTrimming/trimReads.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C
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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores overlapBasedTrimming/splitReads.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores overlapBasedTrimming/adjustFlipped.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores overlapBasedTrimming/mergeRanges.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C
overlapBasedTrimming/mergeRanges.C: In function ‘int main(int, char**)’:
overlapBasedTrimming/mergeRanges.C:77:19: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
77 | err.push_back("ERROR: no sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapAlign/overlapAlign.C:39:
utility/bits.H: In member function ‘void stuffedBits::updateBlk(uint64)’:
utility/bits.H:791:44: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapAlign/computeOverlapAlignment.C:32:
utility/bits.H: In member function ‘void stuffedBits::updateBlk(uint64)’:
utility/bits.H:791:44: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
overlapAlign/computeOverlapAlignment.C: In member function ‘void maComputation::computeOverlapAlignment(uint32, uint32, double, uint32, uint32)’:
overlapAlign/computeOverlapAlignment.C:581:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
581 | if (computeAlignment(_bRead, bbgn, bend, blen, "B", _bID, // Align all of sequence B into
| ^~~
overlapAlign/computeOverlapAlignment.C:582:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
582 | _aRead, abgn, aend, alen, "A", _aID, // sequence A with free ends.
| ^~~
overlapAlign/computeOverlapAlignment.C:626:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
626 | if (computeAlignment(_aRead, abgn, aend, alen, "A", _aID, // Align all of sequence A into
| ^~~
overlapAlign/computeOverlapAlignment.C:627:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
627 | _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends.
| ^~~
overlapAlign/computeOverlapAlignment.C:674:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
674 | if (computeAlignment(_bRead, bbgn, bend, blen, "B", _bID, // Align all of sequence B into
| ^~~
overlapAlign/computeOverlapAlignment.C:675:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
675 | _aRead, abgn, aend, alen, "A", _aID, // sequence A with free ends.
| ^~~
overlapAlign/computeOverlapAlignment.C:719:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
719 | if (computeAlignment(_aRead, abgn, aend, alen, "A", _aID, // Align all of sequence A into
| ^~~
overlapAlign/computeOverlapAlignment.C:720:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
720 | _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends.
| ^~~
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
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from overlapErrorAdjustment/findErrors.H:34,
from overlapErrorAdjustment/findErrors.C:30:
/usr/include/c++/11/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++/11/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C
/usr/include/c++/11/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++/11/bits/stl_heap.h:355:29: 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++/11/bits/stl_heap.h:263:25: note: parameter passing for argument of type ‘_ValueType’ {aka ‘Olap_Info_t’} changed in GCC 9.1
263 | std::__adjust_heap(__first, _DistanceType(0),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
264 | _DistanceType(__last - __first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
265 | _GLIBCXX_MOVE(__value), __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/bogart.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/bogart.C:46:
utility/stddev.H: In member function ‘void histogramStatistics::finalizeData()’:
utility/stddev.H:451:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
bogart/bogart.C: In function ‘int main(int, char**)’:
bogart/bogart.C:338:46: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
338 | if (erateGraph < 0.0) err.push_back("Invalid overlap error threshold (-eg option); must be at least 0.0.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:339:46: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
339 | if (erateMax < 0.0) err.push_back("Invalid overlap error threshold (-eM option); must be at least 0.0.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:340:46: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
340 | if (prefix == NULL) err.push_back("No output prefix name (-o option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:341:46: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
341 | if (seqStorePath == NULL) err.push_back("No sequence store (-S option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:342:46: warning: ISO C++ forbids converting a string constant to ‘std::vector<char*>::value_type’ {aka ‘char*’} [-Wwrite-strings]
342 | if (ovlStorePath == NULL) err.push_back("No overlap store (-O option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C
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);
| ^~~~~
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/AS_BAT_AssemblyGraph.C:28:
utility/stddev.H: In member function ‘void histogramStatistics::finalizeData()’:
utility/stddev.H:451:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_AssemblyGraph.C:26:
/usr/include/c++/11/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++/11/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++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_AssemblyGraph.C:26:
/usr/include/c++/11/bits/stl_vector.h: In function ‘_ZN13AssemblyGraph10buildGraphEPKcdR9TigVector._omp_fn.0’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: 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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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
| ^~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_algo.h:1861:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1861 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1861:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/AS_BAT_CreateUnitigs.C:29:
utility/stddev.H: In member function ‘void histogramStatistics::finalizeData()’:
utility/stddev.H:451:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_DetectSpurs.C:31:
utility/stddev.H: In member function ‘void histogramStatistics::finalizeData()’:
utility/stddev.H:451:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_Instrumentation.C
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++/11/bits/vector.tcc: In member function ‘void BestOverlapGraph::findErrorRateThreshold()’:
/usr/include/c++/11/bits/vector.tcc:121:28: 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++/11/bits/vector.tcc:121:28: 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++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/11/bits/stl_vector.h:1198:28: 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++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1957:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1957 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/11/bits/vector.tcc:121:28: 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++/11/bits/vector.tcc:121:28: 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++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1957:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1957 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_Logging.C
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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.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:866,
from /<<PKGBUILDDIR>>/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:71:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4115 bytes into a destination of size 4096
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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_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
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
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_MergeOrphans.C:30:
/usr/include/c++/11/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++/11/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++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_MergeOrphans.C:30:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void assignReadsToTargets(Unitig*, std::vector<overlapPlacement>*, std::vector<candidatePop*>)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: 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++/11/bits/stl_vector.h: In function ‘_Z24findOrphanReadPlacementsR9TigVectorRSt3mapIjSt6vectorIjSaIjEESt4lessIjESaISt4pairIKjS4_EEEdd._omp_fn.0’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: 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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_OverlapCache.C:49:
utility/stddev.H: In member function ‘void histogramStatistics::finalizeData()’:
utility/stddev.H:451:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from 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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_PromoteToSingleton.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_ReadInfo.C
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39:
/usr/include/c++/11/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++/11/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++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39:
/usr/include/c++/11/bits/stl_vector.h: In function ‘bool placeReadUsingOverlaps(TigVector&, Unitig*, uint32, std::vector<overlapPlacement>&, uint32)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: 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_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
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_SetParentAndHang.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_SplitDiscontinuous.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_TigGraph.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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_AssemblyGraph.H:32,
from bogart/AS_BAT_TigGraph.C:28:
utility/stddev.H: In member function ‘void histogramStatistics::finalizeData()’:
utility/stddev.H:451:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_TigVector.C:28:
utility/stddev.H: In member function ‘void histogramStatistics::finalizeData()’:
utility/stddev.H:451:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_Unitig.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_Unitig_AddRead.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogus/bogus/bogus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogus/bogus.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
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
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_Unitig_AddRead.C:43:
utility/stddev.H: In member function ‘void histogramStatistics::finalizeData()’:
utility/stddev.H:451:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogus/bogus/bogusUtil.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores bogus/bogusUtil.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.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
In file included from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >’ changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/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 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/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
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/11/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++/11/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,
| ^~~~~~~~~~~~~
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}
In file included from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_algo.h:1949:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >’ changed in GCC 7.1
1949 | __sort(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~
/usr/include/c++/11/bits/stl_algo.h:1949:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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++/11/bits/stl_algo.h: In function ‘int main(int, char**)’:
/usr/include/c++/11/bits/stl_algo.h:4875:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >’ changed in GCC 7.1
4875 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__comp));
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:4875:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<genomeAlignment*, std::vector<genomeAlignment> >’ changed in GCC 7.1
4875 | 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
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogus/bogusUtil.H:42,
from bogus/bogusUtil.C:43:
/usr/include/c++/11/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++/11/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++/11/vector:67,
from /usr/include/c++/11/functional:62,
from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13,
from /usr/include/c++/11/algorithm:74,
from utility/arrays.H:33,
from /<<PKGBUILDDIR>>/src/AS_global.H:105,
from bogus/bogusUtil.H:42,
from bogus/bogusUtil.C:43:
/usr/include/c++/11/bits/stl_vector.h: In function ‘void addAlignment(std::vector<genomeAlignment>&, int32, int32, int32, bool, int32, int32, double, int32, int32, int32)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: 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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C
/usr/include/c++/11/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++/11/bits/stl_vector.h:1198:28: 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++/11/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++/11/bits/stl_vector.h:1198:28: 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 /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/src -Iutility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C
cp -pf pipelines/canu.pl /<<PKGBUILDDIR>>/Linux-armv7l/bin/canu
chmod +x /<<PKGBUILDDIR>>/Linux-armv7l/bin/canu
cp -pf pipelines/canu-time.pl /<<PKGBUILDDIR>>/Linux-armv7l/bin/canu-time
chmod +x /<<PKGBUILDDIR>>/Linux-armv7l/bin/canu-time
echo > /<<PKGBUILDDIR>>/Linux-armv7l/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here."
chmod -x /<<PKGBUILDDIR>>/Linux-armv7l/bin/canu.defaults
cp -pf sequence/share/ultra-long-nanopore /<<PKGBUILDDIR>>/Linux-armv7l/share/sequence/ultra-long-nanopore
cp -pf sequence/share/pacbio /<<PKGBUILDDIR>>/Linux-armv7l/share/sequence/pacbio
cp -pf sequence/share/pacbio-hifi /<<PKGBUILDDIR>>/Linux-armv7l/share/sequence/pacbio-hifi
cp -pf pipelines/canu/Consensus.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/CorrectReads.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/HaplotypeReads.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Configure.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Defaults.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Execution.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/SequenceStore.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_Cloud.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_DNANexus.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_LSF.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_PBSTorque.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_SGE.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_Slurm.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Meryl.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Output.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapBasedTrimming.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapErrorAdjustment.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapInCore.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapMhap.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapMMap.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapStore.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Report.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
cp -pf pipelines/canu/Unitig.pm /<<PKGBUILDDIR>>/Linux-armv7l/lib/site_perl/canu/
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/AS_global.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<PKGBUILDDIR>>/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);
| ~~~~~~^~~~~~~
ar rv /<<PKGBUILDDIR>>/Linux-armv7l/lib/libcanu.a /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/AS_global.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/edlib.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/files.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/files-buffered.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/files-compressed.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/files-memoryMapped.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/logging.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/strings.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/system.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/system-stackTrace.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/sequence.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-reader.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-block.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-stream.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-statistics.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-exact.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/bits.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/hexDump.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/md5.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/mt19937ar.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/objectStore.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/speedCounter.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/sweatShop.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/correction/computeGlobalScore.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqCache.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqLibrary.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadData.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadDataWriter.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqStore.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreBlob.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreConstructor.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreInfo.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovOverlap.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStore.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreWriter.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFilter.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFile.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreHistogram.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/tgStore.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/tgTig.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/gfa/gfa.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/gfa/bed.o
ar: creating /<<PKGBUILDDIR>>/Linux-armv7l/lib/libcanu.a
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/AS_global.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/edlib.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/files.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/files-buffered.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/files-compressed.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/files-memoryMapped.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/logging.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/strings.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/system.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/system-stackTrace.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/sequence.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-reader.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-block.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-stream.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-statistics.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-exact.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/bits.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/hexDump.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/md5.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/mt19937ar.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/objectStore.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/speedCounter.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utility/sweatShop.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/correction/computeGlobalScore.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqCache.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqLibrary.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadData.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadDataWriter.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqStore.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreBlob.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreConstructor.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreInfo.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovOverlap.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStore.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreWriter.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFilter.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFile.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreHistogram.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/tgStore.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/tgTig.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/gfa/gfa.o
a - /<<PKGBUILDDIR>>/Linux-armv7l/obj/lib/libcanu.a/gfa/bed.o
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from utgcns/unitigConsensus.H:67,
from utgcns/unitigConsensus.C:74:
utility/bits.H: In member function ‘void stuffedBits::updateBlk(uint64)’:
utility/bits.H:791:44: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64’ {aka ‘long long unsigned int’} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
gfa/alignGFA.C: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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from gfa/alignGFA.C:30:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 8199 bytes into a destination of size 4097
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from gfa/alignGFA.C:30:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 10 and 8202 bytes into a destination of size 4097
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 | __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:866,
from /<<PKGBUILDDIR>>/src/AS_global.H:67,
from gfa/alignGFA.C:30:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 13 and 8205 bytes into a destination of size 4097
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/dumpBlob -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/ovStoreBuild -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/ovStoreConfig -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/ovStoreBucketizer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/ovStoreSorter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/ovStoreIndexer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/ovStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/ovStoreStats -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/sqStoreCreate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/sqStoreDumpFASTQ -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/sqStoreDumpMetaData -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/tgStoreCompress -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/tgStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/tgStoreDump/stores/tgStoreDump.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/tgStoreLoad -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/tgStoreFilter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/tgTigDisplay -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/loadCorrectedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/loadTrimmedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/loadErates -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/loadErates/stores/loadErates.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/meryl -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/meryl.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylCountArray.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylInput.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylOp-count.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylOp-countSimple.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylOp-histogram.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylOp-nextMer.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl/meryl/merylOp.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/meryl-import -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl-import/meryl/meryl-import.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl-import/meryl/merylCountArray.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/meryl-lookup -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/meryl-lookup/meryl/meryl-lookup.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/sequence -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-extract.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-generate.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-mutate.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-sample.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-simulate.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/sequence/sequence/sequence-summarize.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/overlapInCore -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/overlapInCorePartition -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/overlapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/overlapImport -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapImport/overlapInCore/overlapImport.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/overlapPair -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapPair/overlapInCore/overlapPair.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/edalign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/edalign/overlapInCore/edalign.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/prefixEditDistance-matchLimitGenerate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/mhapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/mhapConvert/mhap/mhapConvert.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/mmapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/mmapConvert/minimap/mmapConvert.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/wtdbgConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/filterCorrectionOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/generateCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/filterCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/falconsense -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/falconsense/correction/falconsense.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/falconsense/utgcns/stashContains.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/errorEstimate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/splitHaplotype -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/trimReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/splitReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/mergeRanges -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/overlapAlign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/trimRead.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/findErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/bogart -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/bogart.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Logging.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Outputs.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigVector.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/bogus -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogus/bogus/bogus.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/bogus/bogus/bogusUtil.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/alignGFA/gfa/alignGFA.o -lcanu
g++ -o /<<PKGBUILDDIR>>/Linux-armv7l/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<PKGBUILDDIR>>/Linux-armv7l/lib /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/utgcns/utgcns/utgcns.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/utgcns/utgcns/stashContains.o /<<PKGBUILDDIR>>/Linux-armv7l/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu
Success!
canu installed in /<<PKGBUILDDIR>>/Linux-armv7l/bin/canu
make[2]: Leaving directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>'
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 --destdir=debian/canu/ -a -O--sourcedirectory=src/
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
dh_installdocs -a -O--sourcedirectory=src/
dh_installchangelogs -a -O--sourcedirectory=src/
dh_installman -a -O--sourcedirectory=src/
dh_installsystemduser -a -O--sourcedirectory=src/
dh_perl -a -O--sourcedirectory=src/
dh_link -a -O--sourcedirectory=src/
dh_strip_nondeterminism -a -O--sourcedirectory=src/
dh_compress -a -O--sourcedirectory=src/
dh_fixperms -a -O--sourcedirectory=src/
dh_missing -a -O--sourcedirectory=src/
dh_dwz -a -O--sourcedirectory=src/
dh_strip -a -O--sourcedirectory=src/
dh_makeshlibs -a -O--sourcedirectory=src/
dh_shlibdeps -a -O--sourcedirectory=src/
dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/overlapPair contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/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/bogus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/bogart 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-2+b4_armhf.deb'.
dpkg-deb: building package 'canu-dbgsym' in '../canu-dbgsym_2.0+dfsg-2+b4_armhf.deb'.
dpkg-genbuildinfo --build=any -O../canu_2.0+dfsg-2+b4_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../canu_2.0+dfsg-2+b4_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 2022-03-17T04:52:08Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
canu_2.0+dfsg-2+b4_armhf.changes:
---------------------------------
Format: 1.8
Date: Thu, 17 Mar 2022 04:44:54 +0000
Source: canu (2.0+dfsg-2)
Binary: canu canu-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 2.0+dfsg-2+b4
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Raspbian pi4 based autobuilder <root@raspbian.org>
Description:
canu - single molecule sequence assembler for genomes
Changes:
canu (2.0+dfsg-2+b4) bookworm-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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e1537e59ad8eee174fe0cfce67d0473c67d54e0e 1040020 canu_2.0+dfsg-2+b4_armhf.deb
Checksums-Sha256:
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7997787ec51304fc95aa51423fe4addd8e5b8bb6e554c2b0d374fc709a7b1169 6835 canu_2.0+dfsg-2+b4_armhf.buildinfo
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Files:
c40ee26072584be751295218da9c47ec 11965696 debug optional canu-dbgsym_2.0+dfsg-2+b4_armhf.deb
d0918c04f9164413d05e84a0f69ec8f1 6835 science optional canu_2.0+dfsg-2+b4_armhf.buildinfo
f7a228663a44d1b9d9ddb3f8164522d3 1040020 science optional canu_2.0+dfsg-2+b4_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: canu (2.0+dfsg-2)
Binary: canu canu-dbgsym
Architecture: armhf
Version: 2.0+dfsg-2+b4
Binary-Only-Changes:
canu (2.0+dfsg-2+b4) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
.
-- Raspbian pi4 based autobuilder <root@raspbian.org> Thu, 17 Mar 2022 04:44:54 +0000
Checksums-Md5:
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f7a228663a44d1b9d9ddb3f8164522d3 1040020 canu_2.0+dfsg-2+b4_armhf.deb
Checksums-Sha1:
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Checksums-Sha256:
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Thu, 17 Mar 2022 04:52:06 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.71-2),
automake (= 1:1.16.5-1.1),
autopoint (= 0.21-4),
autotools-dev (= 20220109.1),
base-files (= 12.2+rpi1),
base-passwd (= 3.5.52),
bash (= 5.1-6),
binfmt-support (= 2.2.1-2),
binutils (= 2.37.90.20220207-1+rpi1),
binutils-arm-linux-gnueabihf (= 2.37.90.20220207-1+rpi1),
binutils-common (= 2.37.90.20220207-1+rpi1),
bsdextrautils (= 2.37.3-1),
bsdutils (= 1:2.37.3-1),
build-essential (= 12.9),
bzip2 (= 1.0.8-5),
ca-certificates (= 20211016),
ca-certificates-java (= 20190909),
coreutils (= 8.32-4.1),
cpp (= 4:11.2.0-2+rpi1),
cpp-11 (= 11.2.0-16+rpi1),
dash (= 0.5.11+git20210903+057cd650a4ed-3),
debconf (= 1.5.79),
debhelper (= 13.6),
debianutils (= 4.11.2),
default-jre-headless (= 2:1.11-72+b4),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.0-1),
diffutils (= 1:3.7-5),
dpkg (= 1.21.1+rpi1),
dpkg-dev (= 1.21.1+rpi1),
dwz (= 0.14-1),
fastjar (= 2:0.98-7),
file (= 1:5.41-2),
findutils (= 4.8.0-1),
fontconfig-config (= 2.13.1-4.4),
fonts-dejavu-core (= 2.37-2),
g++ (= 4:11.2.0-2+rpi1),
g++-11 (= 11.2.0-16+rpi1),
gcc (= 4:11.2.0-2+rpi1),
gcc-11 (= 11.2.0-16+rpi1),
gcc-11-base (= 11.2.0-16+rpi1),
gettext (= 0.21-4),
gettext-base (= 0.21-4),
grep (= 3.7-1),
groff-base (= 1.22.4-8),
gzip (= 1.10-4),
hostname (= 3.23),
init-system-helpers (= 1.61),
intltool-debian (= 0.35.0+20060710.5),
jaligner (= 1.0+dfsg-8),
jarwrapper (= 0.78),
java-common (= 0.72),
libacl1 (= 2.3.1-1),
libapache-pom-java (= 18-1),
libarchive-zip-perl (= 1.68-1),
libasan6 (= 11.2.0-16+rpi1),
libasound2 (= 1.2.6.1-2),
libasound2-data (= 1.2.6.1-2),
libatinject-jsr330-api-java (= 1.0+ds1-5),
libatomic1 (= 11.2.0-16+rpi1),
libattr1 (= 1:2.5.1-1),
libaudit-common (= 1:3.0.7-1),
libaudit1 (= 1:3.0.7-1),
libavahi-client3 (= 0.8-5),
libavahi-common-data (= 0.8-5),
libavahi-common3 (= 0.8-5),
libbinutils (= 2.37.90.20220207-1+rpi1),
libblkid1 (= 2.37.3-1),
libboost-dev (= 1.74.0.3+b4),
libboost1.74-dev (= 1.74.0-14+b1),
libbrotli1 (= 1.0.9-2+b1),
libbz2-1.0 (= 1.0.8-5),
libc-bin (= 2.33-5+rpi1),
libc-dev-bin (= 2.33-5+rpi1),
libc6 (= 2.33-5+rpi1),
libc6-dev (= 2.33-5+rpi1),
libcap-ng0 (= 0.7.9-2.2+b1),
libcap2 (= 1:2.44-1),
libcc1-0 (= 11.2.0-16+rpi1),
libcom-err2 (= 1.46.5-2),
libcommons-compress-java (= 1.21-1),
libcommons-parent-java (= 43-1),
libcrypt-dev (= 1:4.4.27-1.1),
libcrypt1 (= 1:4.4.27-1.1),
libctf-nobfd0 (= 2.37.90.20220207-1+rpi1),
libctf0 (= 2.37.90.20220207-1+rpi1),
libcups2 (= 2.4.1op1-2),
libdb5.3 (= 5.3.28+dfsg1-0.8),
libdbus-1-3 (= 1.14.0-1),
libdebconfclient0 (= 0.261),
libdebhelper-perl (= 13.6),
libdpkg-perl (= 1.21.1+rpi1),
libelf1 (= 0.186-1),
libexpat1 (= 2.4.4-1),
libfastutil-java (= 8.5.8+dfsg-1),
libffi8 (= 3.4.2-4),
libfile-stripnondeterminism-perl (= 1.13.0-1),
libfilesys-df-perl (= 0.92-6+b7),
libfontconfig1 (= 2.13.1-4.4),
libfreetype6 (= 2.11.1+dfsg-1),
libgcc-11-dev (= 11.2.0-16+rpi1),
libgcc-s1 (= 11.2.0-16+rpi1),
libgcrypt20 (= 1.9.4-5),
libgdbm-compat4 (= 1.23-1),
libgdbm6 (= 1.23-1),
libglib2.0-0 (= 2.70.4-1),
libgmp10 (= 2:6.2.1+dfsg-3),
libgnutls30 (= 3.7.3-4),
libgomp1 (= 11.2.0-16+rpi1),
libgpg-error0 (= 1.43-3),
libgraphite2-3 (= 1.3.14-1),
libgssapi-krb5-2 (= 1.18.3-7),
libguava-java (= 29.0-6),
libharfbuzz0b (= 2.7.4-1),
libhogweed6 (= 3.7.3-1),
libicu67 (= 67.1-7),
libidn2-0 (= 2.3.2-2),
libisl23 (= 0.24-2),
libjpeg62-turbo (= 1:2.1.2-1),
libjsr305-java (= 0.1~+svn49-11),
libk5crypto3 (= 1.18.3-7),
libkeyutils1 (= 1.6.1-2),
libkrb5-3 (= 1.18.3-7),
libkrb5support0 (= 1.18.3-7),
liblcms2-2 (= 2.12~rc1-2),
liblz4-1 (= 1.9.3-2),
liblzma5 (= 5.2.5-2),
libmagic-mgc (= 1:5.41-2),
libmagic1 (= 1:5.41-2),
libmeryl-dev (= 0~20150903+r2013-8+b1),
libmount1 (= 2.37.3-1),
libmpc3 (= 1.2.1-1),
libmpfr6 (= 4.1.0-3),
libnettle8 (= 3.7.3-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libnspr4 (= 2:4.32-3),
libnss3 (= 2:3.75-1),
libp11-kit0 (= 0.24.0-6),
libpam-modules (= 1.4.0-11),
libpam-modules-bin (= 1.4.0-11),
libpam-runtime (= 1.4.0-11),
libpam0g (= 1.4.0-11),
libpcre2-8-0 (= 10.39-3),
libpcre3 (= 2:8.39-13),
libpcsclite1 (= 1.9.5-3),
libperl5.34 (= 5.34.0-3),
libpipeline1 (= 1.5.5-1),
libpng16-16 (= 1.6.37-3),
libseccomp2 (= 2.5.3-2+rpi1),
libselinux1 (= 3.3-1),
libsigsegv2 (= 2.14-1),
libsmartcols1 (= 2.37.3-1),
libsqlite3-0 (= 3.37.2-2),
libssl1.1 (= 1.1.1m-1),
libssw-java (= 1.1-13),
libstdc++-11-dev (= 11.2.0-16+rpi1),
libstdc++6 (= 11.2.0-16+rpi1),
libsub-override-perl (= 0.09-2),
libsystemd0 (= 250.3-2+rpi1),
libtasn1-6 (= 4.18.0-4),
libtinfo6 (= 6.3-2),
libtirpc-common (= 1.3.2-2),
libtirpc-dev (= 1.3.2-2),
libtirpc3 (= 1.3.2-2),
libtool (= 2.4.6-15),
libubsan1 (= 11.2.0-16+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 250.3-2+rpi1),
libunistring2 (= 1.0-1),
libuuid1 (= 2.37.3-1),
libxml2 (= 2.9.13+dfsg-1),
libzstd1 (= 1.4.8+dfsg-3+rpi1),
linux-libc-dev (= 5.15.15-2+rpi1),
login (= 1:4.11.1+dfsg1-1),
lsb-base (= 11.1.0+rpi1),
m4 (= 1.4.18-5),
make (= 4.3-4.1),
man-db (= 2.10.1-1),
mawk (= 1.3.4.20200120-3),
mhap (= 2.1.3+dfsg-3),
ncurses-base (= 6.3-2),
ncurses-bin (= 6.3-2),
openjdk-11-jre-headless (= 11.0.14+9-1),
openssl (= 1.1.1m-1),
patch (= 2.7.6-7),
perl (= 5.34.0-3),
perl-base (= 5.34.0-3),
perl-modules-5.34 (= 5.34.0-3),
po-debconf (= 1.0.21+nmu1),
rpcsvc-proto (= 1.4.2-4),
sed (= 4.8-1),
sensible-utils (= 0.0.17),
sysvinit-utils (= 3.01-1),
tar (= 1.34+dfsg-1),
ucf (= 3.0043),
util-linux (= 2.37.3-1),
xz-utils (= 5.2.5-2),
zlib1g (= 1:1.2.11.dfsg-2)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1647492294"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
canu-dbgsym_2.0+dfsg-2+b4_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 11965696 bytes: control archive=2868 bytes.
2394 bytes, 12 lines control
5384 bytes, 51 lines md5sums
Package: canu-dbgsym
Source: canu (2.0+dfsg-2)
Version: 2.0+dfsg-2+b4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 13137
Depends: canu (= 2.0+dfsg-2+b4)
Section: debug
Priority: optional
Description: debug symbols for canu
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lrwxrwxrwx root/root 0 2022-03-17 04:44 ./usr/share/doc/canu-dbgsym -> canu
canu_2.0+dfsg-2+b4_armhf.deb
----------------------------
new Debian package, version 2.0.
size 1040020 bytes: control archive=3100 bytes.
891 bytes, 22 lines control
5892 bytes, 85 lines md5sums
Package: canu
Source: canu (2.0+dfsg-2)
Version: 2.0+dfsg-2+b4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8024
Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libstdc++6 (>= 11), perl:any, libfilesys-df-perl, mhap, 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 140940 2022-03-17 04:44 ./usr/lib/canu/bin/ovStoreSorter
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-rwxr-xr-x root/root 112220 2022-03-17 04:44 ./usr/lib/canu/bin/tgStoreCompress
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-rwxr-xr-x root/root 247444 2022-03-17 04:44 ./usr/lib/canu/bin/utgcns
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drwxr-xr-x root/root 0 2022-03-17 04:44 ./usr/lib/canu/lib/
-rw-r--r-- root/root 750326 2022-03-17 04:44 ./usr/lib/canu/lib/libcanu.a
drwxr-xr-x root/root 0 2022-03-17 04:44 ./usr/lib/canu/lib/site_perl/
drwxr-xr-x root/root 0 2022-03-17 04:44 ./usr/lib/canu/lib/site_perl/canu/
-rw-r--r-- root/root 44094 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Configure.pm
-rw-r--r-- root/root 24229 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Consensus.pm
-rw-r--r-- root/root 26771 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/CorrectReads.pm
-rw-r--r-- root/root 69874 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Defaults.pm
-rw-r--r-- root/root 53634 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Execution.pm
-rw-r--r-- root/root 2483 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Grid.pm
-rw-r--r-- root/root 37789 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Grid_Cloud.pm
-rw-r--r-- root/root 7033 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Grid_DNANexus.pm
-rw-r--r-- root/root 6219 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Grid_LSF.pm
-rw-r--r-- root/root 7188 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Grid_PBSTorque.pm
-rw-r--r-- root/root 13874 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Grid_SGE.pm
-rw-r--r-- root/root 5503 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Grid_Slurm.pm
-rw-r--r-- root/root 37097 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/HaplotypeReads.pm
-rw-r--r-- root/root 30367 2022-03-17 04:44 ./usr/lib/canu/lib/site_perl/canu/Meryl.pm
-rw-r--r-- root/root 7066 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Output.pm
-rw-r--r-- root/root 10484 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/OverlapBasedTrimming.pm
-rw-r--r-- root/root 25151 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/OverlapErrorAdjustment.pm
-rw-r--r-- root/root 16396 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/OverlapInCore.pm
-rw-r--r-- root/root 24524 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/OverlapMMap.pm
-rw-r--r-- root/root 30586 2022-03-17 04:44 ./usr/lib/canu/lib/site_perl/canu/OverlapMhap.pm
-rw-r--r-- root/root 31532 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/OverlapStore.pm
-rw-r--r-- root/root 5978 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Report.pm
-rw-r--r-- root/root 18579 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/SequenceStore.pm
-rw-r--r-- root/root 12888 2020-03-18 07:51 ./usr/lib/canu/lib/site_perl/canu/Unitig.pm
drwxr-xr-x root/root 0 2022-03-17 04:44 ./usr/share/
drwxr-xr-x root/root 0 2022-03-17 04:44 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-03-17 04:44 ./usr/share/doc/canu/
-rw-r--r-- root/root 219 2020-03-18 07:51 ./usr/share/doc/canu/README.citation
-rw-r--r-- root/root 2155 2020-03-18 07:51 ./usr/share/doc/canu/README.md
-rw-r--r-- root/root 218 2022-03-17 04:44 ./usr/share/doc/canu/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1051 2022-03-17 04:44 ./usr/share/doc/canu/changelog.Debian.gz
-rw-r--r-- root/root 6019 2021-10-28 20:27 ./usr/share/doc/canu/copyright
drwxr-xr-x root/root 0 2022-03-17 04:44 ./usr/share/man/
drwxr-xr-x root/root 0 2022-03-17 04:44 ./usr/share/man/man1/
-rw-r--r-- root/root 325 2022-03-17 04:44 ./usr/share/man/man1/canu.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 153216
Build-Time: 433
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 456
Job: canu_2.0+dfsg-2
Machine Architecture: armhf
Package: canu
Package-Time: 917
Source-Version: 2.0+dfsg-2
Space: 153216
Status: successful
Version: 2.0+dfsg-2+b4
--------------------------------------------------------------------------------
Finished at 2022-03-17T04:52:08Z
Build needed 00:15:17, 153216k disk space