canu →
2.0+dfsg-2+b2 →
armhf → 2021-12-28 06:55:20
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| canu 2.0+dfsg-2+b2 (armhf) Tue, 28 Dec 2021 06:46:57 +0000 |
+==============================================================================+
Package: canu
Version: 2.0+dfsg-2+b2
Source Version: 2.0+dfsg-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-54bc10e6-dbc1-43d8-a9f1-18aa3d2a3528' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| 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 [12.6 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [13.5 MB]
Fetched 26.2 MB in 10s (2545 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'canu' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/canu.git
Please use:
git clone https://salsa.debian.org/med-team/canu.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1262 kB of source archives.
Get:1 http://172.17.4.1/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 (3708 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/canu-iXVX1N/canu-2.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/canu-iXVX1N' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-KG9Dbz/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-KG9Dbz/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive ./ Packages [430 B]
Fetched 2106 B in 0s (10.3 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 40 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (68.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12559 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap
Filtered Build-Depends: debhelper-compat (= 13), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap
dpkg-deb: building package 'sbuild-build-depends-canu-dummy' in '/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive/sbuild-build-depends-canu-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-canu-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive ./ Sources [517 B]
Get:5 copy:/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive ./ Packages [597 B]
Fetched 2447 B in 0s (11.9 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install canu build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
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 gcc-10-base 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 libgcc-10-dev 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 libstdc++-10-dev
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
libstdc++-10-doc 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 gcc-10-base 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 libgcc-10-dev 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 libstdc++-10-dev
libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mhap
openjdk-11-jre-headless openssl po-debconf sbuild-build-depends-canu-dummy
ucf
0 upgraded, 80 newly installed, 0 to remove and 40 not upgraded.
Need to get 94.5 MB of archives.
After this operation, 428 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-KG9Dbz/apt_archive ./ sbuild-build-depends-canu-dummy 0.invalid.0 [888 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.4-1 [31.6 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf gcc-10-base armhf 10.3.0-13+rpi1 [206 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-2 [295 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-2 [119 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-2 [65.8 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf binfmt-support armhf 2.2.1-1 [55.0 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 1.1.1m-1 [815 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates all 20210119 [158 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf java-common all 0.72 [14.5 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libavahi-common-data armhf 0.8-5 [123 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libavahi-common3 armhf 0.8-5 [55.3 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libdbus-1-3 armhf 1.12.20-3 [195 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libavahi-client3 armhf 0.8-5 [57.9 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libcups2 armhf 2.3.3op2-7+b1 [311 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf liblcms2-2 armhf 2.12~rc1-2 [121 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-3 [80.1 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.11.0+dfsg-1 [386 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libnspr4 armhf 2:4.32-3 [90.8 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libnss3 armhf 2:3.73.1-1 [1093 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libasound2-data all 1.2.5.1-1 [38.6 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libasound2 armhf 1.2.5.1-1 [316 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.2-1 [1210 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libharfbuzz0b armhf 2.7.4-1 [1422 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libpcsclite1 armhf 1.9.5-1 [57.6 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf openjdk-11-jre-headless armhf 11.0.13+8-1 [32.8 MB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf default-jre-headless armhf 2:1.11-72+b4 [11.2 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates-java all 20190909 [15.7 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.186-1 [174 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf fastjar armhf 2:0.98-7 [42.7 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf jaligner all 1.0+dfsg-8 [136 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf jarwrapper all 0.78 [21.8 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libapache-pom-java all 18-1 [4676 B]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libgcc-10-dev armhf 10.3.0-13+rpi1 [679 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libstdc++-10-dev armhf 10.3.0-13+rpi1 [1758 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-13 [9537 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libboost-dev armhf 1.74.0.3+b2 [4824 B]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libcommons-parent-java all 43-1 [10.8 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libcommons-compress-java all 1.21-1 [600 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libfastutil-java all 8.5.6+dfsg-1 [19.3 MB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libfilesys-df-perl armhf 0.92-6+b6 [12.9 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libjsr305-java all 0.1~+svn49-11 [26.9 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libguava-java all 29.0-6 [2419 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libmeryl-dev armhf 0~20150903+r2013-8+b1 [59.6 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libssw-java armhf 1.1-13 [19.2 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf mhap all 2.1.3+dfsg-3 [160 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 12559 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.37.2-4_armhf.deb ...
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update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
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Setting up libjpeg62-turbo:armhf (1:2.1.2-1) ...
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invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of start.
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Updating certificates in /etc/ssl/certs...
129 added, 0 removed; done.
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up ca-certificates-java (20190909) ...
head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certigna.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Chambers_of_Commerce_Root_-_2008.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:Cybertrust_Global_Root.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DST_Root_CA_X3.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:EC-ACC.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R2.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:Global_Chambersign_Root_-_2008.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:Hongkong_Post_Root_CA_3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian: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
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
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.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Sonera_Class_2_Root_CA.pem
Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:TrustCor_ECA-1.pem
Adding debian:TrustCor_RootCert_CA-1.pem
Adding debian:TrustCor_RootCert_CA-2.pem
Adding debian:Trustis_FPS_Root_CA.pem
Adding debian: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:VeriSign_Universal_Root_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-canu-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
Processing triggers for ca-certificates (20210119) ...
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 (11.0.13+8-1) ...
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
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-163-generic armhf (armv8l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-11_11.2.0-10+rpi1 gcc-11_11.2.0-10+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-13+rpi1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 linux-libc-dev_5.14.16-1+rpi1
Package versions: adduser_3.118 apt_2.3.12 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-3.1 binfmt-support_2.2.1-1 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 ca-certificates_20210119 ca-certificates-java_20190909 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.5.2 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_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 fastjar_2:0.98-7 file_1:5.41-2 findutils_4.8.0-1 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-10+rpi1 gcc_4:11.2.0-2+rpi1 gcc-10-base_10.3.0-13+rpi1 gcc-11_11.2.0-10+rpi1 gcc-11-base_11.2.0-10+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_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 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_2.3.12 libarchive-zip-perl_1.68-1 libasan6_11.2.0-10+rpi1 libasound2_1.2.5.1-1 libasound2-data_1.2.5.1-1 libassuan0_2.5.5-1 libatinject-jsr330-api-java_1.0+ds1-5 libatomic1_11.2.0-10+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libavahi-client3_0.8-5 libavahi-common-data_0.8-5 libavahi-common3_0.8-5 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-4 libboost-dev_1.74.0.3+b2 libboost1.74-dev_1.74.0-13 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-10+rpi1 libcom-err2_1.46.4-1 libcommons-compress-java_1.21-1 libcommons-parent-java_43-1 libcrypt-dev_1:4.4.26-1 libcrypt1_1:4.4.26-1 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcups2_2.3.3op2-7+b1 libdb5.3_5.3.28+dfsg1-0.8 libdbus-1-3_1.12.20-3 libdebconfclient0_0.261 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libelf1_0.186-1 libexpat1_2.4.1-3 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libfastutil-java_8.5.6+dfsg-1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.13.0-1 libfilesys-df-perl_0.92-6+b6 libfontconfig1_2.13.1-4.2 libfreetype6_2.11.0+dfsg-1 libgcc-10-dev_10.3.0-13+rpi1 libgcc-11-dev_11.2.0-10+rpi1 libgcc-s1_11.2.0-10+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libglib2.0-0_2.70.2-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.2-2 libgomp1_11.2.0-10+rpi1 libgpg-error0_1.42-3 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 liblocale-gettext-perl_1.07-4+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_2.37.2-4 libmpc3_1.2.1-1 libmpfr6_4.1.0-3 libncursesw6_6.3-1 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_2:3.73.1-1 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libpcsclite1_1.9.5-1 libperl5.32_5.32.1-6 libpipeline1_1.5.4-1 libpng16-16_1.6.37-3 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg2-2 libsasl2-modules-db_2.1.27+dfsg2-2 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_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libssw-java_1.1-13 libstdc++-10-dev_10.3.0-13+rpi1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 libsub-override-perl_0.09-2 libsystemd0_249.7-1+rpi1 libtasn1-6_4.18.0-4 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.3-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_249.7-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.16-1+rpi1 login_1:4.8.1-2 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mhap_2.1.3+dfsg-3 mount_2.37.2-4 ncurses-base_6.3-1 ncurses-bin_6.3-1 netbase_6.3 openjdk-11-jre-headless_11.0.13+8-1 openssl_1.1.1m-1 passwd_1:4.8.1-2 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-canu-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 ucf_3.0043 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.QlUIvHbm/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: failed to verify signature on ./canu_2.0+dfsg-2.dsc
dpkg-source: info: extracting canu in /<<BUILDDIR>>/canu-2.0+dfsg
dpkg-source: info: unpacking canu_2.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking canu_2.0+dfsg-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+b2
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-54bc10e6-dbc1-43d8-a9f1-18aa3d2a3528
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package canu
dpkg-buildpackage: info: source version 2.0+dfsg-2+b2
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 '/<<BUILDDIR>>/canu-2.0+dfsg'
rm -rf Linux-*
rm -f src/canu_version.H
make[1]: Leaving directory '/<<BUILDDIR>>/canu-2.0+dfsg'
dh_autoreconf_clean -O--sourcedirectory=src/
dh_clean -O--sourcedirectory=src/
debian/rules build-arch
dh build-arch --sourcedirectory=src/
dh_update_autotools_config -a -O--sourcedirectory=src/
dh_autoreconf -a -O--sourcedirectory=src/
dh_auto_configure -a -O--sourcedirectory=src/
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/canu-2.0+dfsg'
dh_auto_build
cd src && make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<BUILDDIR>>/canu-2.0+dfsg/src'
WARNING:
WARNING: g++ 11 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher.
WARNING:
Building for 'Linux' '4.15.0-163-generic' as 'armv8l' into '/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/{bin,obj}'.
Using '/usr/bin/g++' version '11'.
Using user-supplied CXXFLAGS '-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security'.
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/edlib.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-buffered.C
Building release v2.0
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-compressed.C
utility/files.C: In function 'void writeToFile(void*, const char*, uint64, uint64, FILE*)':
utility/files.C:89:56: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
90 | nWritten, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:89:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
90 | nWritten, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:89:85: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
90 | nWritten, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:94:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
94 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): Short write\n",
| ~~^
| |
| long unsigned int
| %llu
95 | nWritten, nObjects, description, objectSize), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:94:65: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
94 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): Short write\n",
| ~~^
| |
| long unsigned int
| %llu
95 | nWritten, nObjects, description, objectSize), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:94:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
94 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): Short write\n",
| ~~^
| |
| long unsigned int
| %llu
95 | nWritten, nObjects, description, objectSize), exit(1);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C: In function 'uint64 loadFromFile(void*, const char*, uint64, uint64, FILE*, bool)':
utility/files.C:134:59: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
134 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): End of file\n",
| ~~^
| |
| long unsigned int
| %llu
135 | nLoaded, nObjects, description, objectSize);
| ~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:134:70: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
134 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): End of file\n",
| ~~^
| |
| long unsigned int
| %llu
135 | nLoaded, nObjects, description, objectSize);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:134:88: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
134 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): End of file\n",
| ~~^
| |
| long unsigned int
| %llu
135 | nLoaded, nObjects, description, objectSize);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:150:57: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
150 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
151 | nLoaded, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:150:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
150 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
151 | nLoaded, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C:150:86: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
150 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): %s\n",
| ~~^
| |
| long unsigned int
| %llu
151 | nLoaded, nObjects, description, objectSize, strerror(errno)), exit(1);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/files.C: In function 'void AS_UTL_symlink(const char*, const char*)':
utility/files.C:311:10: warning: ignoring return value of 'int symlink(const char*, const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
311 | symlink(pathToFile, pathToLink);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
utility/files.C: In function 'void AS_UTL_loadFileList(char*, std::vector<char*>&)':
utility/files.C:678:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
678 | fgets(line, FILENAME_MAX, F);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
utility/files.C:684:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
684 | fgets(line, FILENAME_MAX, F);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/logging.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/strings.C
utility/files-memoryMapped.C: In constructor 'memoryMappedFile::memoryMappedFile(const char*, memoryMappedFileType)':
utility/files-memoryMapped.C:76:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result]
76 | read(_fd, _data, _length);
| ~~~~^~~~~~~~~~~~~~~~~~~~~
utility/files-memoryMapped.C: In destructor 'memoryMappedFile::~memoryMappedFile()':
utility/files-memoryMapped.C:102:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result]
102 | write(_fd, _data, _length), close(_fd);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system.C
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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from utility/logging.H:29,
from utility/logging.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 6 and 8205 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utility/logging.C:161:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
161 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name);
| ^
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from utility/logging.H:29,
from utility/logging.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 6 and 8205 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utility/logging.C:157:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
157 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name);
| ^
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from utility/logging.H:29,
from utility/logging.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 6 and 8205 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utility/logging.C:158:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID);
| ^
utility/logging.C:158:43: note: using the range [-2147483648, 2147483647] for directive argument
158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from utility/logging.H:29,
from utility/logging.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 13 and 8220 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'void logFileInstance::rotateMessage()' at utility/logging.C:173:15:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: warning: 'int __builtin___snprintf_chk(char*, unsigned int, int, unsigned int, const char*, ...)' specified bound 1024 exceeds destination size 256 [-Wstringop-overflow=]
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system-stackTrace.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sequence.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-reader.C
In file included from utility/kmers.H:32,
from utility/kmers-reader.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer.C
In file included from utility/kmers-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}
In file included from utility/kmers.H:32,
from utility/kmers.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)':
utility/kmers-reader.C:208:46: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m);
| ~~~~~^ ~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
utility/kmers-reader.C:208:52: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m);
| ~~~~~^ ~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
utility/kmers-reader.C: In function 'void dumpMerylDataFile(char*)':
utility/kmers-reader.C:342:29: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2);
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-reader.C:342:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n",
| ~~~^
| |
| long unsigned int
| %8llu
343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2);
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-reader.C:342:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2);
| ~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-reader.C:342:68: warning: format '%lx' expects argument of type 'long unsigned int', but argument 10 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2);
| ~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-reader.C:342:77: warning: format '%lx' expects argument of type 'long unsigned int', but argument 11 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2);
| ~~
| |
| uint64 {aka long long unsigned int}
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?
| ^~~~~~~
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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from utility/kmers.H:29,
from utility/kmers-reader.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-block.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-stream.C
In file included from utility/kmers.H:32,
from utility/kmers-writer.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from utility/kmers-writer.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-writer.C: In member function 'void kmerCountFileWriter::initialize(uint32, bool)':
utility/kmers-writer.C:78:117: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
78 | fprintf(stderr, "kmerCountFileWriter()-- Creating '%s' for %u-mers, with prefixSize %u suffixSize %u numFiles %lu\n",
| ~~^
| |
| long unsigned int
| %llu
79 | _outName, (_prefixSize + _suffixSize) / 2, _prefixSize, _suffixSize, _numFiles);
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers-writer.C: In member function 'uint32 kmerCountFileWriter::fileNumber(uint64)':
utility/kmers-writer.C:169:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
169 | fprintf(stderr, "kmerCountFileWriter()-- Formed invalid file number %lu >= number of files %lu:\n", oi, _numFiles);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/kmers-writer.C:169:98: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
169 | fprintf(stderr, "kmerCountFileWriter()-- Formed invalid file number %lu >= number of files %lu:\n", oi, _numFiles);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/kmers-writer.C:170:71: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
170 | fprintf(stderr, "kmerCountFileWriter()-- prefix 0x%016lx\n", prefix);
| ~~~~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from utility/kmers.H:29,
from utility/kmers-writer.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-statistics.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-exact.C
In file included from utility/kmers.H:32,
from utility/kmers-writer-stream.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from utility/kmers-writer-stream.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from /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:2426:7: 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
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<>());
| ~~~~~~~~~~~~~~~
/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<>());
| ~~~~~~~~~~~~~~~
/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<>());
| ~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/bits.C
In file included from utility/kmers.H:32,
from utility/kmers-exact.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from utility/kmers.H:32,
from utility/kmers-statistics.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/hexDump.C
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}
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}
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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/md5.C
In file included from utility/bits.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/objectStore.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C
utility/objectStore.C: In function 'bool fetchFromObjectStore(char*)':
utility/objectStore.C:257:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
257 | args[1] = "download";
| ^~~~~~~~~~
utility/objectStore.C:258:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
258 | args[2] = "--overwrite";
| ^~~~~~~~~~~~~
utility/objectStore.C:259:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
259 | args[3] = "--no-progress";
| ^~~~~~~~~~~~~~~
utility/objectStore.C:260:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
260 | args[4] = "--output";
| ^~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from correction/falconConsensus.H:75,
from correction/falconConsensus.C:73:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from correction/falconConsensus.H:75,
from correction/falconConsensus-alignTag.C:73:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from stores/sqCache.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C
stores/sqCache.C: In constructor 'sqCache::sqCache(sqStore*, sqRead_which, uint64)':
stores/sqCache.C:108:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
108 | fprintf(stderr, "sqCache: found %u %s reads with %lu bases.\n", nReads, toString(_which), nBases);
| ~~^ ~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
stores/sqCache.C: In member function 'void sqCache::sqCache_loadReads(uint32, uint32, bool)':
stores/sqCache.C:356:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
356 | fprintf(stderr, "Loading %u reads and %lu bases from range %u-%u inclusive.\n",
| ~~^
| |
| long unsigned int
| %llu
357 | nReads, nBases, bgnID, endID);
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C
stores/sqReadDataWriter.C: In member function 'void sqReadDataWriter::sqReadDataWriter_writeBlob(writeBuffer*)':
stores/sqReadDataWriter.C:109:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
109 | buffer->writeIFFchunk("BLOB");
| ^~~~~~
stores/sqReadDataWriter.C:110:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
110 | buffer->writeIFFchunk("NAME", _name, _nameLen);
| ^~~~~~
stores/sqReadDataWriter.C:115:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
115 | buffer->writeIFFchunk("2SQR", rseq, rseq2Len); // Two-bit encoded sequence (ACGT only)
| ^~~~~~
stores/sqReadDataWriter.C:117:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
117 | buffer->writeIFFchunk("3SQR", rseq, rseq3Len); // Three-bit encoded sequence (ACGTN)
| ^~~~~~
stores/sqReadDataWriter.C:119:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
119 | buffer->writeIFFchunk("USQR", rseq, rseqULen); // Unencoded sequence
| ^~~~~~
stores/sqReadDataWriter.C:124:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
124 | buffer->writeIFFchunk("2SQC", cseq, cseq2Len); // Two-bit encoded sequence (ACGT only)
| ^~~~~~
stores/sqReadDataWriter.C:126:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
126 | buffer->writeIFFchunk("3SQC", cseq, cseq3Len); // Three-bit encoded sequence (ACGTN)
| ^~~~~~
stores/sqReadDataWriter.C:128:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
128 | buffer->writeIFFchunk("USQC", cseq, cseqULen); // Unencoded sequence
| ^~~~~~
stores/sqReadDataWriter.C:132:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
132 | buffer->closeIFFchunk("BLOB");
| ^~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C
In file included from stores/sqStoreBlob.C:26:
stores/sqStore.H: In constructor 'sqStoreBlobWriter::sqStoreBlobWriter(const char*, sqStoreInfo*)':
stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber);
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreBlob.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/sqStoreBlob.C:26:
stores/sqStore.H: In member function 'void sqStoreBlobWriter::writeData(sqReadDataWriter*)':
stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber);
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreBlob.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/sqStoreBlob.C:26:
stores/sqStore.H: In member function 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)':
stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber);
stores/sqStore.H:126:36: note: directive argument in the range [0, 65535]
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreBlob.C:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4109 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C
stores/sqStoreInfo.C: In member function 'bool sqStoreInfo::checkInfo()':
stores/sqStoreInfo.C:82:31: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 4 has type 'long unsigned int' [-Wformat=]
82 | failed += fprintf(stderr, "ERROR: sqVersion in store = 0x%016" F_X64P ", differs from executable = 0x%016" F_X64P "\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreInfo.C: In member function 'bool sqStoreInfo::readInfo8(char*)':
stores/sqStoreInfo.C:229:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
229 | fprintf(stderr, "sqStore_loadInfo()-- Error: Unsupported historical version %lu detected.\n", _sqVersion);
| ~~^ ~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
stores/sqStoreInfo.C: In member function 'void sqStoreInfo::writeInfo(char*)':
stores/sqStoreInfo.C:333:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
333 | B->writeIFFobject("MAGC", _sqMagic);
| ^~~~~~
stores/sqStoreInfo.C:334:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
334 | B->writeIFFobject("VERS", _sqVersion);
| ^~~~~~
stores/sqStoreInfo.C:336:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
336 | B->writeIFFobject("LSIZ", _sqLibrarySize);
| ^~~~~~
stores/sqStoreInfo.C:337:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
337 | B->writeIFFobject("RSIZ", _sqReadSize);
| ^~~~~~
stores/sqStoreInfo.C:338:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
338 | B->writeIFFobject("MLB ", _sqMaxLibrariesBits);
| ^~~~~~
stores/sqStoreInfo.C:339:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
339 | B->writeIFFobject("LNS ", _sqLibraryNameSize);
| ^~~~~~
stores/sqStoreInfo.C:340:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
340 | B->writeIFFobject("MRB ", _sqMaxReadBits);
| ^~~~~~
stores/sqStoreInfo.C:341:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
341 | B->writeIFFobject("MRLB", _sqMaxReadLenBits);
| ^~~~~~
stores/sqStoreInfo.C:343:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
343 | B->writeIFFobject("NLIB", _numLibraries);
| ^~~~~~
stores/sqStoreInfo.C:344:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
344 | B->writeIFFobject("NREA", _numReads);
| ^~~~~~
stores/sqStoreInfo.C:345:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
345 | B->writeIFFobject("NBLO", _numBlobs);
| ^~~~~~
stores/sqStoreInfo.C:347:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
347 | B->writeIFFarray("READ", _reads, sqRead_largest);
| ^~~~~~
stores/sqStoreInfo.C:348:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
348 | B->writeIFFarray("BASE", _bases, sqRead_largest);
| ^~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C
stores/sqStoreConstructor.C: In 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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 13 and 4109 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:212:35: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
212 | snprintf(No, FILENAME_MAX, "%s/libraries", _storePath);
| ^~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 11 and 4107 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:213:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
213 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/libraries", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:216:35: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
216 | snprintf(No, FILENAME_MAX, "%s/reads", _storePath);
| ^~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:217:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
217 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 19 and 4122 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:220:35: warning: '/reads-rawu' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
220 | snprintf(No, FILENAME_MAX, "%s/reads-rawu", _storePath);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:221:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
221 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-rawu", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 24 and 4127 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:224:35: warning: '/reads-rawc' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
224 | snprintf(No, FILENAME_MAX, "%s/reads-rawc", _storePath);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:225:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
225 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-rawc", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 24 and 4127 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:228:35: warning: '/reads-coru' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
228 | snprintf(No, FILENAME_MAX, "%s/reads-coru", _storePath);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:229:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
229 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-coru", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 24 and 4127 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:232:35: warning: '/reads-corc' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
232 | snprintf(No, FILENAME_MAX, "%s/reads-corc", _storePath);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:233:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
233 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-corc", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 24 and 4127 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:236:35: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
236 | snprintf(No, FILENAME_MAX, "%s/info", _storePath);
| ^~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:237:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
237 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/info", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 18 and 4121 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:240:35: warning: '/info.txt' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
240 | snprintf(No, FILENAME_MAX, "%s/info.txt", _storePath);
| ^~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 10 and 4106 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:241:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
241 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/info.txt", _storePath, V);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 22 and 4125 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:207:34: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
207 | snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, _storePath, V);
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 13 and 4116 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovOverlap.C:217:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp]
217 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING
| ^~~~~~~
stores/sqStoreConstructor.C: 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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:290:35: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
290 | snprintf(path, FILENAME_MAX, "%s/libraries", _storePath); AS_UTL_unlink(path);
| ^~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 11 and 4107 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:291:35: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
291 | snprintf(path, FILENAME_MAX, "%s/reads", _storePath); AS_UTL_unlink(path);
| ^~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:292:35: warning: '/reads-rawu' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
292 | snprintf(path, FILENAME_MAX, "%s/reads-rawu", _storePath); AS_UTL_unlink(path);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:293:35: warning: '/reads-rawc' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
293 | snprintf(path, FILENAME_MAX, "%s/reads-rawc", _storePath); AS_UTL_unlink(path);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:294:35: warning: '/reads-coru' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
294 | snprintf(path, FILENAME_MAX, "%s/reads-coru", _storePath); AS_UTL_unlink(path);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:295:35: warning: '/reads-corc' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
295 | snprintf(path, FILENAME_MAX, "%s/reads-corc", _storePath); AS_UTL_unlink(path);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreConstructor.C:296:35: warning: '/blobs' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
296 | snprintf(path, FILENAME_MAX, "%s/blobs", _storePath); AS_UTL_unlink(path);
| ^~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStore.H:37,
from stores/sqStoreConstructor.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C
stores/ovStoreWriter.C:71:2: warning: #warning not failing if a valid store [-Wcpp]
71 | #warning not failing if a valid store
| ^~~~~~~
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}
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
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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStore.C:59:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStore.C:109:35: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
109 | snprintf(name, FILENAME_MAX, "%s/evalues", _storePath);
| ^~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStore.C:59:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C
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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 22 and 4129 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:237:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
237 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i);
| ^~~~~~~
stores/ovStoreWriter.C:237:34: note: directive argument in the range [0, 536870910]
237 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 23 and 4124 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)':
stores/ovStoreWriter.C:260:35: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
260 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bucket, _sliceNum);
| ^~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C
stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/ovStoreWriter.C:56:
stores/ovStore.H:104:39: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
104 | snprintf(name, FILENAME_MAX, "%s/%04u.info", path, index);
| ^
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/ovStoreWriter.C:56:
stores/ovStore.H: In member function 'void ovStoreSliceWriter::mergeInfoFiles()':
stores/ovStore.H:79:39: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
79 | snprintf(name, FILENAME_MAX, "%s/%04u.info", path, index);
| ^
stores/ovStore.H:79:36: note: directive argument in the range [1, 107374183]
79 | snprintf(name, FILENAME_MAX, "%s/%04u.info", path, index);
| ^~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 11 and 4112 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:404:42: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
404 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, ss);
| ^
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/ovStoreWriter.C:56:
stores/ovStore.H:102:39: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
102 | snprintf(name, FILENAME_MAX, "%s/info", path);
| ^~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeOverlapSlice()':
stores/ovStoreWriter.C:486:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
486 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, _sliceNum);
| ^~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::checkSortingIsComplete()':
stores/ovStoreWriter.C:505:38: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
505 | snprintf(nameF, FILENAME_MAX, "%s/%04u.info", _storePath, i);
| ^
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:506:38: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
506 | snprintf(nameI, FILENAME_MAX, "%s/%04u.index", _storePath, i);
| ^
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()':
stores/ovStoreWriter.C:537:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
537 | snprintf(name, FILENAME_MAX, "%s/%04u.index", _storePath, ss);
| ^
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:540:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=]
540 | snprintf(name, FILENAME_MAX, "%s/%04u.info", _storePath, ss);
| ^
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:557:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
557 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, bb);
| ^~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:561:39: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
561 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, ss);
| ^~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreWriter.C:565:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
565 | snprintf(name, FILENAME_MAX, "%s/bucket%04u", _storePath, bb);
| ^~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreWriter.C:56:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C
stores/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
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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C:192:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
192 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name);
| ^~~~~~~~
stores/tgStore.C:192:33: note: using the range [-2147483648, 2147483647] for directive argument
192 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C:193:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
193 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name);
| ^~~~~~~~
stores/tgStore.C:193:33: note: using the range [-2147483648, 2147483647] for directive argument
193 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C: In member function 'void tgStore::dumpMASR(tgStore::tgStoreEntry*&, uint32&, uint32)':
stores/tgStore.C:594:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
594 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V);
| ^~~~~~~~
stores/tgStore.C:594:33: note: using the range [-2147483648, 2147483647] for directive argument
594 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C: In member function 'void tgStore::loadMASR(tgStore::tgStoreEntry*&, uint32&, uint32&, uint32)':
stores/tgStore.C:626:40: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
626 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, i);
| ^~~~~~~~
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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C:637:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
637 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V);
| ^~~~~~~~
stores/tgStore.C:637:33: note: using the range [-2147483648, 2147483647] for directive argument
637 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C:641:38: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
641 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V);
| ^~~~~~~~
stores/tgStore.C:641:35: note: using the range [-2147483648, 2147483647] for directive argument
641 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStore.C: In member function 'FILE* tgStore::openDB(uint32)':
stores/tgStore.C:695:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
695 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version);
| ^~~~~~~~
stores/tgStore.C:695:33: note: using the range [-2147483648, 2147483647] for directive argument
695 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version);
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/tgStore.C:42:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/ovStore.H:37,
from stores/ovStoreFile.C:47:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 4 and 4100 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgTig.C:34:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
stores/tgTig.C: In member function 'void tgTig::dumpLayout(FILE*, bool)':
stores/tgTig.C:547:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
547 | fprintf(stderr, "ERROR: _bases length %ld\n", strlen(_bases));
| ~~^ ~~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
stores/tgTig.C: In member function 'void tgTig::dumpFASTA(FILE*)':
stores/tgTig.C:806:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
806 | ">tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgTig.C: In member function 'void tgTig::dumpFASTQ(FILE*)':
stores/tgTig.C:826:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
826 | "@tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc
stores/tgTig.C: In member function 'bool tgTig::loadLayout(FILE*)':
stores/tgTig.C:565:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
565 | fgets(LINE, LINEmax, F); LINEnum++;
| ~~~~~^~~~~~~~~~~~~~~~~~
stores/tgTig.C:690:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
690 | fgets(LINE, LINEmax, F); LINEnum++;
| ~~~~~^~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc
In file included from stores/tgTig.H:36,
from stores/tgTigSizeAnalysis.H:41,
from stores/tgTigSizeAnalysis.C:42:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/tgTigMultiAlignDisplay.C:42:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
stores/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);
| ^~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from overlapInCore/overlapReadCache.H:37,
from overlapInCore/overlapReadCache.C:30:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/liboverlap/prefixEditDistance-extend.C:69:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C
In file included from utgcns/libNDalign/NDalign.C:36:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utgcns/libNDalign/NDalign.C: In member function 'bool NDalign::processHits()':
utgcns/libNDalign/NDalign.C:660:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
660 | display("NDalign::processHits()-- ", false);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libNDalign/NDalign.C: In member function 'bool NDalign::scanDeltaForBadness(bool, bool)':
utgcns/libNDalign/NDalign.C:724:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
724 | display("NDalign::scanForDeltaBadness()-- ", true);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libNDalign/NDalign.C: In member function 'void NDalign::realignForward(bool, bool)':
utgcns/libNDalign/NDalign.C:774:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
774 | display("NDalign::realignForward()-- ", displayAlign);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libNDalign/NDalign.C: In member function 'void NDalign::realignBackward(bool, bool)':
utgcns/libNDalign/NDalign.C:838:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
838 | display("NDalign::realignBackward()-- ", displayAlign);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C
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:2426:7: 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
2426 | _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<>());
| ~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C
/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<>());
| ~~~~~~~~~~~~~~~
/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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/dumpBlob.C
gfa/gfa.C: In member function 'void gfaSequence::load(char*)':
gfa/gfa.C:123:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
123 | findGFAtokenI(_features, "LN:i:", _length);
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreBuild.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreConfig.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreBucketizer.C
stores/ovStoreBuild.C: In function 'int main(int, char**)':
stores/ovStoreBuild.C:125:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
125 | err.push_back("ERROR: No overlap store (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreBuild.C:128:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
128 | err.push_back("ERROR: No sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreConfig.C: In member function 'void ovStoreConfig::assignReadsToSlices(sqStore*, uint64, uint64)':
stores/ovStoreConfig.C:288:76: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
288 | fprintf(stderr, "ERROR: expected %u slices, generated %u instead. %lu overlaps per slice allowed.\n",
| ~~^
| |
| long unsigned int
| %llu
289 | _numSlices, slice, olapsPerSlice);
| ~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
stores/ovStoreConfig.C: In function 'int main(int, char**)':
stores/ovStoreConfig.C:372:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
372 | err.push_back("ERROR: No sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreConfig.C:375:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
375 | err.push_back("ERROR: No input overlap files (-L or last on the command line) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreConfig.C:378:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
378 | err.push_back("ERROR: Can't both -create -describe a config.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreConfig.C:381:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
381 | err.push_back("ERROR: Must supply one of -create or -describe.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreConfig.C:385:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
385 | err.push_back("ERROR: Memory (-M) must be at least 0.25 GB to account for overhead.\n"); // , OVSTORE_MEMORY_OVERHEAD / 1024.0 / 1024.0 / 1024.0
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreBucketizer.C: In function 'int main(int, char**)':
stores/ovStoreBucketizer.C:139:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
139 | err.push_back("ERROR: No overlap store (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreBucketizer.C:142:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
142 | err.push_back("ERROR: No sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreBucketizer.C:145:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
145 | err.push_back("ERROR: No store configuration (-C) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreBucketizer.C:148:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
148 | err.push_back("ERROR: Invalid or no bucket (-b) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreSorter.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreIndexer.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreDump.C
stores/ovStoreSorter.C: In function 'int main(int, char**)':
stores/ovStoreSorter.C:167:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
167 | err.push_back("ERROR: No overlap store (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreSorter.C:170:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
170 | err.push_back("ERROR: no slice number (-F) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreIndexer.C: In function 'int main(int, char**)':
stores/ovStoreIndexer.C:80:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
80 | err.push_back("ERROR: No overlap store (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreIndexer.C:83:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
83 | err.push_back("ERROR: No sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreIndexer.C:86:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
86 | err.push_back("ERROR: No config (-C) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/ovStoreDump.C:56:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
stores/ovStoreDump.C: In function 'int main(int, char**)':
stores/ovStoreDump.C:832:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
832 | err.push_back("ERROR: no input seqStore (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreDump.C:835:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
835 | err.push_back("ERROR: no input ovlStore (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/ovStoreDump.C:838:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
838 | err.push_back("ERROR: -prefix is necessary for -binary output.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/ovStoreStats.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/sqStoreCreate.C
In file included from stores/ovStoreStats.C:35:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C
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:2426:7: 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
2426 | _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);
| ^~~~~~~
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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStoreDumpFASTQ.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 7 and 8197 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreDumpFASTQ.C:135:37: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size between 0 and 4095 [-Wformat-truncation=]
135 | snprintf(N, FILENAME_MAX, "%s.%s.fastq%s", _p, _n, _s);
| ^~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStoreDumpFASTQ.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 8 and 12293 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTA()':
stores/sqStoreDumpFASTQ.C:167:36: warning: '.fasta' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
167 | snprintf(N, FILENAME_MAX, "%s.fasta%s", _p, _s);
| ^~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStoreDumpFASTQ.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 7 and 8197 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/sqStoreDumpFASTQ.C:165:37: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size between 0 and 4095 [-Wformat-truncation=]
165 | snprintf(N, FILENAME_MAX, "%s.%s.fasta%s", _p, _n, _s);
| ^~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/sqStoreDumpFASTQ.C:39:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 8 and 12293 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Isequence stores/sqStoreDumpMetaData.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Isequence sequence/sequence-summarize.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/tgStoreCompress.C
sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogramSimple(std::vector<long long unsigned int>)':
sequence/sequence-summarize.C:106:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=]
106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn);
| ~~^
| |
| long unsigned int
| %llu
sequence/sequence-summarize.C:106:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn);
| ~~^ ~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
sequence/sequence-summarize.C: In function 'void doSummarize_dumpLengths(std::vector<long long unsigned int>)':
sequence/sequence-summarize.C:120:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=]
120 | fprintf(stdout, "%lu\n", lengths[ii]);
| ~~^
| |
| long unsigned int
| %llu
sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogram(std::vector<long long unsigned int>, uint64, bool)':
sequence/sequence-summarize.C:290:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector<long long unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
290 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", 0.0, lengths.size(), lSum, histPlot[hp++]); // Occurs if only empty sequences in the input!
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| std::vector<long long unsigned int>::size_type {aka unsigned int}
sequence/sequence-summarize.C:292:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector<long long unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
292 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", (double)lSum / genomeSize, lengths.size(), lSum, histPlot[hp++]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| std::vector<long long unsigned int>::size_type {aka unsigned int}
sequence/sequence-summarize.C:294:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector<long long unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
294 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " ||\n", (double)lSum / genomeSize, lengths.size(), lSum);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| std::vector<long long unsigned int>::size_type {aka unsigned int}
stores/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
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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/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 /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from stores/sqStoreDumpMetaData.C:34:
/usr/include/c++/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,
| ^~~~~~~~~~~~~
/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
In file included from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from stores/sqStoreDumpMetaData.C:34:
/usr/include/c++/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::__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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/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>::
| ^~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/tgStoreDump.C
/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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_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: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 /<<BUILDDIR>>/canu-2.0+dfsg/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/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from stores/sqStoreDumpMetaData.C:34:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/tgTigSizeAnalysis.C
In file included from /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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/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/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 /<<BUILDDIR>>/canu-2.0+dfsg/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 /<<BUILDDIR>>/canu-2.0+dfsg/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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
stores/tgStoreDump.C: In function 'int main(int, char**)':
stores/tgStoreDump.C:1166:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1166 | err.push_back("No sequence store (-S option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:1169:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1169 | err.push_back("No tig store (-T option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:1172:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1172 | err.push_back("No tig store version (-T option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:1175:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1175 | err.push_back("-coverage needs and output prefix (-o option).\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreDump.C:1178:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
1178 | err.push_back("No DUMP TYPE supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/tgStoreLoad.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/tgStoreFilter.C
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
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
stores/tgStoreLoad.C: In function 'int main(int, char**)':
stores/tgStoreLoad.C:194:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
194 | err.push_back("ERROR: no sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreLoad.C:196:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
196 | err.push_back("ERROR: no tig store (-T) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/tgStoreLoad.C:198:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
198 | err.push_back("ERROR: no input tig files supplied on command line or via -L option.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/tgTigDisplay.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/loadCorrectedReads.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/tgTigDisplay.C:33:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility stores/loadErates.C
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/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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadCorrectedReads.C: In function 'int main(int, char**)':
stores/loadCorrectedReads.C:76:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
76 | err.push_back("ERROR: no sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadCorrectedReads.C:78:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
78 | err.push_back("ERROR: no tig store (-T) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadCorrectedReads.C:80:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
80 | err.push_back("ERROR: no input tigs supplied on command line and no -L file supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadCorrectedReads.C:185:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'std::vector<char*>::size_type' {aka 'unsigned int'} [-Wformat=]
185 | fprintf(stderr, "%9" F_U64P " %9" F_U64P " %35" F_U64P "\n", nLoadTot, nSkipTot, corInputs.size());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~
| |
| std::vector<char*>::size_type {aka unsigned int}
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl.C
meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp]
261 | #warning HARD CODED NUMBER OF FILES!
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C
stores/loadErates.C: In function 'int main(int, char**)':
stores/loadErates.C:214:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
214 | err.push_back("ERROR: No overlap store (-O) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadErates.C:217:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
217 | err.push_back("ERROR: No sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadErates.C:220:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
220 | err.push_back("ERROR: No input erate files (-L or last on the command line) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylInput.C
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/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 meryl/meryl.H:51,
from meryl/meryl.C:46:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
stores/loadErates.C: In member function 'void ovStore::addEvalues(std::vector<char*>&)':
stores/loadErates.C:86:41: warning: '/evalues.WORKING' directive output may be truncated writing 16 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
86 | snprintf(evalueTemp, FILENAME_MAX, "%s/evalues.WORKING", _storePath);
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/loadErates.C:43:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 17 and 4113 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stores/loadErates.C:87:41: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
87 | snprintf(evalueName, FILENAME_MAX, "%s/evalues", _storePath);
| ^~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from stores/loadErates.C:43:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-count.C
In file included from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylInput.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from 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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:89,
from meryl/meryl.H:49,
from meryl/merylCountArray.C:26:
meryl/merylCountArray.H: In instantiation of 'void swv<VALUE>::set(uint64, VALUE) [with VALUE = unsigned int; uint64 = long long unsigned int]':
meryl/merylCountArray.C:205:23: required from 'swv<VALUE>* merylCountArray<VALUE>::unpackSuffixesAndValues(uint64) [with VALUE = unsigned int; uint64 = long long unsigned int]'
meryl/merylCountArray.C:396:16: required from here
utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow]
77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X)))
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK'
41 | _s2 = suffix & uint64MASK(32);
| ^~~~~~~~~~
meryl/merylCountArray.H: In instantiation of 'void swv<VALUE>::set(uint64, VALUE) [with VALUE = long long unsigned int; uint64 = long long unsigned int]':
meryl/merylCountArray.C:205:23: required from 'swv<VALUE>* merylCountArray<VALUE>::unpackSuffixesAndValues(uint64) [with VALUE = long long unsigned int; uint64 = long long unsigned int]'
meryl/merylCountArray.C:397:16: required from here
utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow]
77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X)))
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK'
41 | _s2 = suffix & uint64MASK(32);
| ^~~~~~~~~~
In file included from meryl/meryl.H:51,
from meryl/merylInput.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
meryl/meryl.C: In function 'int main(int, char**)':
meryl/meryl.C:331:42: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
331 | snprintf(indexName, FILENAME_MAX, "%s/merylIndex", optString);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from meryl/meryl.H:49,
from meryl/meryl.C:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl.C:332:42: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
332 | snprintf(sqInfName, FILENAME_MAX, "%s/info", optString);
| ^~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from meryl/meryl.H:49,
from meryl/meryl.C:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl.C:333:42: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=]
333 | snprintf(sqRdsName, FILENAME_MAX, "%s/reads", optString);
| ^~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from meryl/meryl.H:49,
from meryl/meryl.C:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl.C:594:54: warning: '%s' directive output may be truncated writing up to 4096 bytes into a region of size 996 [-Wformat-truncation=]
594 | snprintf(s, 1024, "Don't know what to do with '%s'.", optString);
| ^~ ~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from meryl/meryl.H:49,
from meryl/meryl.C:46:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 31 and 4127 bytes into a destination of size 1024
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-count.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-countSimple.C
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-count.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylOp-count.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
meryl/merylOp-count.C: In function 'uint64 findMaxInputSizeForMemorySize(uint32, uint64)':
meryl/merylOp-count.C:69:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
69 | fprintf(stderr, "For memory size %lu bytes\n", memSize);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
meryl/merylOp-count.C:112:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %10llu
113 | wp, nKmers,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C:112:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %10llu
113 | wp, nKmers,
114 | nPrefix, nSeg,
| ~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C:112:42: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %10llu
113 | wp, nKmers,
114 | nPrefix, nSeg,
| ~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C:112:48: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %10llu
......
115 | mersPerSeg,
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C:112:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %10llu
......
116 | basicMem, ptrMem, dataMem,
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C:112:60: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %10llu
......
116 | basicMem, ptrMem, dataMem,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C:112:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n",
| ~~~~^
| |
| long unsigned int
| %12llu
......
116 | basicMem, ptrMem, dataMem,
| ~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C: In function 'void findExpectedSimpleSize(uint64, uint64&)':
meryl/merylOp-count.C:157:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
157 | fprintf(stderr, " -> %lu entries for counts up to %u.\n", nEntries, ((uint32)1 << lowBitsSize) - 1);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C:158:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
158 | fprintf(stderr, " -> %lu %cbits memory used\n", scaledNumber(lowMem), scaledUnit(lowMem));
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C:160:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
160 | fprintf(stderr, " %lu input bases\n", nKmerEstimate);
| ~~^ ~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C:161:51: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
161 | fprintf(stderr, " -> expected max count of %lu, needing %lu extra bits.\n", expMaxCount, extraBits);
| ~~^ ~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C:161:64: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
161 | fprintf(stderr, " -> expected max count of %lu, needing %lu extra bits.\n", expMaxCount, extraBits);
| ~~^ ~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C:163:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
163 | fprintf(stderr, " -> %lu %cbits memory used\n", scaledNumber(highMem), scaledUnit(highMem));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C:167:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
167 | fprintf(stderr, " %lu %cB memory needed\n", scaledNumber(totMem), scaledUnit(totMem));
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/merylOp-count.C: In member function 'void merylOperation::configureCounting(uint64, bool&, uint32&, uint64&, uint32&, uint64&)':
meryl/merylOp-count.C:385:19: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
385 | fprintf(stderr, "Counting %lu (estimated)%s %s%s%s " F_U32 "-mers from " F_SIZE_T " input file%s:\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
386 | scaledNumber(_expNumKmers), scaledName(_expNumKmers),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-count.C: In member function 'void merylOperation::count(uint32, uint64, uint32, uint64)':
meryl/merylOp-count.C:603:69: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
603 | fprintf(stderr, "Used %3.3f GB out of %3.3f GB to store %12lu kmers.\n",
| ~~~~^
| |
| long unsigned int
| %12llu
......
606 | kmersAdded);
| ~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-histogram.C
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-countSimple.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-countSimple.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylOp-countSimple.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.C
meryl/merylOp-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
meryl/merylOp-nextMer.C:98:2: warning: #warning "need to decide whic direction we're going?" [-Wcpp]
98 | #warning "need to decide whic direction we're going?"
| ^~~~~~~
meryl/merylOp-nextMer.C:116:2: warning: #warning "rounding issues in word-frequency!" [-Wcpp]
116 | #warning "rounding issues in word-frequency!"
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp.C
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-histogram.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-histogram.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylOp-histogram.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl-import/meryl/meryl-import.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-import.C
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp-nextMer.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
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}
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl-import/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C
In file included from meryl/meryl.H:51,
from meryl/merylOp-nextMer.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
meryl/merylOp-nextMer.C: In member function 'void merylOperation::initializeThreshold()':
meryl/merylOp-nextMer.C:113:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
113 | fprintf(stderr, "For fraction-distinct %f, found threshold %lu\n", _fracDist, _threshold);
| ~~^ ~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
meryl/merylOp-nextMer.C:121:63: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
121 | fprintf(stderr, "For word-frequency %f, found threshold %lu\n", _wordFreq, _threshold);
| ~~^ ~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
meryl/merylOp-nextMer.C: In member function 'bool merylOperation::nextMer()':
meryl/merylOp-nextMer.C:612:46: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n",
| ~~^
| |
| long unsigned int
| %llu
613 | _kmer.toString(str), _actCount[0], _actCount[1]);
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/merylOp-nextMer.C:612:70: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n",
| ~~^
| |
| long unsigned int
| %llu
613 | _kmer.toString(str), _actCount[0], _actCount[1]);
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylOp.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from 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");
| ^
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}
In file included from meryl/meryl.H:51,
from meryl/merylCountArray.H:29,
from meryl/meryl-import.C:31:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
meryl/meryl-import.C: In function 'int main(int, char**)':
meryl/meryl-import.C:92:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
92 | err.push_back("No input kmer file (-kmers) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-import.C:94:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
94 | err.push_back("No output database name (-output) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-import.C:96:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
96 | err.push_back("No kmer size (-k) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-import.C:233:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
233 | fprintf(stderr, "Found %lu kmers in the input.\n", nKmers);
| ~~^ ~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from utility/kmers.H:32,
from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from meryl/merylInput.H:30,
from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
In file included from meryl/meryl.H:51,
from meryl/merylCountArray.C:26:
meryl/merylInput.H: In member function 'char* merylInput::inputType()':
meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
51 | if (_operation) return("meryl-operation");
| ^
meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
52 | if (_stream) return("meryl-database");
| ^
meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
53 | if (_sequence) return("sequence-file");
| ^
meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
55 | if (_store) return("canu-seqStore");
| ^
meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
58 | return("invalid-input");
| ^
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl-lookup/meryl/meryl-lookup.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-lookup.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence.C
In file included from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:89,
from meryl/meryl.H:49,
from meryl/merylCountArray.C:26:
meryl/merylCountArray.H: In instantiation of 'void swv<VALUE>::set(uint64, VALUE) [with VALUE = unsigned int; uint64 = long long unsigned int]':
meryl/merylCountArray.C:205:23: required from 'swv<VALUE>* merylCountArray<VALUE>::unpackSuffixesAndValues(uint64) [with VALUE = unsigned int; uint64 = long long unsigned int]'
meryl/merylCountArray.C:396:16: required from here
utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow]
77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X)))
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK'
41 | _s2 = suffix & uint64MASK(32);
| ^~~~~~~~~~
meryl/merylCountArray.H: In instantiation of 'void swv<VALUE>::set(uint64, VALUE) [with VALUE = long long unsigned int; uint64 = long long unsigned int]':
meryl/merylCountArray.C:205:23: required from 'swv<VALUE>* merylCountArray<VALUE>::unpackSuffixesAndValues(uint64) [with VALUE = long long unsigned int; uint64 = long long unsigned int]'
meryl/merylCountArray.C:397:16: required from here
utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow]
77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X)))
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK'
41 | _s2 = suffix & uint64MASK(32);
| ^~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-extract.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-extract.C
In file included from utility/kmers.H:32,
from meryl/meryl-lookup.C:28:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
sequence/sequence.C: In function 'int main(int, char**)':
sequence/sequence.C:414:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
414 | err.push_back("ERROR: No mode (summarize, extract, generate or simulate) specified.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:418:21: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
418 | err.push_back("ERROR: No input sequence files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:422:21: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
422 | err.push_back("ERROR: No input sequence files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:428:21: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
428 | err.push_back("ERROR: No reference genome sequence (-genome) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence/sequence.C:432:21: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
432 | err.push_back("ERROR: No input sequence files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from meryl/meryl-lookup.C:28:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C: In function 'void dumpExistence(dnaSeqFile*, compressedFileWriter*, std::vector<kmerCountExactLookup*>&, std::vector<const char*>&)':
meryl/meryl-lookup.C:83:43: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
83 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\n",
| ~~^
| |
| long unsigned int
| %llu
......
86 | kiter.position(),
| ~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C:97:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
97 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\t%s\t%lu\t%s\t%lu\t%s\n",
| ~~^
| |
| long unsigned int
| %llu
......
100 | kiter.position(),
| ~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C:97:58: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
97 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\t%s\t%lu\t%s\t%lu\t%s\n",
| ~~^
| |
| long unsigned int
| %llu
......
102 | kiter.fmer().toString(fString), fValue,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C:97:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
97 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\t%s\t%lu\t%s\t%lu\t%s\n",
| ~~^
| |
| long unsigned int
| %llu
......
103 | kiter.rmer().toString(rString), rValue,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
meryl/meryl-lookup.C: In function 'void reportExistence(dnaSeqFile*, compressedFileWriter*, std::vector<kmerCountExactLookup*>&, std::vector<const char*>&)':
meryl/meryl-lookup.C:134:35: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
134 | fprintf(ofile->file(), "%s\t%lu\t%lu\t%lu\n", seq.name(), nKmer, klookup[0]->nKmers(), nKmerFound);
| ~~^ ~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C:134:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
134 | fprintf(ofile->file(), "%s\t%lu\t%lu\t%lu\n", seq.name(), nKmer, klookup[0]->nKmers(), nKmerFound);
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C:134:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
134 | fprintf(ofile->file(), "%s\t%lu\t%lu\t%lu\n", seq.name(), nKmer, klookup[0]->nKmers(), nKmerFound);
| ~~^ ~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C: In function 'void filter(dnaSeqFile*, dnaSeqFile*, compressedFileWriter*, compressedFileWriter*, std::vector<kmerCountExactLookup*>&, bool)':
meryl/meryl-lookup.C:204:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
204 | fprintf(stderr, "\nIncluding %lu reads (or read pairs) out of %lu.\n", nReadsFound, nReads);
| ~~^ ~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C:204:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
204 | fprintf(stderr, "\nIncluding %lu reads (or read pairs) out of %lu.\n", nReadsFound, nReads);
| ~~^ ~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
meryl/meryl-lookup.C: In function 'int main(int, char**)':
meryl/meryl-lookup.C:285:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
285 | err.push_back("No input sequences (-sequence) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-lookup.C:287:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
287 | err.push_back("No query meryl database (-mers) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
meryl/meryl-lookup.C:289:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
289 | err.push_back("No report-type (-existence, etc) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/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 /<<BUILDDIR>>/canu-2.0+dfsg/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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-generate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-generate.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-mutate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-mutate.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-sample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-sample.C
sequence/sequence-generate.C: In function 'void doGenerate(generateParameters&)':
sequence/sequence-generate.C:92:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
92 | ">random%08 " F_U64P "\n", nSeqs);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-shiftregister.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister.C
sequence/sequence-mutate.C: In function 'void doMutate(std::vector<char*>&, mutateParameters&)':
sequence/sequence-mutate.C:160:50: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
160 | AS_UTL_writeFastA(stdout, nBases, oLen, 0, ">%s\n", seq.name());
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-emit-fast.C
sequence/sequence-sample.C: In function 'void doSample_paired(std::vector<char*>&, sampleParameters&)':
sequence/sequence-sample.C:272:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
272 | AS_UTL_writeFastA(outFile1, seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name());
| ^~~~~~~
sequence/sequence-sample.C:273:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
273 | AS_UTL_writeFastA(outFile2, seq2.bases(), seq2.length(), 0, ">%s\n", seq2.name());
| ^~~~~~~
sequence/sequence-sample.C: In function 'void doSample_single(std::vector<char*>&, sampleParameters&)':
sequence/sequence-sample.C:417:73: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
417 | AS_UTL_writeFastA(outFiles[of], seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name());
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-fast.C
In file included from /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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/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
/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from sequence/sequence-shiftregister-emit-fast.C:29:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
sequence/sequence-shiftregister-emit-fast.C: In function 'void emitShiftRegisterFast(shiftRegisterParameters&)':
sequence/sequence-shiftregister-emit-fast.C:52:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
52 | fprintf(stderr, "Emitting %lu bases, plus an extra %u.\n", srPar.length - srPar.order - 1 - 1, srPar.order - 1);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
sequence/sequence-shiftregister-emit-fast.C:53:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
53 | fprintf(stderr, " sr %0*lo\n", srPar.order, expandTo3(sr));
| ~~~~^ ~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %0*llo
sequence/sequence-shiftregister-emit-fast.C:54:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
54 | fprintf(stderr, " cyclen %lu\n", cyclen);
| ~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
sequence/sequence-shiftregister-emit-fast.C:55:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
55 | fprintf(stderr, " cycmax %lu\n", cycmax);
| ~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
sequence/sequence-shiftregister-emit-fast.C:56:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
56 | fprintf(stderr, " sv %0*lo\n", srPar.order, expandTo3(sv));
| ~~~~^ ~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %0*llo
sequence/sequence-shiftregister-emit-fast.C:57:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
57 | fprintf(stderr, " svmax %0*lo\n", srPar.order, expandTo3(svmax));
| ~~~~^ ~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %0*llo
sequence/sequence-shiftregister-emit-fast.C:58:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
58 | fprintf(stderr, " svmask %0*lo\n", srPar.order, expandTo3(svmask));
| ~~~~^ ~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %0*llo
In file included from 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/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);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-sample.C:30:
/usr/include/c++/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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-slow.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-simulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-simulate.C
In file included from sequence/sequence-shiftregister-search-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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility sequence/sequence-summarize.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C
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}
sequence/sequence-simulate.C: In member function 'void simulateParameters::finalize()':
sequence/sequence-simulate.C:44:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
44 | char *path = findSharedFile("share/sequence", distribName);
| ^~~~~~~~~~~~~~~~
sequence/sequence-simulate.C: In function 'void doSimulate_loadSequences(simulateParameters&, std::vector<dnaSeq*>&, uint64&)':
sequence/sequence-simulate.C:89:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<dnaSeq*>::size_type' {aka 'unsigned int'} [-Wformat=]
89 | fprintf(stderr, "Loaded %lu sequences.\n", seqs.size());
| ~~^ ~~~~~~~~~~~
| | |
| long unsigned int std::vector<dnaSeq*>::size_type {aka unsigned int}
| %u
sequence/sequence-simulate.C: In function 'void doSimulate_extract(simulateParameters&, std::vector<dnaSeq*>&, uint64, mtRandom&, uint64, uint64)':
sequence/sequence-simulate.C:194:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
194 | fprintf(stdout, ">read=%lu,%s,position=%lu,length=%u,%s\n",
| ~~^
| |
| long unsigned int
| %llu
195 | nReads+1,
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
sequence/sequence-simulate.C:194:48: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
194 | fprintf(stdout, ">read=%lu,%s,position=%lu,length=%u,%s\n",
| ~~^
| |
| long unsigned int
| %llu
......
197 | position,
| ~~~~~~~~
| |
| uint64 {aka long long unsigned int}
sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogramSimple(std::vector<long long unsigned int>)':
sequence/sequence-summarize.C:106:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=]
106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn);
| ~~^
| |
| long unsigned int
| %llu
sequence/sequence-summarize.C:106:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn);
| ~~^ ~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
sequence/sequence-summarize.C: In function 'void doSummarize_dumpLengths(std::vector<long long unsigned int>)':
sequence/sequence-summarize.C:120:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=]
120 | fprintf(stdout, "%lu\n", lengths[ii]);
| ~~^
| |
| long unsigned int
| %llu
sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogram(std::vector<long long unsigned int>, uint64, bool)':
sequence/sequence-summarize.C:290:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector<long long unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
290 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", 0.0, lengths.size(), lSum, histPlot[hp++]); // Occurs if only empty sequences in the input!
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| std::vector<long long unsigned int>::size_type {aka unsigned int}
sequence/sequence-summarize.C:292:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector<long long unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
292 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", (double)lSum / genomeSize, lengths.size(), lSum, histPlot[hp++]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| std::vector<long long unsigned int>::size_type {aka unsigned int}
sequence/sequence-summarize.C:294:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector<long long unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
294 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " ||\n", (double)lSum / genomeSize, lengths.size(), lSum);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| std::vector<long long unsigned int>::size_type {aka unsigned int}
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C
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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/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 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/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C
In file included from /usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/sequence/sequence.H:30,
from sequence/sequence-summarize.C:30:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C
sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
474 | }
| ^
sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/overlapInCore-Build_Hash_Index.C:67:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/overlapInCore-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
overlapInCore/overlapInCore-Build_Hash_Index.C: In function 'void Mark_Skip_Kmers()':
overlapInCore/overlapInCore-Build_Hash_Index.C:258:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
258 | fgets(line, 1024, F);
| ~~~~~^~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/overlapInCore-Output.C:67:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapInCore/overlapInCore.H:66,
from overlapInCore/overlapInCore-Process_Overlaps.C:71:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C
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
overlapInCore/overlapInCorePartition.C: In function 'int main(int, char**)':
overlapInCore/overlapInCorePartition.C:430:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
430 | FILE *BAT = openOutput(outputPrefix, "ovlbat");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:431:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
431 | FILE *JOB = openOutput(outputPrefix, "ovljob");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:432:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
432 | FILE *OPT = openOutput(outputPrefix, "ovlopt");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:445:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
445 | renameToFinal(outputPrefix, "ovlbat");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:446:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
446 | renameToFinal(outputPrefix, "ovljob");
| ^~~~~~~~
overlapInCore/overlapInCorePartition.C:447:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
447 | renameToFinal(outputPrefix, "ovlopt");
| ^~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C
overlapInCore/overlapImport.C: In function 'int main(int, char**)':
overlapInCore/overlapImport.C:158:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
158 | err.push_back("ERROR: no input seqStore (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
overlapInCore/overlapImport.C:161:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
161 | err.push_back("ERROR: no input overlap files supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
overlapInCore/overlapImport.C:274:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
274 | fgets(S, 1024, in->file());
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
overlapInCore/overlapImport.C:304:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
304 | fgets(S, 1024, in->file());
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
overlapInCore/overlapPair.C:479:2: warning: #warning do we need to check for contained too? [-Wcpp]
479 | #warning do we need to check for contained too?
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from overlapInCore/overlapReadCache.H:37,
from overlapInCore/overlapPair.C:44:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
overlapInCore/overlapPair.C: In function 'void* recomputeOverlaps(void*)':
overlapInCore/overlapPair.C:429:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
429 | if (extendAlignment(bRead, bbgn, bend, blen, "B", bID,
| ^~~
overlapInCore/overlapPair.C:430:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
430 | aRead, abgn, aend, alen, "A", aID,
| ^~~
overlapInCore/overlapPair.C:437:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
437 | if (extendAlignment(aRead, abgn, aend, alen, "A", aID,
| ^~~
overlapInCore/overlapPair.C:438:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
438 | bRead, bbgn, bend, blen, "B", bID,
| ^~~
overlapInCore/overlapPair.C:506:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
506 | if (extendAlignment(bRead, bbgn, bend, blen, "Bb5", bID,
| ^~~~~
overlapInCore/overlapPair.C:507:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
507 | aRead, abgn, aend, alen, "Ab5", aID,
| ^~~~~
overlapInCore/overlapPair.C:532:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
532 | if (extendAlignment(aRead, abgn, aend, alen, "Aa5", aID,
| ^~~~~
overlapInCore/overlapPair.C:533:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
533 | bRead, bbgn, bend, blen, "Ba5", bID,
| ^~~~~
overlapInCore/overlapPair.C:560:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
560 | if (extendAlignment(aRead, abgn, aend, alen, "Aa3", aID,
| ^~~~~
overlapInCore/overlapPair.C:561:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
561 | bRead, bbgn, bend, blen, "Ba3", bID,
| ^~~~~
overlapInCore/overlapPair.C:586:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
586 | if (extendAlignment(bRead, bbgn, bend, blen, "Bb3", bID,
| ^~~~~
overlapInCore/overlapPair.C:587:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
587 | aRead, abgn, aend, alen, "Ab3", aID,
| ^~~~~
overlapInCore/edalign.C: In function 'bool readLine(FILE*, char*, int32, int32&, splitToWords&)':
overlapInCore/edalign.C:38:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
38 | fgets(line, lineMax, file);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C
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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionOverlaps.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C
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
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from wtdbg/wtdbgConvert.C:33:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from correction/generateCorrectionLayouts.C:37:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
correction/generateCorrectionLayouts.C: In function 'void generateLayout(tgTig*, uint16*, uint32, double, double, ovOverlap*, uint32, FILE*)':
correction/generateCorrectionLayouts.C:118:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
118 | fprintf(logFile, " filter read %9u at position %6u,%6u length %5lu erate %.3f - low quality (threshold %.2f)\n",
| ~~~^
| |
| long unsigned int
| %5llu
119 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate(), maxEvidenceErate);
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
correction/generateCorrectionLayouts.C:125:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
125 | fprintf(logFile, " filter read %9u at position %6u,%6u length %5lu erate %.3f - too short (threshold %u)\n",
| ~~~^
| |
| long unsigned int
| %5llu
126 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate(), minEvidenceLength);
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
correction/generateCorrectionLayouts.C:133:26: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
133 | fprintf(logFile, " filter read %9u at position %6u,%6u length %5lu erate %.3f - filtered by global filter (threshold " F_U16 ")\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
134 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate(), olapThresh[ovl[oo].b_iid]);
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
correction/generateCorrectionLayouts.C:140:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
140 | fprintf(logFile, " filter read %9u at position %6u,%6u length %5lu erate %.3f - duplicate\n",
| ~~~^
| |
| long unsigned int
| %5llu
141 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate());
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
correction/generateCorrectionLayouts.C:146:73: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
146 | fprintf(logFile, " allow read %9u at position %6u,%6u length %5lu erate %.3f\n",
| ~~~^
| |
| long unsigned int
| %5llu
147 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate());
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionLayouts.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from 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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from 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/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:2426:7: 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
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<>());
| ~~~~~~~~~~~~~~~
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
/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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C
correction/falconsense.C: In function 'void generateFalconConsensus(falconConsensus*, tgTig*, sqCache*, std::map<unsigned int, sqRead*>&, bool, uint32)':
correction/falconsense.C:207:41: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
207 | fprintf(stdout, "(%6u) memory act %10lu est %10lu act/est %.2f", len, fc->getRSS(), mem, fc->getRSS() * 100.0 / mem);
| ~~~~^ ~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %10llu
correction/falconsense.C:207:51: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
207 | fprintf(stdout, "(%6u) memory act %10lu est %10lu act/est %.2f", len, fc->getRSS(), mem, fc->getRSS() * 100.0 / mem);
| ~~~~^ ~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %10llu
correction/falconsense.C: In function 'int main(int, char**)':
correction/falconsense.C:359:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
359 | err.push_back("ERROR: no seqStore input (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
correction/falconsense.C:362:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
362 | err.push_back("ERROR: no corStore input (-C) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
correction/falconsense.C: In function 'void loadReadList(char*, uint32, uint32, std::set<unsigned int>&)':
correction/falconsense.C:70:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
70 | for (fgets(L, 1024, R);
| ~~~~~^~~~~~~~~~~~
correction/falconsense.C:72:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
72 | fgets(L, 1024, R)) {
| ~~~~~^~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from utgcns/stashContains.H:35,
from utgcns/stashContains.C:30:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C
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 utility/kmers.H:32,
from haplotyping/splitHaplotype.C:34:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from haplotyping/splitHaplotype.C:34:
utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)':
utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
| ~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~~~^
| |
| long unsigned int
| %016llx
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
595 | prefix,
596 | _blockPrefix, _blockPosition, _numKmers,
| ~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n",
| ~~~^
| |
| long unsigned int
| %8llu
......
597 | AS_UTL_ftell(F), _numKmers + nKmers);
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
haplotyping/splitHaplotype.C: In member function 'void hapData::initializeKmerTable(uint32)':
haplotyping/splitHaplotype.C:443:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
443 | fprintf(stderr, "-- loaded %lu kmers.\n", nKmers);
| ~~^ ~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
haplotyping/splitHaplotype.C: In function 'void outputReadBatch(void*, void*)':
haplotyping/splitHaplotype.C:707:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
707 | ">%s\n", s->_names[ii].string());
| ^~~~~~~
haplotyping/splitHaplotype.C: In function 'int main(int, char**)':
haplotyping/splitHaplotype.C:771:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
771 | err.push_back("No input sequences supplied with either (-S) or (-R).\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplotyping/splitHaplotype.C:773:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
773 | err.push_back("Only one type of input reads (-S or -R) supported.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplotyping/splitHaplotype.C:775:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
775 | err.push_back("Not enough haplotypes (-H) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplotyping/splitHaplotype.C:854:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
854 | fprintf(stdout, "-- %8u reads %12lu bases written to haplotype file %s.\n", G->_haps[ii]->nReads, G->_haps[ii]->nBases, G->_haps[ii]->outputName);
| ~~~~^
| |
| long unsigned int
| %12llu
haplotyping/splitHaplotype.C:855:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
855 | fprintf(stdout, "-- %8u reads %12lu bases written to haplotype file %s.\n", G->_ambiguousReads, G->_ambiguousBases, G->_ambiguousName);
| ~~~~^ ~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %12llu
haplotyping/splitHaplotype.C:857:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
857 | fprintf(stdout, "-- %8u reads %12lu bases filtered for being too short.\n", G->_filteredReads, G->_filteredBases);
| ~~~~^ ~~~~~~~~~~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %12llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C
overlapBasedTrimming/trimReads.C: In function 'int main(int, char**)':
overlapBasedTrimming/trimReads.C:480:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
480 | readsIn .generatePlots(outputPrefix, "inputReads", 250);
| ^~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:481:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
481 | deletedIn.generatePlots(outputPrefix, "inputDeletedReads", 250);
| ^~~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:482:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
482 | noTrimIn .generatePlots(outputPrefix, "inputNoTrimReads", 250);
| ^~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:492:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
492 | readsOut .generatePlots(outputPrefix, "outputTrimmedReads", 250);
| ^~~~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:493:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
493 | noOvlOut .generatePlots(outputPrefix, "outputNoOvlReads", 250);
| ^~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:494:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
494 | deletedOut .generatePlots(outputPrefix, "outputDeletedReads", 250);
| ^~~~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:495:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
495 | noChangeOut.generatePlots(outputPrefix, "outputUnchangedReads", 250);
| ^~~~~~~~~~~~~~~~~~~~~~
overlapBasedTrimming/trimReads.C:503:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
503 | trim5.generatePlots(outputPrefix, "trim5", 25);
| ^~~~~~~
overlapBasedTrimming/trimReads.C:504:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
504 | trim3.generatePlots(outputPrefix, "trim3", 25);
| ^~~~~~~
In file included from overlapBasedTrimming/trimReads.C:31:
overlapBasedTrimming/trimStat.H: In member function 'void trimStat::generatePlots(char*, char*, uint32)':
overlapBasedTrimming/trimStat.H:74:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
74 | system(N);
| ~~~~~~^~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustFlipped.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/mergeRanges.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C
overlapBasedTrimming/mergeRanges.C: In function 'int main(int, char**)':
overlapBasedTrimming/mergeRanges.C:77:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
77 | err.push_back("ERROR: no sequence store (-S) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapAlign/computeOverlapAlignment.C:32:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
overlapAlign/computeOverlapAlignment.C: In member function 'void maComputation::computeOverlapAlignment(uint32, uint32, double, uint32, uint32)':
overlapAlign/computeOverlapAlignment.C:581:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
581 | if (computeAlignment(_bRead, bbgn, bend, blen, "B", _bID, // Align all of sequence B into
| ^~~
overlapAlign/computeOverlapAlignment.C:582:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
582 | _aRead, abgn, aend, alen, "A", _aID, // sequence A with free ends.
| ^~~
overlapAlign/computeOverlapAlignment.C:626:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
626 | if (computeAlignment(_aRead, abgn, aend, alen, "A", _aID, // Align all of sequence A into
| ^~~
overlapAlign/computeOverlapAlignment.C:627:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
627 | _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends.
| ^~~
overlapAlign/computeOverlapAlignment.C:674:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
674 | if (computeAlignment(_bRead, bbgn, bend, blen, "B", _bID, // Align all of sequence B into
| ^~~
overlapAlign/computeOverlapAlignment.C:675:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
675 | _aRead, abgn, aend, alen, "A", _aID, // sequence A with free ends.
| ^~~
overlapAlign/computeOverlapAlignment.C:719:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
719 | if (computeAlignment(_aRead, abgn, aend, alen, "A", _aID, // Align all of sequence A into
| ^~~
overlapAlign/computeOverlapAlignment.C:720:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
720 | _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends.
| ^~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C
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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from stores/sqCache.H:30,
from overlapAlign/computeAlignments.C:36:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from overlapErrorAdjustment/findErrors.H:34,
from overlapErrorAdjustment/findErrors.C:30:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C
overlapErrorAdjustment/findErrors-Dump.C: In function 'int main(int, char**)':
overlapErrorAdjustment/findErrors-Dump.C:66:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
66 | char *typeName[13] = { "IDENT",
| ^~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:67:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
67 | "DELETE",
| ^~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:68:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
68 | "A_SUBST",
| ^~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:69:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
69 | "C_SUBST",
| ^~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:70:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
70 | "G_SUBST",
| ^~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:71:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
71 | "T_SUBST",
| ^~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:72:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
72 | "A_INSERT",
| ^~~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:73:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
73 | "C_INSERT",
| ^~~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:74:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
74 | "G_INSERT",
| ^~~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:75:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
75 | "T_INSERT",
| ^~~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:76:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
76 | "NO_VOTE",
| ^~~~~~~~~
overlapErrorAdjustment/findErrors-Dump.C:77:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
77 | "EXTENSION",
| ^~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C
overlapErrorAdjustment/correctOverlaps-Correct_Frags.C: In function 'void Correct_Frags(coParameters*, sqStore*, FILE*)':
overlapErrorAdjustment/correctOverlaps-Correct_Frags.C:281:74: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
281 | AS_UTL_writeFastA(correctedReads, read.bases, read.basesLen, 60, ">%d\n", curID);
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/bogart.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/bogart.C:46:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
bogart/bogart.C: In function 'int main(int, char**)':
bogart/bogart.C:338:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
338 | if (erateGraph < 0.0) err.push_back("Invalid overlap error threshold (-eg option); must be at least 0.0.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:339:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
339 | if (erateMax < 0.0) err.push_back("Invalid overlap error threshold (-eM option); must be at least 0.0.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:340:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
340 | if (prefix == NULL) err.push_back("No output prefix name (-o option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:341:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
341 | if (seqStorePath == NULL) err.push_back("No sequence store (-S option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:342:46: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
342 | if (ovlStorePath == NULL) err.push_back("No overlap store (-O option) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bogart/bogart.C:736:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
736 | writeTigsToStore(contigs, prefix, "ctg", true);
| ^~~~~
bogart/bogart.C:756:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
756 | writeTigsToStore(unitigs, prefix, "utg", true);
| ^~~~~
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/AS_BAT_AssemblyGraph.C:28:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C
In file included from /usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/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 /<<BUILDDIR>>/canu-2.0+dfsg/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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DetectSpurs.C
bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp]
486 | #warning deviationGraph hard coded
| ^~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/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
/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogart/AS_BAT_ReadInfo.H:29,
from bogart/AS_BAT_BestOverlapGraph.C:42:
/usr/include/c++/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 bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/AS_BAT_DropDeadEnds.C:29:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Instrumentation.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_Instrumentation.C:43:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
bogart/AS_BAT_Instrumentation.C: In function 'void reportTigs(TigVector&, const char*, const char*, uint64)':
bogart/AS_BAT_Instrumentation.C:421:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
421 | writeTigsToStore(tigs, getLogFilePrefix(), "tig", false);
| ^~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C
bogart/AS_BAT_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 /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:67,
from bogart/AS_BAT_Logging.H:41,
from bogart/AS_BAT_Logging.C:38:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 12 and 4115 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OptimizePositions.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/AS_BAT_MarkRepeatReads.C:29:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
bogart/AS_BAT_MarkRepeatReads.C: In function 'uint32 splitTig(TigVector&, Unitig*, std::vector<breakPointCoords>&, Unitig**, int32*, uint32*, uint32*, bool)':
bogart/AS_BAT_MarkRepeatReads.C:170:64: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'std::vector<breakPointCoords>::size_type' {aka 'unsigned int'} [-Wformat=]
170 | fprintf(stderr, "Failed to place read %u at %d-%d with %lu BPs:\n", frg.ident, frgbgn, frgend, BP.size());
| ~~^ ~~~~~~~~~
| | |
| long unsigned int std::vector<breakPointCoords>::size_type {aka unsigned int}
| %u
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_MergeOrphans.C:35:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
bogart/AS_BAT_MergeOrphans.C: In function 'void findPotentialOrphans(TigVector&, BubTargetList&)':
bogart/AS_BAT_MergeOrphans.C:196:69: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'int' [-Wformat=]
196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n",
| ~~^
| |
| long int
| %d
197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end,
198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang,
| ~~~~~~~~~~~~~~
| |
| int
bogart/AS_BAT_MergeOrphans.C:196:73: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'int' [-Wformat=]
196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n",
| ~~^
| |
| long int
| %d
197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end,
198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang,
| ~~~~~~~~~~~~~~
| |
| int
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_OptimizePositions.C:44:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Outputs.C
In file included from /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 /<<BUILDDIR>>/canu-2.0+dfsg/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 /<<BUILDDIR>>/canu-2.0+dfsg/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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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
/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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PromoteToSingleton.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ReadInfo.C
In file included from /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 /<<BUILDDIR>>/canu-2.0+dfsg/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 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 /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 /<<BUILDDIR>>/canu-2.0+dfsg/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_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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SetParentAndHang.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SplitDiscontinuous.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_TigGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigGraph.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigVector.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_SetParentAndHang.C:41:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_SplitDiscontinuous.C:41:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_TigVector.C:28:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_AssemblyGraph.H:32,
from bogart/AS_BAT_TigGraph.C:28:
utility/stddev.H: In member function 'void histogramStatistics::finalizeData()':
utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax);
| ~~^ ~~~~~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median);
| ~~^ ~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation);
| ~~^ ~~~~~~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_AddRead.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogus/bogus/bogus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogus/bogus.C
In file included from bogart/AS_BAT_Unitig.H:49,
from bogart/AS_BAT_Unitig.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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogus/bogus/bogusUtil.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores bogus/bogusUtil.C
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from utgcns/utgcns.C:46:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
utgcns/utgcns.C: In function 'uint32 createPartitions_greedilyPartition(cnsParameters&, tigInfo*, uint32)':
utgcns/utgcns.C:294:35: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
294 | fprintf(stderr, "%9u %9lu %9lu %12lu %9.3f %9u\n",
| ~~~^
| |
| long unsigned int
| %9llu
295 | tigs[ti].tigID,
296 | tigs[ti].tigChildren,
| ~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utgcns/utgcns.C:294:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
294 | fprintf(stderr, "%9u %9lu %9lu %12lu %9.3f %9u\n",
| ~~~^
| |
| long unsigned int
| %9llu
......
297 | tigs[ti].tigLength,
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utgcns/utgcns.C:294:46: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
294 | fprintf(stderr, "%9u %9lu %9lu %12lu %9.3f %9u\n",
| ~~~~^
| |
| long unsigned int
| %12llu
......
298 | tigs[ti].consensusArea,
| ~~~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utgcns/utgcns.C: In function 'uint64* createPartitions_outputPartitions(cnsParameters&, tigInfo*, uint32, uint32)':
utgcns/utgcns.C:363:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
363 | parts[pi]->writeIFFobject("MAGC", magc);
| ^~~~~~
utgcns/utgcns.C:364:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
364 | parts[pi]->writeIFFobject("VERS", vers);
| ^~~~~~
utgcns/utgcns.C:365:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
365 | parts[pi]->writeIFFobject("DEFV", defv);
| ^~~~~~
utgcns/utgcns.C: In function 'void createPartitions(cnsParameters&)':
utgcns/utgcns.C:419:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
419 | fprintf(partFile, "%9u %9lu %9lu %12lu %9.3f %9u %9.3f\n",
| ~~~^
| |
| long unsigned int
| %9llu
420 | tigs[ti].tigID,
421 | tigs[ti].tigChildren,
| ~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utgcns/utgcns.C:419:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
419 | fprintf(partFile, "%9u %9lu %9lu %12lu %9.3f %9u %9.3f\n",
| ~~~^
| |
| long unsigned int
| %9llu
......
422 | tigs[ti].tigLength,
| ~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utgcns/utgcns.C:419:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
419 | fprintf(partFile, "%9u %9lu %9lu %12lu %9.3f %9u %9.3f\n",
| ~~~~^
| |
| long unsigned int
| %12llu
......
423 | tigs[ti].consensusArea,
| ~~~~~~~~~~~~~~~~~~~~~~
| |
| uint64 {aka long long unsigned int}
utgcns/utgcns.C: In function 'std::map<unsigned int, sqRead*>* loadPartitionedReads(char*)':
utgcns/utgcns.C:582:75: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
582 | fprintf(stderr, "File '%s' isn't a utgcns seqFile: found magic 0x%016lx.\n", seqFile, magc), exit(1);
| ~~~~~^ ~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %016llx
utgcns/utgcns.C:588:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
588 | fprintf(stderr, "File '%s' is a utgcns seqFile, but an unsupported version %lu.\n", seqFile, vers), exit(1);
| ~~^ ~~~~
| | |
| | uint64 {aka long long unsigned int}
| long unsigned int
| %llu
utgcns/utgcns.C: In function 'int main(int, char**)':
utgcns/utgcns.C:887:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
887 | err.push_back("ERROR: No sequence data! Need one of seqStore (-S), read file (-R) or package (-p).\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/utgcns.C:890:19: warning: ISO C++ forbids converting a string constant to 'std::vector<char*>::value_type' {aka 'char*'} [-Wwrite-strings]
890 | err.push_back("ERROR: No tigStore (-T) OR no test tig (-t) OR no package (-p) supplied.\n");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/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
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/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,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from utility/arrays.H:33,
from /<<BUILDDIR>>/canu-2.0+dfsg/src/AS_global.H:105,
from bogus/bogusUtil.H:42,
from bogus/bogus.C:38:
/usr/include/c++/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 '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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/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 /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 /<<BUILDDIR>>/canu-2.0+dfsg/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 /<<BUILDDIR>>/canu-2.0+dfsg/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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from utgcns/stashContains.H:35,
from utgcns/stashContains.C:30:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
/usr/include/c++/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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C
/usr/include/c++/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 /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C
cp -pf pipelines/canu.pl /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/canu
chmod +x /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/canu
cp -pf pipelines/canu-time.pl /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/canu-time
chmod +x /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/canu-time
echo > /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here."
chmod -x /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/canu.defaults
cp -pf sequence/share/ultra-long-nanopore /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/share/sequence/ultra-long-nanopore
cp -pf sequence/share/pacbio /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/share/sequence/pacbio
cp -pf sequence/share/pacbio-hifi /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/share/sequence/pacbio-hifi
cp -pf pipelines/canu/Consensus.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/CorrectReads.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/HaplotypeReads.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Configure.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Defaults.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Execution.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/SequenceStore.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_Cloud.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_DNANexus.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_LSF.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_PBSTorque.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_SGE.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Grid_Slurm.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Meryl.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Output.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapBasedTrimming.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapErrorAdjustment.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapInCore.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapMhap.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapMMap.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/OverlapStore.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Report.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
cp -pf pipelines/canu/Unitig.pm /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/site_perl/canu/
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/AS_global.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/<<BUILDDIR>>/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap AS_global.C
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from gfa/alignGFA.C:32:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
gfa/alignGFA.C: In function 'bool checkRecord(bedRecord*, sequences&, sequences&, sequences&, bool, bool)':
gfa/alignGFA.C:507:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
507 | success &= checkRecord_align("ALL",
| ^~~~~
gfa/alignGFA.C:535:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
535 | success &= checkRecord_align("LEFT",
| ^~~~~~
gfa/alignGFA.C:541:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
541 | success &= checkRecord_align("RIGHT",
| ^~~~~~~
gfa/alignGFA.C: In function 'void processBEDtoGFA(char*, uint32, char*, char*, double, uint32)':
gfa/alignGFA.C:782:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
782 | gfaFile *gfa = new gfaFile("H\tVN:Z:1.0");
| ^~~~~~~~~~~~~
gfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)':
gfa/alignGFA.C:162:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
162 | system(Pfile);
| ~~~~~~^~~~~~~
ar rv /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/libcanu.a /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/AS_global.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/edlib.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-buffered.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-compressed.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-memoryMapped.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/logging.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/strings.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/system.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/system-stackTrace.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/sequence.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-reader.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer-block.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer-stream.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-statistics.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-exact.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/bits.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/hexDump.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/md5.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/mt19937ar.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/objectStore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/speedCounter.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/sweatShop.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/computeGlobalScore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/falconConsensus.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqCache.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqLibrary.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqReadData.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqReadDataWriter.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreBlob.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreConstructor.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreInfo.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovOverlap.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreWriter.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreFilter.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreFile.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreHistogram.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgStore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTig.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/gfa/gfa.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/gfa/bed.o
ar: creating /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib/libcanu.a
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/AS_global.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/edlib.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-buffered.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-compressed.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/files-memoryMapped.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/logging.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/strings.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/system.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/system-stackTrace.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/sequence.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-reader.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer-block.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-writer-stream.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-statistics.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/kmers-exact.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/bits.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/hexDump.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/md5.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/mt19937ar.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/objectStore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/speedCounter.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utility/sweatShop.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/computeGlobalScore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/falconConsensus.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqCache.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqLibrary.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqReadData.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqReadDataWriter.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreBlob.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreConstructor.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/sqStoreInfo.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovOverlap.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreWriter.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreFilter.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreFile.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/ovStoreHistogram.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgStore.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTig.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/objgfa/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 /<<BUILDDIR>>/canu-2.0+dfsg/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 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gfa/alignGFA.C:141:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=]
141 | sprintf(Pfile, "plot-%s-%s.sh", Aname, Bname);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/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 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gfa/alignGFA.C:160:27: warning: '%s' directive writing up to 4096 bytes into a region of size 4089 [-Wformat-overflow=]
160 | sprintf(Pfile, "sh plot-%s-%s.sh", Aname, Bname);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:866,
from /<<BUILDDIR>>/canu-2.0+dfsg/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 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/stores/libsnappy/snappy.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/gfa/gfa.o
a - /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/lib/libcanu.a/gfa/bed.o
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/dumpBlob -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreBuild -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreConfig -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreBucketizer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreSorter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -lcanu
In file included from stores/tgTig.H:36,
from stores/tgStore.H:43,
from utgcns/unitigConsensus.H:67,
from utgcns/unitigConsensus.C:74:
utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)':
utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen);
| ~~^ ~~~~~~~~
| | |
| long unsigned int uint64 {aka long long unsigned int}
| %llu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreIndexer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/ovStoreStats -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/sqStoreCreate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/sqStoreDumpFASTQ -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/sqStoreDumpMetaData -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/tgStoreCompress -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/tgStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreDump/stores/tgStoreDump.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/tgStoreLoad -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/tgStoreFilter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/tgTigDisplay -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/loadCorrectedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/loadTrimmedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/loadErates -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/loadErates/stores/loadErates.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/meryl -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/meryl.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylCountArray.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylInput.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp-count.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp-countSimple.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp-histogram.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp-nextMer.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl/meryl/merylOp.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/meryl-import -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl-import/meryl/meryl-import.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl-import/meryl/merylCountArray.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/meryl-lookup -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/meryl-lookup/meryl/meryl-lookup.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/sequence -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-extract.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-generate.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-mutate.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-sample.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-shiftregister.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-simulate.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/sequence/sequence/sequence-summarize.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/overlapInCore -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/overlapInCorePartition -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/overlapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/overlapImport -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapImport/overlapInCore/overlapImport.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/overlapPair -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapPair/overlapInCore/overlapPair.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/edalign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/edalign/overlapInCore/edalign.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/prefixEditDistance-matchLimitGenerate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/mhapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/mhapConvert/mhap/mhapConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/mmapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/mmapConvert/minimap/mmapConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/wtdbgConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/filterCorrectionOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/generateCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/filterCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/falconsense -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/falconsense/correction/falconsense.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/falconsense/utgcns/stashContains.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/errorEstimate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/splitHaplotype -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/trimReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/splitReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/mergeRanges -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/overlapAlign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/trimRead.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/findErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/bogart -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/bogart.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Logging.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Outputs.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_TigVector.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Unitig.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/bogus -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogus/bogus/bogus.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/bogus/bogus/bogusUtil.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/alignGFA/gfa/alignGFA.o -lcanu
g++ -o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/lib /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/utgcns/utgcns/utgcns.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/utgcns/utgcns/stashContains.o /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu
Success!
canu installed in /<<BUILDDIR>>/canu-2.0+dfsg/Linux-armv8l/bin/canu
make[2]: Leaving directory '/<<BUILDDIR>>/canu-2.0+dfsg/src'
builddir=*-*/; \
find $builddir \
-name OverlapMhap.pm \
-exec sed -i 's#\(\s*my \$javaPath = \).*#\1 "/usr/lib/jvm/java-8-openjdk-armhf/bin/java";#' {} +
make[1]: Leaving directory '/<<BUILDDIR>>/canu-2.0+dfsg'
dh_auto_test -a -O--sourcedirectory=src/
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --sourcedirectory=src/
dh_testroot -a -O--sourcedirectory=src/
dh_prep -a -O--sourcedirectory=src/
dh_auto_install --destdir=debian/canu/ -a -O--sourcedirectory=src/
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/canu-2.0+dfsg'
dh_install
for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/canu-2.0+dfsg'
dh_installdocs -a -O--sourcedirectory=src/
dh_installchangelogs -a -O--sourcedirectory=src/
dh_installman -a -O--sourcedirectory=src/
dh_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-dbgsym' in '../canu-dbgsym_2.0+dfsg-2+b2_armhf.deb'.
dpkg-deb: building package 'canu' in '../canu_2.0+dfsg-2+b2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../canu_2.0+dfsg-2+b2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-12-28T06:55:16Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
canu_2.0+dfsg-2+b2_armhf.changes:
---------------------------------
Format: 1.8
Date: Fri, 29 Oct 2021 01:57:43 +0530
Source: canu (2.0+dfsg-2)
Binary: canu canu-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 2.0+dfsg-2+b2
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
canu - single molecule sequence assembler for genomes
Changes:
canu (2.0+dfsg-2+b2) 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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Checksums-Sha256:
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8f722380b64883eb1ef308baf8653adf5fca8a4763dbb3093fa117429c822a4b 6853 canu_2.0+dfsg-2+b2_armhf.buildinfo
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Files:
36acaaac8d784582f5b769aa81218d8c 11990904 debug optional canu-dbgsym_2.0+dfsg-2+b2_armhf.deb
9ea36ab7f92ea4a8f35bd261b72072e2 6853 science optional canu_2.0+dfsg-2+b2_armhf.buildinfo
1480dbf9197a68e6d85fdd861f8fb3fd 1038528 science optional canu_2.0+dfsg-2+b2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
canu-dbgsym_2.0+dfsg-2+b2_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 11990904 bytes: control archive=2872 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+b2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 13163
Depends: canu (= 2.0+dfsg-2+b2)
Section: debug
Priority: optional
Description: debug symbols for canu
Build-Ids: 00f016407de0cdc11daa28e0a955f6809a9a578a 01976509406fc28324ad632198714d61ebb361e2 083aa98d904b5e07f2dbfbd3ff3db8fcc71bf381 08610adec925c91e20525f564b42ec4817949710 0ccaa9f7580bcf6eb2f9fc66520be10146f43cb8 145107530c8edaa0121fe82fcdf9646728c1cbaa 198a017cf91e250bb30dae88d9728349d0e98844 1e1325b72d39ef6e161370a7accbe3d867a636a7 1eddc5ea7612b0144a8530b663caec1468ea9acb 24697b76845292978216334fbd1c7904f887380e 2c79eb5f82846e763479aa9e0d3c2cc88a1664aa 36495f2c2404fd6f921394a07ba0d08975415d59 3f9d4d9b4a904e31e1667a635c1265ba6dcde6bd 40a07ea4ea7fe6d821a6b3112254a60bba2de0d7 437a2314fd744bf470611e19cfbe020dfc4af966 437dfa353d7771b825e6129a4c86f1d9dd4968cd 4705155d630ec894e6840184ffb611a9d3d2de98 49eb39a7d8eb4d563b3d73b477326b9742d1962a 530faa0d9f186012ba41163e8ecc4ef74ee9a518 53308d92e6ee1e8e2bbd3d04b53561f9c4cbc0fa 546ab254667c21cd776ec2664e28401887895aa6 5703e4e923896803f49f6692106dba1a3e538cf5 68f44ca66386a053c06de214b33ae2e19ab80f81 71eff731d1962ab2800d6297239a3a9fcf4fdb61 7a609471dc92d751bddec80493b560561412b1a8 7a6307c1b5be94d0203497322bacd99ca82e8aa4 7b224914a92ae11a325cb2b44808c9a30ccd4e7e 7c591b1d0cea9a77a05095b48e905703eab59b3c 936e7200d3fb1354262eaae995ac1602093845ff 93990dc1692ed4808cb73c42a14dde1eac47beff 9ec95f82c21ce67086167d9510b02c602e2711d7 9f69a49ada9551e7aa605ca5c3e5f951bdce8254 aa3f147da6e3746d3179f6d644033e473fa00052 ad5c6c1ce0afffac20c034e810bfdbc342a2e9c4 aeb368b2aa38a5270ada98d54379b7d631a82b4b bc64dc8b7740da871036bb026a8f9805f8893fc9 c21122b7c887a59ff73c5640fe33007b9fb88954 c57bd17187c10a13bd9be83616e2c7e056f44c63 c8ff08486eeea76448da751b041a3765bc9f6b30 d858773aadce6e0a1f6aaba03a5c38c4610477ba dae0b7448ccc202ee21f8c7fbc80ca9cb00d9479 dbbb912c2bd364565d5d66798a96278c47fff6cd dfc535a8f5cf82a5855a0f0b57f6cae9ae594d9f e43e2f57645fb03fe9eac9026c7ee7238330cf85 e5fed1f901fc00c2d317dbbfd2bbd8efe43505a3 e650dbb4df3c484f9f38c12974e509994a5e8a09 ec5fef99f48ac58eb22a6e77eb4ebe4f8ceefae3 ed7d62e4038eaf6754e7cdf15488ecef34e1b02b f53234e2da96cf8350e4145ed4db2a13498f0db8 fa1850b770f46c6bc9e5edb93f0ada7e2c010aad
drwxr-xr-x root/root 0 2021-10-28 20:27 ./
drwxr-xr-x root/root 0 2021-10-28 20:27 ./usr/
drwxr-xr-x root/root 0 2021-10-28 20:27 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-28 20:27 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-28 20:27 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-28 20:27 ./usr/lib/debug/.build-id/00/
-rw-r--r-- root/root 148472 2021-10-28 20:27 ./usr/lib/debug/.build-id/00/f016407de0cdc11daa28e0a955f6809a9a578a.debug
drwxr-xr-x root/root 0 2021-10-28 20:27 ./usr/lib/debug/.build-id/01/
-rw-r--r-- root/root 407576 2021-10-28 20:27 ./usr/lib/debug/.build-id/01/976509406fc28324ad632198714d61ebb361e2.debug
drwxr-xr-x root/root 0 2021-10-28 20:27 ./usr/lib/debug/.build-id/08/
-rw-r--r-- root/root 146396 2021-10-28 20:27 ./usr/lib/debug/.build-id/08/3aa98d904b5e07f2dbfbd3ff3db8fcc71bf381.debug
-rw-r--r-- root/root 166048 2021-10-28 20:27 ./usr/lib/debug/.build-id/08/610adec925c91e20525f564b42ec4817949710.debug
drwxr-xr-x root/root 0 2021-10-28 20:27 ./usr/lib/debug/.build-id/0c/
-rw-r--r-- root/root 347216 2021-10-28 20:27 ./usr/lib/debug/.build-id/0c/caa9f7580bcf6eb2f9fc66520be10146f43cb8.debug
drwxr-xr-x root/root 0 2021-10-28 20:27 ./usr/lib/debug/.build-id/14/
-rw-r--r-- root/root 297316 2021-10-28 20:27 ./usr/lib/debug/.build-id/14/5107530c8edaa0121fe82fcdf9646728c1cbaa.debug
drwxr-xr-x root/root 0 2021-10-28 20:27 ./usr/lib/debug/.build-id/19/
-rw-r--r-- root/root 207424 2021-10-28 20:27 ./usr/lib/debug/.build-id/19/8a017cf91e250bb30dae88d9728349d0e98844.debug
drwxr-xr-x root/root 0 2021-10-28 20:27 ./usr/lib/debug/.build-id/1e/
-rw-r--r-- root/root 34764 2021-10-28 20:27 ./usr/lib/debug/.build-id/1e/1325b72d39ef6e161370a7accbe3d867a636a7.debug
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drwxr-xr-x root/root 0 2021-10-28 20:27 ./usr/lib/debug/.build-id/24/
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-rw-r--r-- root/root 77496 2021-10-28 20:27 ./usr/lib/debug/.build-id/2c/79eb5f82846e763479aa9e0d3c2cc88a1664aa.debug
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drwxr-xr-x root/root 0 2021-10-28 20:27 ./usr/lib/debug/.build-id/40/
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canu_2.0+dfsg-2+b2_armhf.deb
----------------------------
new Debian package, version 2.0.
size 1038528 bytes: control archive=3104 bytes.
891 bytes, 22 lines control
5892 bytes, 85 lines md5sums
Package: canu
Source: canu (2.0+dfsg-2)
Version: 2.0+dfsg-2+b2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8020
Depends: libc6 (>= 2.29), 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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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 153272
Build-Time: 204
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 277
Job: canu_2.0+dfsg-2
Machine Architecture: armhf
Package: canu
Package-Time: 499
Source-Version: 2.0+dfsg-2
Space: 153272
Status: successful
Version: 2.0+dfsg-2+b2
--------------------------------------------------------------------------------
Finished at 2021-12-28T06:55:16Z
Build needed 00:08:19, 153272k disk space