I: pbuilder: network access will be disabled during build
I: Current time: Wed Feb 19 14:27:29 -12 2025
I: pbuilder-time-stamp: 1740018449
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [snap-aligner_2.0.3+dfsg-2.dsc]
I: copying [./snap-aligner_2.0.3+dfsg.orig.tar.xz]
I: copying [./snap-aligner_2.0.3+dfsg-2.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./snap-aligner_2.0.3+dfsg-2.dsc: unsupported subcommand
dpkg-source: info: extracting snap-aligner in snap-aligner-2.0.3+dfsg
dpkg-source: info: unpacking snap-aligner_2.0.3+dfsg.orig.tar.xz
dpkg-source: info: unpacking snap-aligner_2.0.3+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying non-x86-and-kfreebsd
dpkg-source: info: applying drop-msse
dpkg-source: info: applying simde
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/3708746/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='arm64'
IFS='
'
INVOCATION_ID='074231572da04b1d82ed902c07ed804d'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='3708746'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.GLqPIdtv/pbuilderrc_wbFl --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.GLqPIdtv/b1 --logfile b1/build.log snap-aligner_2.0.3+dfsg-2.dsc'
SUDO_GID='109'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.4:3128'
I: uname -a
Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/3708746/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), help2man, zlib1g-dev, libsimde-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19912 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libsimde-dev; however:
Package libsimde-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded.
Need to get 21.7 MB of archives. After unpacking 90.9 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB]
Get: 2 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 4 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 5 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 6 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
Get: 7 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 8 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 9 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-4 [92.1 kB]
Get: 10 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 11 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 12 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB]
Get: 13 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB]
Get: 14 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 15 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB]
Get: 16 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB]
Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-3 [539 kB]
Get: 19 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 25 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 26 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 27 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
Get: 28 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 29 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB]
Get: 32 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB]
Get: 33 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-2 [467 kB]
Get: 34 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Fetched 21.7 MB in 0s (108 MB/s)
Preconfiguring packages ...
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(Reading database ... 19912 files and directories currently installed.)
Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_arm64.deb ...
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Setting up libpipeline1:arm64 (1.5.8-1) ...
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Setting up libmagic-mgc (1:5.45-3+b1) ...
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Setting up libdebhelper-perl (13.24.1) ...
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Setting up gettext-base (0.23.1-1) ...
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Setting up autoconf (2.72-3) ...
Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up dwz (0.15-1+b1) ...
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Setting up libuchardet0:arm64 (0.0.8-1+b2) ...
Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up liblocale-gettext-perl (1.07-7+b1) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up help2man (1.49.3+b1) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/snap-aligner-2.0.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../snap-aligner_2.0.3+dfsg-2_source.changes
dpkg-buildpackage: info: source package snap-aligner
dpkg-buildpackage: info: source version 2.0.3+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg'
dh_auto_clean
make -j12 clean
make[2]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg'
rm -f SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o snap-aligner unit_tests SNAPCommand snap SNAP
make[2]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg'
rm -f debian/*.1
rm -f */*.d */*/*.d
make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg'
dh_auto_build
make -j12 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg'
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGap.o SNAPLib/AffineGap.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGapVectorized.o SNAPLib/AffineGapVectorized.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerContext.o SNAPLib/AlignerContext.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerOptions.o SNAPLib/AlignerOptions.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerStats.o SNAPLib/AlignerStats.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentAdjuster.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentResult.o SNAPLib/AlignmentResult.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ApproximateCounter.o SNAPLib/ApproximateCounter.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Bam.o SNAPLib/Bam.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BaseAligner.o SNAPLib/BaseAligner.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BigAlloc.o SNAPLib/BigAlloc.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BufferedAsync.o SNAPLib/BufferedAsync.cpp
In file included from SNAPLib/AffineGap.cpp:2:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/ApproximateCounter.h:3,
from SNAPLib/ApproximateCounter.cpp:3:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/BigAlloc.cpp:24:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from SNAPLib/AlignerContext.cpp:27:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/AffineGapVectorized.cpp:2:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/AlignerStats.h:29,
from SNAPLib/AlignerStats.cpp:27:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/Genome.h:26,
from SNAPLib/AlignerOptions.h:29,
from SNAPLib/AlignerOptions.cpp:27:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/HashTable.h:23,
from SNAPLib/GenomeIndex.h:27,
from SNAPLib/AlignmentAdjuster.h:27,
from SNAPLib/AlignmentAdjuster.cpp:26:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/Genome.h:26,
from SNAPLib/AlignmentResult.h:29,
from SNAPLib/AlignmentResult.cpp:23:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from SNAPLib/Genome.h:26,
from SNAPLib/AlignmentResult.h:29,
from SNAPLib/BaseAligner.h:30,
from SNAPLib/BaseAligner.cpp:29:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/SAM.h:22,
from SNAPLib/Bam.cpp:20:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/BufferedAsync.cpp:21:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ChimericPairedEndAligner.o SNAPLib/ChimericPairedEndAligner.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/CommandProcessor.o SNAPLib/CommandProcessor.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Compat.o SNAPLib/Compat.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataReader.o SNAPLib/DataReader.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataWriter.o SNAPLib/DataWriter.cpp
In file included from SNAPLib/Genome.h:26,
from SNAPLib/AlignmentResult.h:29,
from SNAPLib/PairedEndAligner.h:25,
from SNAPLib/ChimericPairedEndAligner.h:27,
from SNAPLib/ChimericPairedEndAligner.cpp:27:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
In file included from SNAPLib/Compat.cpp:26:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Error.o SNAPLib/Error.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTA.o SNAPLib/FASTA.cpp
In file included from SNAPLib/Genome.h:26,
from SNAPLib/FASTA.h:27,
from SNAPLib/CommandProcessor.cpp:27:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTQ.o SNAPLib/FASTQ.cpp
In file included from SNAPLib/DataWriter.cpp:21:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/DataReader.cpp:22:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp
In file included from SNAPLib/Error.cpp:25:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/FASTQ.h:30,
from SNAPLib/FASTQ.cpp:29:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/GenericFile.cpp:27:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/FASTA.cpp:26:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
SNAPLib/DataReader.cpp: In static member function 'static bool DecompressDataReader::decompress(z_stream*, ThreadHeap*, char*, _int64, _int64*, char*, _int64, _int64*, DecompressMode)':
SNAPLib/DataReader.cpp:2052:53: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=]
2052 | fprintf(stderr, "\n0x%llx\t", offset);
| ~~~^ ~~~~~~
| | |
| | _int64 {aka long int}
| long long unsigned int
| %lx
SNAPLib/DataReader.cpp: In member function 'char* DecompressDataReader::findPointer(void*)':
SNAPLib/DataReader.cpp:2105:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=]
2105 | sprintf(result, "compressed #%d @ %lld", i, (char*)p - e->compressed);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int long int
| %ld
SNAPLib/DataReader.cpp:2109:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=]
2109 | sprintf(result, "decompressed #%d %lld", i, (char*) p - e->decompressed);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int long int
| %ld
SNAPLib/DataReader.cpp:2113:43: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=]
2113 | sprintf(result, "extra #%d %lld", i, (char*) p - e->decompressed - extraBytes);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int long int
| %ld
SNAPLib/DataReader.cpp: In static member function 'static void DecompressDataReader::decompressThread(void*)':
SNAPLib/DataReader.cpp:2261:174: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=]
2261 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int _int64 {aka long int}
| %ld
SNAPLib/DataReader.cpp:2261:198: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=]
2261 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry);
| ~~~^ ~~~~~~
| | |
| long long int _int64 {aka long int}
| %ld
SNAPLib/DataReader.cpp:2265:74: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=]
2265 | fprintf(stderr, "error reading BAM file at offset %lld\n", reader->getFileOffset());
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int _int64 {aka long int}
| %ld
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_Blob.cpp
SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)':
SNAPLib/Error.cpp:96:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=]
96 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment);
| ~~~^ ~~~~~~~~~
| | |
| long long int _int64 {aka long int}
| %ld
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_HDFS.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp
In file included from SNAPLib/GenericFile.h:25,
from SNAPLib/GenericFile_Blob.h:26,
from SNAPLib/GenericFile_Blob.cpp:25:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp
In file included from SNAPLib/GenericFile.h:25,
from SNAPLib/GenericFile_Blob.h:26,
from SNAPLib/GenericFile_map.h:26,
from SNAPLib/GenericFile_map.cpp:25:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.cpp
In file included from SNAPLib/Genome.h:26,
from SNAPLib/Genome.cpp:26:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp
In file included from SNAPLib/GenericFile_stdio.cpp:25:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp
In file included from SNAPLib/ApproximateCounter.h:3,
from SNAPLib/GenomeIndex.cpp:26:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Histogram.o SNAPLib/Histogram.cpp
In file included from SNAPLib/HashTable.h:23,
from SNAPLib/HashTable.cpp:20:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/GzipDataWriter.h:25,
from SNAPLib/GzipDataWriter.cpp:20:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HitDepth.o SNAPLib/HitDepth.cpp
In file included from SNAPLib/Histogram.cpp:27:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp
In file included from SNAPLib/Genome.h:26,
from SNAPLib/AlignmentResult.h:29,
from SNAPLib/PairedEndAligner.h:25,
from SNAPLib/IntersectingPairedEndAligner.h:25,
from SNAPLib/IntersectingPairedEndAligner.cpp:24:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/HitDepth.cpp:25:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
SNAPLib/GenomeIndex.cpp: In static member function 'static bool GenomeIndex::BuildIndexToDirectory(const Genome*, int, double, const char*, unsigned int, unsigned int, bool, unsigned int, bool, const char*, unsigned int, bool)':
SNAPLib/GenomeIndex.cpp:952:36: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=]
952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int _uint64 {aka long unsigned int}
| %ld
SNAPLib/GenomeIndex.cpp:952:61: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type '_uint64' {aka 'long unsigned int'} [-Wformat=]
952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int _uint64 {aka long unsigned int}
| %ld
SNAPLib/GenomeIndex.cpp:952:103: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=]
952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed);
| ~~~^ ~~~~~~~~~~~
| | |
| long long int _uint64 {aka long unsigned int}
| %ld
SNAPLib/GenomeIndex.cpp:1007:36: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=]
1007 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables,
| ~~~^
| |
| long long int
| %ld
1008 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| _uint64 {aka long unsigned int}
SNAPLib/GenomeIndex.cpp:1007:50: warning: format '%lld' expects argument of type 'long long int', but argument 10 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
1007 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables,
| ~~~^
| |
| long long int
| %ld
1008 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize);
| ~~~~~~~~~~~~~~~~~
| |
| size_t {aka long unsigned int}
SNAPLib/GenomeIndex.cpp: In static member function 'static GenomeIndex* GenomeIndex::loadFromDirectory(char*, bool, bool)':
SNAPLib/GenomeIndex.cpp:1879:57: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=]
1879 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding,
| ~~~^ ~~~~~~~~~~~~~~~~~~
| | |
| long long int* _int64* {aka long int*}
| %ld
SNAPLib/GenomeIndex.cpp:1879:71: warning: format '%lld' expects argument of type 'long long int*', but argument 10 has type 'size_t*' {aka 'long unsigned int*'} [-Wformat=]
1879 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding,
| ~~~^
| |
| long long int*
| %ld
1880 | &hashTableKeySize, &hashTablesFileSize, &smallHashTable, &locationSize))) {
| ~~~~~~~~~~~~~~~~~~~
| |
| size_t* {aka long unsigned int*}
SNAPLib/Genome.cpp: In member function 'bool Genome::saveToFile(const char*) const':
SNAPLib/Genome.cpp:216:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'long int' [-Wformat=]
216 | fprintf(saveFile,"%lld %d %d\n",nBases, nContigs, GENOME_FLAG_ALT_CONTIGS_MARKED);
| ~~~^ ~~~~~~
| | |
| | long int
| long long int
| %ld
SNAPLib/Genome.cpp:226:31: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=]
226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation),
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int _int64 {aka long int}
| %ld
SNAPLib/Genome.cpp:226:42: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_int64' {aka 'long int'} [-Wformat=]
226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation),
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int _int64 {aka long int}
| %ld
SNAPLib/Genome.cpp: In static member function 'static const Genome* Genome::loadFromFile(const char*, unsigned int, GenomeLocation, GenomeDistance, bool)':
SNAPLib/Genome.cpp:356:47: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type '_int64*' {aka 'long int*'} [-Wformat=]
356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) {
| ~~~^ ~~~~~~~~~~~~
| | |
| long long int* _int64* {aka long int*}
| %ld
SNAPLib/Genome.cpp:356:58: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=]
356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) {
| ~~~^ ~~~~~~~~~~~~~~~~
| | |
| long long int* _int64* {aka long int*}
| %ld
SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool)':
SNAPLib/Genome.cpp:497:51: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=]
497 | if (NULL == retval || 3 != sscanf(linebuf,"%lld %d %d\n", nBases, nContigs, &flags)) {
| ~~~^ ~~~~~~
| | |
| | GenomeDistance* {aka long int*}
| long long int*
| %ld
In file included from SNAPLib/LandauVishkin.cpp:2:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp
In file included from SNAPLib/Read.h:28,
from SNAPLib/MultiInputReadSupplier.cpp:25:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp
SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions]
767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} };
| ^
SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions]
767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} };
| ^
In file included from SNAPLib/PairedAligner.cpp:34:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp
In file included from SNAPLib/ParallelTask.h:25,
from SNAPLib/ParallelTask.cpp:18:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/PairedReadMatcher.cpp:26:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp
In file included from SNAPLib/Read.h:28,
from SNAPLib/ProbabilityDistance.h:3,
from SNAPLib/ProbabilityDistance.cpp:2:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/RangeSplitter.h:29,
from SNAPLib/RangeSplitter.cpp:28:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/ReadReader.cpp:19:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/PairedAligner.cpp:47:
SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions]
767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} };
| ^
SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions]
767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} };
| ^
SNAPLib/PairedAligner.cpp: In member function 'void PairedAlignerContext::runIterationThreadImpl(Read**)':
SNAPLib/PairedAligner.cpp:673:72: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
673 | fprintf(stderr, "reporter:counter:SNAP,readsAligned,%llu\n", stats->totalReads - readsWhenLastReported);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int long unsigned int
| %lu
In file included from SNAPLib/Read.h:28,
from SNAPLib/Read.cpp:25:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp
In file included from SNAPLib/Read.h:28,
from SNAPLib/ReadSupplierQueue.cpp:25:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp
SNAPLib/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)':
SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type]
44 | }
| ^
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp
In file included from SNAPLib/ReadWriter.cpp:21:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/SAM.cpp:21:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp
In file included from SNAPLib/Seed.h:27,
from SNAPLib/Seed.cpp:26:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp
In file included from SNAPLib/Seed.h:27,
from SNAPLib/SeedSequencer.h:27,
from SNAPLib/SeedSequencer.cpp:25:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Tables.o SNAPLib/Tables.cpp
In file included from SNAPLib/Genome.h:26,
from SNAPLib/AlignmentResult.h:29,
from SNAPLib/BaseAligner.h:30,
from SNAPLib/SingleAligner.cpp:27:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp
In file included from SNAPLib/SortedDataWriter.cpp:21:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const':
SNAPLib/SAM.cpp:1292:116: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'long int' [-Wformat=]
1292 | bytesConsumed += snprintf(header + bytesConsumed, headerBufferSize - bytesConsumed, "@SQ\tSN:%s\tLN:%llu%s\n", contig->name, contig->length - context.genome->getChromosomePadding(), contig->isALT ? "\tAH:*":"");
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int long int
| %lu
In file included from SNAPLib/Util.h:5,
from SNAPLib/Util.cpp:26:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writePairs(const ReaderContext&, LandauVishkinWithCigar*, AffineGapVectorizedWithCigar*, bool, char*, size_t, size_t*, size_t*, Read**, GenomeLocation*, PairedAlignmentResult*, bool, bool, char*, bool, int*, int*, bool*, bool*) const':
SNAPLib/SAM.cpp:1854:77: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
1854 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%s%s%.*s\n",
| ~~~^
| |
| long long unsigned int
| %lu
......
1858 | positionInContig[whichRead],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| GenomeDistance {aka long int}
SNAPLib/SAM.cpp:1854:95: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
1854 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%s%s%.*s\n",
| ~~~^
| |
| long long unsigned int
| %lu
......
1862 | matePositionInContig[whichRead],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| GenomeDistance {aka long int}
SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, LandauVishkinWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, bool, char*, bool, _int64, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const':
SNAPLib/SAM.cpp:2076:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n",
| ~~~^
| |
| long long unsigned int
| %lu
......
2080 | positionInContig,
| ~~~~~~~~~~~~~~~~
| |
| GenomeDistance {aka long int}
SNAPLib/SAM.cpp:2076:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n",
| ~~~^
| |
| long long unsigned int
| %lu
......
2084 | matePositionInContig,
| ~~~~~~~~~~~~~~~~~~~~
| |
| GenomeDistance {aka long int}
SNAPLib/SAM.cpp:2076:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=]
2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n",
| ~~~^
| |
| long long int
| %ld
......
2085 | templateLength,
| ~~~~~~~~~~~~~~
| |
| _int64 {aka long int}
SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, AffineGapVectorizedWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, int, bool, char*, bool, _int64, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const':
SNAPLib/SAM.cpp:2312:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n",
| ~~~^
| |
| long long unsigned int
| %lu
......
2316 | positionInContig,
| ~~~~~~~~~~~~~~~~
| |
| GenomeDistance {aka long int}
SNAPLib/SAM.cpp:2312:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n",
| ~~~^
| |
| long long unsigned int
| %lu
......
2320 | matePositionInContig,
| ~~~~~~~~~~~~~~~~~~~~
| |
| GenomeDistance {aka long int}
SNAPLib/SAM.cpp:2312:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=]
2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n",
| ~~~^
| |
| long long int
| %ld
......
2321 | templateLength,
| ~~~~~~~~~~~~~~
| |
| _int64 {aka long int}
SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)':
SNAPLib/SAM.cpp:2650:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int GenomeDistance {aka long int}
| %lu
SNAPLib/SAM.cpp:2654:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int GenomeDistance {aka long int}
| %lu
SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)':
SNAPLib/SAM.cpp:2745:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int GenomeDistance {aka long int}
| %lu
SNAPLib/SAM.cpp:2749:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int GenomeDistance {aka long int}
| %lu
SNAPLib/SAM.cpp: In static member function 'static void SAMFormat::printRead(const Genome*, Read*, GenomeLocation)':
SNAPLib/SAM.cpp:2820:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'GenomeLocation' {aka 'long int'} [-Wformat=]
2820 | printf("Aligned location %s:%llu\n",
| ~~~^
| |
| long long unsigned int
| %lu
2821 | genome->getContigAtLocation(location)->name,
2822 | location - genome->getContigAtLocation(location)->beginningLocation);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| GenomeLocation {aka long int}
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp
In file included from SNAPLib/mapq.cpp:25:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/Error.h:25,
from SNAPLib/exit.cpp:26:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
SNAPLib/SingleAligner.cpp: In member function 'virtual void SingleAlignerContext::runIterationThreadImpl(Read*&)':
SNAPLib/SingleAligner.cpp:207:67: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
207 | fprintf(stderr,"reporter:counter:SNAP,readsAligned,%llu\n",stats->totalReads - readsWhenLastReported);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int long unsigned int
| %lu
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp
SNAPLib/Util.cpp: In function 'char* FormatUIntWithCommas(_uint64, char*, size_t, size_t)':
SNAPLib/Util.cpp:167:49: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=]
167 | sprintf(tempBuf, ",%03lld", x % 1000);
| ~~~~~^ ~~~~~~~~
| | |
| | _uint64 {aka long unsigned int}
| long long int
| %03ld
SNAPLib/Util.cpp:170:46: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=]
170 | sprintf(tempBuf, "%lld", x);
| ~~~^ ~
| | |
| | _uint64 {aka long unsigned int}
| long long int
| %ld
In file included from SNAPLib/CommandProcessor.h:24,
from apps/snap/Main.cpp:26:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp
In file included from SNAPLib/AffineGap.h:3,
from tests/AffineGapTest.cpp:3:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp
In file included from SNAPLib/LandauVishkin.h:2,
from tests/EventTest.cpp:3:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from SNAPLib/AffineGapVectorized.h:7,
from tests/AffineGapVectorizedTest.cpp:3:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp
In file included from SNAPLib/LandauVishkin.h:2,
from tests/LandauVishkinTest.cpp:3:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp
In file included from tests/ProbabilityDistanceTest.cpp:2:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
In file included from apps/SNAPCommand/SNAPCommand.cpp:26:
SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined
87 | # define _MM_HINT_T0 1
| ^~~~~~~~~~~
In file included from /usr/include/simde/x86/sse2.h:35,
from SNAPLib/Compat.h:81:
/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition
3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0
| ^~~~~~~~~~~
SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined
88 | # define _MM_HINT_T1 2
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition
3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1
| ^~~~~~~~~~~
SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined
89 | # define _MM_HINT_T2 3
| ^~~~~~~~~~~
/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition
3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2
| ^~~~~~~~~~~
SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)':
SNAPLib/SAM.cpp:2650:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=]
2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore);
| ^~~~
SNAPLib/SAM.cpp:2650:54: note: directive argument in the range [1, 9223372036854775807]
2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore);
| ^~~~~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/fstream:43,
from SNAPLib/stdafx.h:14,
from SNAPLib/SAM.cpp:19:
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2650:21:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16
68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
69 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)':
SNAPLib/SAM.cpp:2654:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=]
2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter);
| ^~~~
SNAPLib/SAM.cpp:2654:52: note: directive argument in the range [1, 9223372036854775807]
2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter);
| ^~~~~~~
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2654:21:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16
68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
69 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)':
SNAPLib/SAM.cpp:2745:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=]
2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore);
| ^~~~
SNAPLib/SAM.cpp:2745:54: note: directive argument in the range [1, 9223372036854775807]
2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore);
| ^~~~~~~
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2745:21:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16
68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
69 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)':
SNAPLib/SAM.cpp:2749:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=]
2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter);
| ^~~~
SNAPLib/SAM.cpp:2749:52: note: directive argument in the range [1, 9223372036854775807]
2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter);
| ^~~~~~~
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2749:21:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16
68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
69 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -o snap-aligner -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o -lrt -lz
echo SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o
SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o
echo SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o
SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o
g++ -o SNAPCommand -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o -lrt -lz
g++ -o unit_tests -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o -lrt -lz
make[2]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg'
help2man --no-discard-stderr --no-info --version-string="2.0.3" \
--name "scalable nucleotide alignment program" \
--help-option=" " ./snap-aligner > debian/snap-aligner.1
for option in index single paired; do help2man \
--no-discard-stderr --no-info --version-string="2.0.3" \
--include=debian/snap-aligner-${option}-man-include \
--help-option=" " "./snap-aligner ${option}" > \
debian/snap-aligner-${option}.1; done
help2man --no-discard-stderr --no-info --version-string="2.0.3" \
--name "scalable nucleotide alignment program" \
--help-option=" " ./SNAPCommand > debian/SNAPCommand.1
make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg'
dh_auto_test
./unit_tests
AffineGapTest:
- synthetic: [OK]
AffineGapVectorizedTest:
- equal strings: [OK]
- one deletion: [OK]
- long deletion: [OK]
- long insertion: [OK]
- synthetic: [OK]
EventTest:
- many waiters: [OK]
- single waiters: [OK]
LandauVishkinTest:
- equal strings: [OK]
- prefixes: [OK]
- non-equal strings: [OK]
- overly distant strings: [OK]
- CIGAR strings: [OK]
ProbabilityDistanceTest:
- basic probabilities: [OK]
- indels: [OK]
15 / 15 tests passed.
make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/snap-aligner/
dh_install
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'snap-aligner' in '../snap-aligner_2.0.3+dfsg-2_arm64.deb'.
dpkg-deb: building package 'snap-aligner-dbgsym' in '../snap-aligner-dbgsym_2.0.3+dfsg-2_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../snap-aligner_2.0.3+dfsg-2_arm64.buildinfo
dpkg-genchanges --build=binary -O../snap-aligner_2.0.3+dfsg-2_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/3708746 and its subdirectories
I: Current time: Wed Feb 19 14:29:13 -12 2025
I: pbuilder-time-stamp: 1740018553