Sat May 23 00:01:25 UTC 2020 I: starting to build parsinsert/buster/armhf on jenkins on '2020-05-23 00:00' Sat May 23 00:01:26 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_19/2002/console.log Sat May 23 00:01:26 UTC 2020 I: Downloading source for buster/parsinsert=1.04-4 --2020-05-23 00:01:26-- http://deb.debian.org/debian/pool/main/p/parsinsert/parsinsert_1.04-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2090 (2.0K) Saving to: ‘parsinsert_1.04-4.dsc’ 0K .. 100% 9.95M=0s 2020-05-23 00:01:26 (9.95 MB/s) - ‘parsinsert_1.04-4.dsc’ saved [2090/2090] Sat May 23 00:01:26 UTC 2020 I: parsinsert_1.04-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: parsinsert Binary: parsinsert, parsinsert-testdata Architecture: any all Version: 1.04-4 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Homepage: http://sourceforge.net/projects/parsinsert/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/parsinsert Vcs-Git: https://salsa.debian.org/med-team/parsinsert.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~) Package-List: parsinsert deb science optional arch=any parsinsert-testdata deb science optional arch=all Checksums-Sha1: 197c6f3f87c96d7c2104db3c530b0e0bc04a70f4 53700 parsinsert_1.04.orig.tar.gz 92df61c5270e066cb48ff1763d098595506cf846 2826308 parsinsert_1.04-4.debian.tar.xz Checksums-Sha256: 06977f23a08b1a0a6657f5c4c5c6a1bb699ab28335ff06c081f9ecf82e8f84c0 53700 parsinsert_1.04.orig.tar.gz 5d1fa17043664764b40e84029ba45a6d877b4e14c3d7e155e09935b859487d17 2826308 parsinsert_1.04-4.debian.tar.xz Files: 3e4997e279325e13860996758c2aed7e 53700 parsinsert_1.04.orig.tar.gz 11ec1917be8cb6150502317526ad0e80 2826308 parsinsert_1.04-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAluoALQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEWWw/9FUvkKElvT4mftWfYhMJ+FX8IB6/TgjBg nPGddgunKGM8e6iCkugYoHE6d3hDKK7VcPcLE1rJv93r7DfJvX2nUHD0MOSgnbOG UhcLEWkH6eyrW5NCWpNXmxssiA4Wu67ar7hgPVUAYficH8592Snl4t4PO/zqE6ED 19rKb6BIaepaGoTarMtEqRgHfspCP5kdFgWNFPbDlD7Nl+ErFEd0I3ev/vNpFUx0 nfbAgEcCLIVXfnfOlAHF79UCgFTY27qDL5yvLy49Bsh+GkGol3va67XP2sBw7kQZ g/nUdXDtwxOIWLtHaKPDRku0h4uOQTLwDa/pd3AXNrNwU5uw5F+y+zs/O4V8NVqS 4akuwkHzYLPIYzaklba3xJr28qJ0jLoDWFvpa/H30PrQSsuWdPL7GkuzA6d8TUmF EEZNdMPsYdbFJr0i4A4De0ow7JnbO9ysJyghKyNZtkOqG0p+KyBTOfrPF6JO9bZk I2eEES+yfarKb9Mwlan42saFW02cmr675g8MCGMgUQhzAlqQtvKo4mjd6jALe3pE 2uACrTpkGglYthozzI7b/vc5m0fT/lJ76b9NQCq92N37D+WQjCygtNO0IlzCffhV /u63sJI0RgtztIO/eRAX0AcUV5JQt2TdNQJb1+8yuYK0DOnxE6bsJdkQV7dCV4+K ucLv9E6PW7w= =t9QO -----END PGP SIGNATURE----- Sat May 23 00:01:26 UTC 2020 I: Checking whether the package is not for us Sat May 23 00:01:26 UTC 2020 I: Starting 1st build on remote node jtk1b-armhf-rb.debian.net. Sat May 23 00:01:26 UTC 2020 I: Preparing to do remote build '1' on jtk1b-armhf-rb.debian.net. Sat May 23 00:07:34 UTC 2020 I: Deleting $TMPDIR on jtk1b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 22 12:01:38 -12 2020 I: pbuilder-time-stamp: 1590192098 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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 [parsinsert_1.04-4.dsc] I: copying [./parsinsert_1.04.orig.tar.gz] I: copying [./parsinsert_1.04-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Sep 23 09:08:04 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./parsinsert_1.04-4.dsc dpkg-source: info: extracting parsinsert in parsinsert-1.04 dpkg-source: info: unpacking parsinsert_1.04.orig.tar.gz dpkg-source: info: unpacking parsinsert_1.04-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix-gcc6.patch I: using fakeroot in build. I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team 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 (>= 11~) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 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 (>= 11~); however: Package debhelper 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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 18.2 MB of archives. After unpacking 63.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 24 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 30 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 31 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Fetched 18.2 MB in 13s (1417 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... 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Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../11-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. 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Preparing to unpack .../27-libcroco3_0.6.12-3_armhf.deb ... Unpacking libcroco3:armhf (0.6.12-3) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../28-libncurses6_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses6:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_armhf.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Setting up libpipeline1:armhf (1.5.1-2) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/parsinsert-1.04/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package parsinsert dpkg-buildpackage: info: source version 1.04-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/parsinsert-1.04' mv parsinsert ParsInsert || true mv: cannot stat 'parsinsert': No such file or directory dh_auto_clean make -j3 clean make[2]: Entering directory '/build/parsinsert-1.04' rm -f ParsInsert AttrList.o Knox_Stddef.o PNode.o SeqList.o Taxonomy.o ParsInsert.o *.fasta *.log *.results *.tree make[2]: Leaving directory '/build/parsinsert-1.04' make[1]: Leaving directory '/build/parsinsert-1.04' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/parsinsert-1.04' dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/parsinsert-1.04' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsinsert-1.04=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AttrList.o AttrList.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsinsert-1.04=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Knox_Stddef.o Knox_Stddef.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsinsert-1.04=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PNode.o PNode.cpp AttrList.cpp: In member function 'int CAttrList::AddHex(const char*, long unsigned int)': AttrList.cpp:173:15: warning: format '%X' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] sprintf(buf, "0x%08X", value); ^~~~~~~~ ~~~~~ In file included from PNode.h:31, from PNode.cpp:27: ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': ParsimonySet.h:429:35: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%s [", label); ^ ParsimonySet.h:431:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL(" %3d", segCounts[k]); ^ ParsimonySet.h:432:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("]\n"); ^ PNode.cpp: In member function 'void CPTree::Parse(const char*)': PNode.cpp:299:64: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Could not process all the chars in NEWICK file\n"); ^ PNode.cpp:304:63: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Processed %d chars of %d\n", nProcess, totalProcess); ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsinsert-1.04=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SeqList.o SeqList.cpp In file included from PNode.h:31, from SeqList.cpp:27: ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': ParsimonySet.h:429:35: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%s [", label); ^ ParsimonySet.h:431:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL(" %3d", segCounts[k]); ^ ParsimonySet.h:432:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("]\n"); ^ SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceIndexFile(const char*)': SeqList.cpp:490:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Loading sequence %d [%s]\n", count, name); ^ SeqList.cpp:492:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Loading sequence %d\n", count); ^ SeqList.cpp:496:61: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Loaded %d sequences from [%s]\n", count, filename); ^ SeqList.cpp: In member function 'int CSequenceFile::ReadTaxonomyFile()': SeqList.cpp:529:71: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); ^ SeqList.cpp:531:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Loading sequence %d\n", seqCount); ^ SeqList.cpp: In member function 'int CSequenceFile::ReadSequenceFile(int)': SeqList.cpp:565:72: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); ^ SeqList.cpp:580:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Duplicate sequence found [%s]\n", seq->name.c_str()); ^ SeqList.cpp:605:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Loading sequence %d [%s]\n", seqCount, seq->name.c_str()); ^ SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqHeader(FILE*)': SeqList.cpp:202:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer, sizeof(buffer)-1, f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SeqList.cpp: In member function 'const char* CSequenceItem::ReadSeqData(FILE*)': SeqList.cpp:229:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer, sizeof(buffer)-1, f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsinsert-1.04=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Taxonomy.o Taxonomy.cpp Taxonomy.cpp: In member function 'int CTaxEntry::Display(const char*, int)': Taxonomy.cpp:96:54: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%s[%s] %d\n", leader, name.c_str(), count); ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsinsert-1.04=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ParsInsert.o ParsInsert.cpp ParsInsert.cpp:411:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] DisplayL("%s\nCommand Line:[%s]\n", VERSION, cmd.c_str()); ^~~~~~~ ParsInsert.cpp:56:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] #define VERSION APPNAME " Version 1.04 " __DATE__ " " __TIME__ ^~~~~~~~ ParsInsert.cpp:411:38: note: in expansion of macro 'VERSION' DisplayL("%s\nCommand Line:[%s]\n", VERSION, cmd.c_str()); ^~~~~~~ ParsInsert.cpp:416:25: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] DisplayT(USAGE, VERSION, APPNAME); ^~~~~~~ ParsInsert.cpp:56:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] #define VERSION APPNAME " Version 1.04 " __DATE__ " " __TIME__ ^~~~~~~~ ParsInsert.cpp:416:25: note: in expansion of macro 'VERSION' DisplayT(USAGE, VERSION, APPNAME); ^~~~~~~ In file included from ParsInsert.h:29, from ParsInsert.cpp:34: ParsimonySet.h: In member function 'void CParsimonySet::TraceSegments(const char*)': ParsimonySet.h:429:35: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%s [", label); ^ ParsimonySet.h:431:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL(" %3d", segCounts[k]); ^ ParsimonySet.h:432:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("]\n"); ^ ParsInsert.cpp: At global scope: ParsInsert.cpp:92:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] char *statsName = "PI_Results.log"; ^~~~~~~~~~~~~~~~ ParsInsert.cpp:93:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] char *logFilename = "ParsInsert.log"; ^~~~~~~~~~~~~~~~ ParsInsert.cpp:94:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] char *treeFilename = "PI_Tree.tree"; ^~~~~~~~~~~~~~ ParsInsert.cpp:95:39: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] char *seqFilename = "PI_Tree.fasta"; ^~~~~~~~~~~~~~~ ParsInsert.cpp: In function 'int main(int, char**)': ParsInsert.cpp:247:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%s\n", COPYRIGHT); ^ ParsInsert.cpp:288:81: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Setting Tree Floating Point Precision to %d\n", v); ^ ParsInsert.cpp:388:73: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("invalid command option '%c'\n", argv[i][1]); ^ ParsInsert.cpp:411:58: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%s\nCommand Line:[%s]\n", VERSION, cmd.c_str()); ^ ParsInsert.cpp:415:54: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("ERROR - missing files to process\n"); ^ ParsInsert.cpp:416:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT(USAGE, VERSION, APPNAME); ^ ParsInsert.cpp:424:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL(" tree file: %s\n", treeFilename); ^ ParsInsert.cpp:429:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL(" tree sequence file: %s\n", seqFilename); ^ ParsInsert.cpp:434:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL(" mask file: %s\n", maskName); ^ ParsInsert.cpp:438:51: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Cannot open mask file [%s]", maskName); ^ ParsInsert.cpp:447:49: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL(" taxomony index file: %s\n", taxName); ^ ParsInsert.cpp:451:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Cannot open taxomony index FASTA file [%s]", taxName); ^ ParsInsert.cpp:455:77: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL(" taxomony index file: %d taxa\n", taxonomy->GetCount()); ^ ParsInsert.cpp:484:58: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Process Completed: %d sec\n", time(NULL)-start); ^ ParsInsert.cpp: In function 'int ParsimonyInsertion()': ParsInsert.cpp:532:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Reading Newick Tree: [%s]\n", treeFilename); ^ ParsInsert.cpp:537:73: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Error accessing Newick Tree file [%s]\n", treeFilename); ^ ParsInsert.cpp:541:112: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Newick Tree Read Completed: %d taxa, %d sec\n", (tree->nodeList.size()+1)/2, time(NULL)-stage); ^ ParsInsert.cpp:552:58: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Found duplicate name: [%s]/n", name.c_str()); ^ ParsInsert.cpp:558:58: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Tree Sequence Reading: [%s]\n", seqFilename); ^ ParsInsert.cpp:564:115: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Tree Sequence Read Completed: %d sequences, %d sec\n", treeSeqfile->seqlist.size(), time(NULL)-stage); ^ ParsInsert.cpp:567:65: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Reading sequences for insertion: [%s]\n", files[0]); ^ ParsInsert.cpp:573:50: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("No insertion sequences found\n"); ^ ParsInsert.cpp:576:115: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Insert Sequecne Read Completed: %d sequences, %d sec\n", insertSeqfile->GetCount(), time(NULL)-stage); ^ ParsInsert.cpp:579:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Checking Taxa Taxonomy\n"); ^ ParsInsert.cpp:581:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Setting Internal Taxonomy\n"); ^ ParsInsert.cpp:584:71: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Internal Taxonomy Completed: %d sec\n", time(NULL)-stage); ^ ParsInsert.cpp:587:58: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Setting internal parsimony sequences ...\n"); ^ ParsInsert.cpp:590:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Parsimony Calculation Completed: %d sec\n", time(NULL)-stage); ^ ParsInsert.cpp:595:84: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("[%d sec elapsed] Searching for insertion points:\n", time(NULL)-start); ^ ParsInsert.cpp:623:105: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("[%d sec elapsed] Insert Locations Completed: %d sec\n", time(NULL)-start, time(NULL)-stage); ^ ParsInsert.cpp:641:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Writing Newick tree file: [%s]\n", treename.c_str()); ^ ParsInsert.cpp:647:115: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("CalcCost calls[%d] = %d / %d (%d)\n", useCalcCost, nCalcCostFull, nCalcCost,nCalcCost-nCalcCostFull); ^ ParsInsert.cpp:649:97: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Insert Time = %d, %d per hour\n", insertTime, 3600 * inserts.size() / insertTime ); ^ ParsInsert.cpp: In function 'int CheckTreeSequences(CPTree*, CSequenceFile*)': ParsInsert.cpp:674:88: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Error accessing Tree Sequencefile [%s]\n", treeSeqfile->fname.c_str()); ^ ParsInsert.cpp:693:90: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("ERROR - tree member sequence is not available [%s]\n", name.c_str()); ^ ParsInsert.cpp: In function 'int CreateParsimonySets(const char*, CPTree*)': ParsInsert.cpp:711:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL(" parsimony index file: %s\n", parsName); ^ ParsInsert.cpp:715:77: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Cannot open parsimony index FASTA file [%s]", parsName); ^ ParsInsert.cpp:718:79: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL(" parsimony file: %d internal nodes\n", parsimony->GetCount()); ^ ParsInsert.cpp:755:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Calculating internal parsimony sequences ...\n"); ^ ParsInsert.cpp: In function 'CPTree* ReadNewickTree(const char*)': ParsInsert.cpp:861:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] Display("Could not open source file: [%s]\n", filename); ^ ParsInsert.cpp:870:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Opening file: %s\t...", filename); ^ ParsInsert.cpp:897:61: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] Display("Opening file: %s\tLines:%d", filename, linecount); ^ ParsInsert.cpp:902:51: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Parsing Newick file: %s\t...", filename); ^ ParsInsert.cpp: In function 'int CheckLeafTaxonomy(CPTree*)': ParsInsert.cpp:949:76: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%d of %d nodes are missing taxonomy\n\t", n, nodes.size()); ^ ParsInsert.cpp:955:84: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL(" %-12.12s%s", node->title.c_str(), (++count%8 == 0 ? "\n\t" :"")); ^ ParsInsert.cpp:957:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("\n"); ^ ParsInsert.cpp: In function 'int SetInternalTaxonomy(CPTree*)': ParsInsert.cpp:1091:81: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("\rSetting Internal Taxonomy %d nodes remaining ", nSeqRemaining); ^ ParsInsert.cpp:1099:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("\n"); ^ ParsInsert.cpp: In function 'void FindInsertLocations_Serial(CSequenceFile*, CPTree*, CSequenceFile*, CInsertPosArray&)': ParsInsert.cpp:1125:77: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("**** Sequence is already in core tree: %s\n", seq->name.c_str()); ^ ParsInsert.cpp:1132:68: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("**** Cannot find sequence for %s\n", seq->name.c_str()); ^ ParsInsert.cpp:1170:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] tax.c_str()); ^ ParsInsert.cpp:1187:156: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Searching for position to insert %d sequences in tree of %d nodes. {Setup: %d sec}\n", inserts.size(), tree->nodeList.size(), time(NULL)-start+1); ^ ParsInsert.cpp:1193:111: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("[%10d/%d] {%d sec} [%s]\n", count, tree->nodeList.size(), time(NULL)-start+1, node->title.c_str()); ^ ParsInsert.cpp:1224:84: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Insertion of %d sequences in [%d sec]\n", inserts.size(), finish-start+1); ^ ParsInsert.cpp: In function 'void FindInsertLocations(CSequenceFile*, CPNode*, CSequenceItem*, CInsertPos*)': ParsInsert.cpp:1244:60: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("**** Error: could not generate Parsimony Set\n"); ^ ParsInsert.cpp: In function 'void FindInsertLocations(CSequenceFile*, CPTree*, CSequenceFile*, CInsertPosArray&)': ParsInsert.cpp:1324:77: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("**** Sequence is already in core tree: %s\n", seq->name.c_str()); ^ ParsInsert.cpp:1331:68: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("**** Cannot find sequence for %s\n", seq->name.c_str()); ^ ParsInsert.cpp:1343:77: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("**** Cannot find sequence taxonomy for %s\n", seq->name.c_str()); ^ ParsInsert.cpp:1368:111: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("[%10d/%d] {%d sec} [%s]\n", count, insertSeqfile->seqCount, time(NULL)-start+1, seq->name.c_str()); ^ ParsInsert.cpp:1378:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] tax.c_str()); ^ ParsInsert.cpp:1384:83: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("(%d sec) [%5d skipped]\n", time(NULL)-start_item, nSeqRemaining); ^ ParsInsert.cpp:1386:54: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("(%d sec)\n", time(NULL)-start_item); ^ ParsInsert.cpp:1394:84: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Insertion of %d sequences in [%d sec]\n", inserts.size(), finish-start+1); ^ ParsInsert.cpp: In function 'void BuildScoreMatrix()': ParsInsert.cpp:1432:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("BAD BAD COMPUTER"); ^ ParsInsert.cpp: In function 'int CalcAncestorParsimony(CPTree*)': ParsInsert.cpp:1640:38: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("Calculating Parsimony ..."); ^ ParsInsert.cpp:1644:64: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("*** Cannot calc parsimony, no sequence file loaded"); ^ ParsInsert.cpp:1658:74: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Applying parsimonious selections back down the tree.\n"); ^ ParsInsert.cpp:1660:53: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%d nodes were modified\n", changes); ^ ParsInsert.cpp:1684:108: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("\nProcessed %d nodes in %d seconds, %.0f nodes per sec\n", tree->nodeList.size(), delta, npersec); ^ ParsInsert.cpp: In function 'int ForceNodeParsimony(CPNode*)': ParsInsert.cpp:1709:73: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("***** Child not found [%s]\n", node->title.c_str()); ^ ParsInsert.cpp: In function 'int CalcNodeParsimony(CPNode*)': ParsInsert.cpp:1748:65: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("***** Child not found [%s]\n", node->title.c_str()); ^ ParsInsert.cpp:1801:68: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("\rCalcParsimony %d nodes remaining ", nSeqRemaining); ^ ParsInsert.cpp: In function 'int WriteParsimonySet(CPNode*, CSequenceFile*)': ParsInsert.cpp:1829:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayT("\r %d nodes remaining to be written ", nSeqRemaining); ^ ParsInsert.cpp: In function 'void DisplayInsertLocations(CInsertPosArray&, int)': ParsInsert.cpp:1880:96: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("======================================================================\n"); ^ ParsInsert.cpp:1884:61: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] inserts[i]->best.list.size(), tax.c_str()); ^ ParsInsert.cpp:1892:48: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("\tNO MATCHES found\n"); ^ ParsInsert.cpp:1942:77: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] iterB->node->title.c_str(), taxBest.c_str()); ^ ParsInsert.cpp:1978:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 0); ^ ParsInsert.cpp:1989:81: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%12.12s\t Seq[%s]\n", marker.c_str(), tax.c_str()); ^ ParsInsert.cpp:1990:70: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%12.12s\t [%s]\n", "", diff.c_str()); ^ ParsInsert.cpp:1991:73: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%12.12s\t Best[%s]\n", "", taxBest.c_str()); ^ ParsInsert.cpp:1993:67: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("\tFirst[%s]\n", taxFirst.c_str()); ^ ParsInsert.cpp: In function 'void DisplayBestInsertLocations(CInsertPos*, int)': ParsInsert.cpp:2010:88: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("======================================================================\n"); ^ ParsInsert.cpp:2013:86: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] item->seq->name.c_str(), item->nSites, item->best.list.size(), tax.c_str()); ^ ParsInsert.cpp:2021:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("\tNO MATCHES found\n"); ^ ParsInsert.cpp:2072:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] iterB->node->title.c_str(), taxBest.c_str()); ^ ParsInsert.cpp:2107:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 0); ^ ParsInsert.cpp:2118:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%12.12s\t Seq[%s]\n", marker.c_str(), tax.c_str()); ^ ParsInsert.cpp:2119:58: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%12.12s\t [%s]\n", "", diff.c_str()); ^ ParsInsert.cpp:2120:61: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%12.12s\t Best[%s]\n", "", taxBest.c_str()); ^ ParsInsert.cpp:2122:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("\tFirst[%s]\n", taxFirst.c_str()); ^ ParsInsert.cpp: In function 'void DisplayRankCounts(const char*, int (*)[4])': ParsInsert.cpp:2134:109: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("\n%s\n _________Precision________ __________Recall__________\n", header); ^ ParsInsert.cpp:2142:91: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] rankNames[r], counts[r][0], counts[r][1], per, counts[r][3], counts[r][2], per2); ^ ParsInsert.cpp: In function 'void OutputInsertLocations(CInsertPosArray&, int)': ParsInsert.cpp:2182:92: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("======================================================================\n"); ^ ParsInsert.cpp:2183:90: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("\nInsertion: [%20.20s] [%5d sites]\n", name.c_str(), inserts[i]->nSites); ^ ParsInsert.cpp:2187:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("\tNO MATCHES found\n"); ^ ParsInsert.cpp:2231:117: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("\t\t%5d [%5f] [%s][%s]\n", iterB->score, dist, iterB->node->title.c_str(), iterB->tax.c_str()); ^ ParsInsert.cpp:2261:118: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("\t\t%5d [%3d%%] [%s][%s]\n", iterB->score, per, iterB->node->title.c_str(), iterB->tax.c_str()); ^ ParsInsert.cpp:2268:111: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] iterB->node->title.c_str(),(iterB->node->IsBranchNode()?'^':' '), taxBest.c_str()); ^ ParsInsert.cpp:2307:64: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] cost, diffs, parts, indel, taxBest.c_str()); ^ ParsInsert.cpp:2324:71: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%18s[%s]\n", leader.c_str(), taxVoteList[knox].c_str()); ^ ParsInsert.cpp:2331:60: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("%18s[%s]\n", leader.c_str(), taxBest.c_str()); ^ ParsInsert.cpp:2353:73: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("no assignment (%d%% < %d%%)", per, scoreThresh); ^ ParsInsert.cpp:2363:72: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL(" Correct Taxonomy:[%s]\n", taxCorrect.c_str()); ^ ParsInsert.cpp:2407:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Taxonomies List:\n"); ^ ParsInsert.cpp: In function 'int BuildInsertTree(CTreeInserts*, CPTree*)': ParsInsert.cpp:2647:107: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("[%s] at %d%% does not meet threshold (%d%%)\n", in->seq->name.c_str(), score, 100-scoreThresh); ^ ParsInsert.cpp: In function 'int SetMyTaxonomy(CPNode*)': ParsInsert.cpp:2804:89: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("No Taxnomy for [%s][%s]\n", name.c_str(), child->title.c_str()); ^ ParsInsert.cpp:2810:85: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("No Taxnomy for [%s][%s]\n", name.c_str(), child->title.c_str()); ^ ParsInsert.cpp:2834:80: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("No Taxnomy for [%s][%s]\n", name.c_str(), node->title.c_str()); ^ ParsInsert.cpp: In function 'double ComparePosition(const char*, CPNode*, CPTree*, CPTree*)': ParsInsert.cpp:3011:93: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Could not find core position for [%s][%s]\n", core1.c_str(), core2.c_str()); ^ ParsInsert.cpp: In function 'void ComparePositions(CInsertPosArray&, CPTree*, CPTree*)': ParsInsert.cpp:3036:92: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("======================================================================\n"); ^ ParsInsert.cpp:3037:112: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("\nDistance to Insertion: [%20.20s] [%5d sites]\n", name.c_str(), inserts[i]->best.list.size()); ^ ParsInsert.cpp:3041:67: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("\tNO MATCHES found for [%s]\n", name.c_str()); ^ ParsInsert.cpp:3054:83: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("\tDistance error from [%20.20s] = %d\n", pname.c_str(), dist); ^ ParsInsert.cpp: In function 'int FullTree_Initialization()': ParsInsert.cpp:3069:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Reading Newick Tree: [%s]\n", fullTreeName); ^ ParsInsert.cpp:3073:73: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Error accessing Newick Tree file [%s]\n", fullTreeName); ^ ParsInsert.cpp:3077:86: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] DisplayL("Newick Tree Read Completed: %d taxa\n", (fullTree->nodeList.size()+1)/2); ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/parsinsert-1.04=. -fstack-protector-strong -Wformat -Werror=format-security -o ParsInsert AttrList.o Knox_Stddef.o PNode.o SeqList.o Taxonomy.o ParsInsert.o -lm -lc -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/parsinsert-1.04' mv ParsInsert parsinsert make[1]: Leaving directory '/build/parsinsert-1.04' debian/rules override_dh_auto_test make[1]: Entering directory '/build/parsinsert-1.04' echo "Upstream tarball lacks Test.cpp so we can not run the test." Upstream tarball lacks Test.cpp so we can not run the test. make[1]: Leaving directory '/build/parsinsert-1.04' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/parsinsert/usr/bin/parsinsert contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'parsinsert-dbgsym' in '../parsinsert-dbgsym_1.04-4_armhf.deb'. dpkg-deb: building package 'parsinsert' in '../parsinsert_1.04-4_armhf.deb'. dpkg-deb: building package 'parsinsert-testdata' in '../parsinsert-testdata_1.04-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../parsinsert_1.04-4_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/5621 and its subdirectories I: Current time: Fri May 22 12:07:19 -12 2020 I: pbuilder-time-stamp: 1590192440 Sat May 23 00:07:37 UTC 2020 I: 1st build successful. Starting 2nd build on remote node opi2b-armhf-rb.debian.net. Sat May 23 00:07:37 UTC 2020 I: Preparing to do remote build '2' on opi2b-armhf-rb.debian.net. Sat May 23 00:18:17 UTC 2020 I: Deleting $TMPDIR on opi2b-armhf-rb.debian.net. Sat May 23 00:18:20 UTC 2020 I: parsinsert_1.04-4_armhf.changes: Format: 1.8 Date: Sun, 23 Sep 2018 22:58:01 +0200 Source: parsinsert Binary: parsinsert parsinsert-dbgsym parsinsert-testdata Architecture: armhf all Version: 1.04-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: parsinsert - Parsimonious Insertion of unclassified sequences into phylogeneti parsinsert-testdata - Test data for parsinsert Changes: parsinsert (1.04-4) unstable; urgency=medium . * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 Checksums-Sha1: 14fe3dab51c90da882956a6be0102d20078ee605 799316 parsinsert-dbgsym_1.04-4_armhf.deb d08c0b3751186cc5de240b3ad4beca2e6c9c2d10 4138624 parsinsert-testdata_1.04-4_all.deb f55025e0c0be64837b637956f802c4b744d52955 4785 parsinsert_1.04-4_armhf.buildinfo 33f44cbf7c2a1cc10fbe4b1dd45d9d15b94707a5 53856 parsinsert_1.04-4_armhf.deb Checksums-Sha256: 31fae827d310e654f0e1d49c7d7586a6cfbc8609fac9aaef59ad9139cd666ff0 799316 parsinsert-dbgsym_1.04-4_armhf.deb 68dae6353a09b1f03202ea006e43e94e963d690cd03cd4d49f77f9234b92180f 4138624 parsinsert-testdata_1.04-4_all.deb 4abb9f8a1453075471573585e62fac40c10f7c5a8fd39b718348d93938b3f357 4785 parsinsert_1.04-4_armhf.buildinfo 993a17528096eee2fb77e65ce18e338ecf93777be7d1df5f790e9a2fac7e646c 53856 parsinsert_1.04-4_armhf.deb Files: 00b4ce100fdf369f2b4df1c23ac1ca16 799316 debug optional parsinsert-dbgsym_1.04-4_armhf.deb a87e80b07798752cf40fd82369041f44 4138624 science optional parsinsert-testdata_1.04-4_all.deb 976a3a0d7390a8b4036e3f8845c589b5 4785 science optional parsinsert_1.04-4_armhf.buildinfo e8e9f51d45c5bc0db214a39bd11309a9 53856 science optional parsinsert_1.04-4_armhf.deb Sat May 23 00:18:22 UTC 2020 I: diffoscope 144 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.9uHTrYZdud/parsinsert_1.04-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.9uHTrYZdud/parsinsert_1.04-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.9uHTrYZdud/parsinsert_1.04-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.9uHTrYZdud/b1/parsinsert_1.04-4_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.9uHTrYZdud/b2/parsinsert_1.04-4_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.604s) 0.604s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.217s) 0.217s 10 calls diffoscope.comparators.binary.FilesystemFile Sat May 23 00:23:58 UTC 2020 I: diffoscope 144 found no differences in the changes files, and a .buildinfo file also exists. Sat May 23 00:23:58 UTC 2020 I: parsinsert from buster built successfully and reproducibly on armhf. Sat May 23 00:24:00 UTC 2020 I: Submitting .buildinfo files to external archives: Sat May 23 00:24:00 UTC 2020 I: Submitting 8.0K b1/parsinsert_1.04-4_armhf.buildinfo.asc Sat May 23 00:24:01 UTC 2020 I: Submitting 8.0K b2/parsinsert_1.04-4_armhf.buildinfo.asc Sat May 23 00:24:02 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 23 00:24:02 UTC 2020 I: Done submitting .buildinfo files. Sat May 23 00:24:02 UTC 2020 I: Removing signed parsinsert_1.04-4_armhf.buildinfo.asc files: removed './b1/parsinsert_1.04-4_armhf.buildinfo.asc' removed './b2/parsinsert_1.04-4_armhf.buildinfo.asc'