{"app_name":"Debian Janitor","binary_packages":[],"branch_url":"git+ssh://git@salsa.debian.org/med-team/sideretro.git","build_log_highlight_lines":[1434,1435,1436,1437,1438,1439,1440,1441,1442,1443,1444,1507,1508,1509,1510,1511,1654,1655,1656,1657,1658,1659,1660,1661,1662,1663,1664,1727,1728,1729,1730,1731,1749,1750,1751,1791],"build_log_include_lines":[1776,1791],"build_log_line_count":1791,"build_log_name":"build.log","campaign":"lintian-fixes","change_set":"78e6644a-220b-49f9-8976-4648d26c4474","codebase":"sideretro","codemod_log_name":"codemod.log","command":"DEB_UPDATE_CHANGELOG=auto lintian-brush","current_year":"2026","description":"Unidentified error: ","failure_excerpt":{"full_log_url":"/lintian-fixes/c/sideretro/78e6644a-220b-49f9-8976-4648d26c4474/logs/build.log","highlighted_indices":[604],"lines":["","","Unpack source","-------------","","Format: 3.0 (quilt)","Source: sideretro","Binary: sideretro","Architecture: any","Version: 1.1.6-4~jan+lint1","Maintainer: Debian Med Packaging Team ","Uploaders: Daniela Moreira Mombach ","Homepage: https://github.com/galantelab/sideRETRO","Standards-Version: 4.7.4","Vcs-Browser: https://salsa.debian.org/med-team/sideretro","Vcs-Git: https://salsa.debian.org/med-team/sideretro.git","Build-Depends: check , cmake, debhelper-compat (= 13), libhts-dev, libsqlite3-dev, meson, pkgconf, python3-sphinx , zlib1g-dev","Package-List:"," sideretro deb science optional arch=any","Checksums-Sha1:"," 20a0572585b0b16ca71ed76b08b8fcbce3f33aca 2109112 sideretro_1.1.6.orig.tar.gz"," 720aa3d2cfe8a6d2b0c984123c4db57bd4a72ea7 7608 sideretro_1.1.6-4~jan+lint1.debian.tar.xz","Checksums-Sha256:"," 378b49030bef1627494c81bbd285d85f3b78843f691f68963bd6e703ae7bac20 2109112 sideretro_1.1.6.orig.tar.gz"," 46b732f4bc1c460c3b02df4c433fdd2fe1d5aaf3c5abff887b6f281e73d4f9b8 7608 sideretro_1.1.6-4~jan+lint1.debian.tar.xz","Files:"," 2ee5b04044bcce8eda2bd8e5bfaa7ea9 2109112 sideretro_1.1.6.orig.tar.gz"," 78308a73b01249278fa138e09bb56b2e 7608 sideretro_1.1.6-4~jan+lint1.debian.tar.xz","","dpkg-source: warning: extracting unsigned source package (sideretro_1.1.6-4~jan+lint1.dsc)","dpkg-source: info: extracting sideretro in /build/reproducible-path/sideretro-1.1.6","dpkg-source: info: unpacking sideretro_1.1.6.orig.tar.gz","dpkg-source: info: unpacking sideretro_1.1.6-4~jan+lint1.debian.tar.xz","","clean up apt cache","------------------","","","Check disk space","----------------","","Sufficient free space for build","","User Environment","----------------","","APT_CONFIG=/var/lib/sbuild/apt.conf","HOME=/sbuild-nonexistent","LANG=C.UTF-8","LC_ALL=C.UTF-8","LOGNAME=sbuild","PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games","SHELL=/bin/sh","SOURCE_DATE_EPOCH=1782656306","USER=sbuild","","dpkg-buildpackage","-----------------","","Command: dpkg-buildpackage --sanitize-env -us -uc","dpkg-buildpackage: info: source package sideretro","dpkg-buildpackage: info: source version 1.1.6-4~jan+lint1","dpkg-buildpackage: info: source distribution lintian-fixes","dpkg-buildpackage: info: source changed by Debian Janitor "," dpkg-source --before-build .","dpkg-buildpackage: info: host architecture amd64"," debian/rules clean","dh clean"," dh_clean"," dpkg-source -b .","dpkg-source: info: using source format '3.0 (quilt)'","dpkg-source: info: building sideretro using existing ../sideretro_1.1.6.orig.tar.gz","dpkg-source: info: building sideretro in ../sideretro_1.1.6-4~jan+lint1.debian.tar.xz","dpkg-source: info: building sideretro in ../sideretro_1.1.6-4~jan+lint1.dsc"," debian/rules binary","dh binary"," dh_update_autotools_config"," dh_autoreconf"," dh_auto_configure","\tcd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu -Dpython.bytecompile=-1","The Meson build system","Version: 1.11.1","Source dir: /build/reproducible-path/sideretro-1.1.6","Build dir: /build/reproducible-path/sideretro-1.1.6/obj-x86_64-linux-gnu","Build type: native build","Project name: sideRETRO","Project version: 1.1.6","C compiler for the host machine: cc (gcc 15.3.0 \"cc (Debian 15.3.0-1) 15.3.0\")","C linker for the host machine: cc ld.bfd 2.46.50.20260617","Host machine cpu family: x86_64","Host machine cpu: x86_64","Configuring config.h.in using configuration","Library m found: YES","Library dl found: YES","Run-time dependency threads found: YES","Found pkg-config: YES (/usr/bin/pkg-config) 2.5.1","Run-time dependency zlib found: YES 1.3.2","Run-time dependency sqlite3 found: YES 3.53.3","Run-time dependency htslib found: YES 1.22.1","Run-time dependency check found: YES 0.15.2","Program sphinx-build found: YES (/usr/bin/sphinx-build)","Message: Generate man page alongside the executable","Build targets in project: 5","","sideRETRO 1.1.6",""," User defined options"," buildtype : plain"," libdir : lib/x86_64-linux-gnu"," localstatedir : /var"," prefix : /usr"," python.bytecompile: -1"," sysconfdir : /etc"," wrap_mode : nodownload","","Found ninja-1.13.2 at /usr/bin/ninja"," dh_auto_build","\tcd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v","[1/70] /usr/bin/meson --internal vcstagger config.h.in config.h 1.1.6 /build/reproducible-path/sideretro-1.1.6 @version@ '(.*)' git describe --tags --dirty=+","[2/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/array.c.o -MF src/libsider.a.p/array.c.o.d -o src/libsider.a.p/array.c.o -c ../src/array.c","[3/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/bed.c.o -MF src/libsider.a.p/bed.c.o.d -o src/libsider.a.p/bed.c.o -c ../src/bed.c","[4/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/abnormal.c.o -MF src/libsider.a.p/abnormal.c.o.d -o src/libsider.a.p/abnormal.c.o -c ../src/abnormal.c","[5/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/blacklist.c.o -MF src/libsider.a.p/blacklist.c.o.d -o src/libsider.a.p/blacklist.c.o -c ../src/blacklist.c","[6/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/bitree.c.o -MF src/libsider.a.p/bitree.c.o.d -o src/libsider.a.p/bitree.c.o -c ../src/bitree.c","[7/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/chr.c.o -MF src/libsider.a.p/chr.c.o.d -o src/libsider.a.p/chr.c.o -c ../src/chr.c","[8/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/correlation.c.o -MF src/libsider.a.p/correlation.c.o.d -o src/libsider.a.p/correlation.c.o -c ../src/correlation.c","[9/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/cluster.c.o -MF src/libsider.a.p/cluster.c.o.d -o src/libsider.a.p/cluster.c.o -c ../src/cluster.c","[10/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/dbscan.c.o -MF src/libsider.a.p/dbscan.c.o.d -o src/libsider.a.p/dbscan.c.o -c ../src/dbscan.c","[11/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/db_merge.c.o -MF src/libsider.a.p/db_merge.c.o.d -o src/libsider.a.p/db_merge.c.o -c ../src/db_merge.c","[12/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/db.c.o -MF src/libsider.a.p/db.c.o.d -o src/libsider.a.p/db.c.o -c ../src/db.c","[13/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/exon.c.o -MF src/libsider.a.p/exon.c.o.d -o src/libsider.a.p/exon.c.o -c ../src/exon.c","[14/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/dedup.c.o -MF src/libsider.a.p/dedup.c.o.d -o src/libsider.a.p/dedup.c.o -c ../src/dedup.c","[15/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/fasta.c.o -MF src/libsider.a.p/fasta.c.o.d -o src/libsider.a.p/fasta.c.o -c ../src/fasta.c","[16/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/gz.c.o -MF src/libsider.a.p/gz.c.o.d -o src/libsider.a.p/gz.c.o -c ../src/gz.c","[17/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/gff.c.o -MF src/libsider.a.p/gff.c.o.d -o src/libsider.a.p/gff.c.o -c ../src/gff.c","[18/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/genotype.c.o -MF src/libsider.a.p/genotype.c.o.d -o src/libsider.a.p/genotype.c.o -c ../src/genotype.c","[19/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/io.c.o -MF src/libsider.a.p/io.c.o.d -o src/libsider.a.p/io.c.o -c ../src/io.c","[20/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/ibitree.c.o -MF src/libsider.a.p/ibitree.c.o.d -o src/libsider.a.p/ibitree.c.o -c ../src/ibitree.c","[21/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/hash.c.o -MF src/libsider.a.p/hash.c.o.d -o src/libsider.a.p/hash.c.o -c ../src/hash.c","[22/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/list.c.o -MF src/libsider.a.p/list.c.o.d -o src/libsider.a.p/list.c.o -c ../src/list.c","[23/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/log.c.o -MF src/libsider.a.p/log.c.o.d -o src/libsider.a.p/log.c.o -c ../src/log.c","[24/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/logger.c.o -MF src/libsider.a.p/logger.c.o.d -o src/libsider.a.p/logger.c.o -c ../src/logger.c","[25/70] /usr/bin/sphinx-build -b man /build/reproducible-path/sideretro-1.1.6/docs /build/reproducible-path/sideretro-1.1.6/obj-x86_64-linux-gnu/docs","Running Sphinx v9.1.0","WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English).","loading translations [en]... done","Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.","building [mo]: targets for 0 po files that are out of date","writing output... ","building [man]: all manpages","updating environment: [new config] 8 added, 0 changed, 0 removed","reading sources... [ 12%] authors","reading sources... [ 25%] index","reading sources... [ 38%] install","reading sources... [ 50%] intro","reading sources... [ 62%] method","reading sources... [ 75%] result","reading sources... [ 88%] retrocopy","reading sources... [100%] usage","","looking for now-outdated files... none found","pickling environment... done","checking consistency... /build/reproducible-path/sideretro-1.1.6/docs/index.rst: WARNING: document isn't included in any toctree [toc.not_included]","done","preparing documents... done","copying assets... ","copying assets: done","writing... sider.1 { ","} done","build succeeded, 2 warnings.","","The manual pages are in docs.","[26/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/make_vcf.c.o -MF src/libsider.a.p/make_vcf.c.o.d -o src/libsider.a.p/make_vcf.c.o -c ../src/make_vcf.c","[27/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/sam.c.o -MF src/libsider.a.p/sam.c.o.d -o src/libsider.a.p/sam.c.o -c ../src/sam.c","[28/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/merge_call.c.o -MF src/libsider.a.p/merge_call.c.o.d -o src/libsider.a.p/merge_call.c.o -c ../src/merge_call.c","[29/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/process_sample.c.o -MF src/libsider.a.p/process_sample.c.o.d -o src/libsider.a.p/process_sample.c.o -c ../src/process_sample.c","[30/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/retrocopy.c.o -MF src/libsider.a.p/retrocopy.c.o.d -o src/libsider.a.p/retrocopy.c.o -c ../src/retrocopy.c","[31/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/set.c.o -MF src/libsider.a.p/set.c.o.d -o src/libsider.a.p/set.c.o -c ../src/set.c","[32/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/str.c.o -MF src/libsider.a.p/str.c.o.d -o src/libsider.a.p/str.c.o -c ../src/str.c","[33/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/thpool.c.o -MF src/libsider.a.p/thpool.c.o.d -o src/libsider.a.p/thpool.c.o -c ../src/thpool.c","[34/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/utils.c.o -MF src/libsider.a.p/utils.c.o.d -o src/libsider.a.p/utils.c.o -c ../src/utils.c","[35/70] cc -Isrc/sider.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ src/sider.p/main.c.o -MF src/sider.p/main.c.o.d -o src/sider.p/main.c.o -c ../src/main.c","[36/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/vcf.c.o -MF src/libsider.a.p/vcf.c.o.d -o src/libsider.a.p/vcf.c.o -c ../src/vcf.c","[37/70] cc -Isrc/libsider.a.p -Isrc -I../src -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -MD -MQ src/libsider.a.p/wrapper.c.o -MF src/libsider.a.p/wrapper.c.o.d -o src/libsider.a.p/wrapper.c.o -c ../src/wrapper.c","[38/70] rm -f src/libsider.a && gcc-ar csrDT src/libsider.a src/libsider.a.p/abnormal.c.o src/libsider.a.p/array.c.o src/libsider.a.p/bed.c.o src/libsider.a.p/bitree.c.o src/libsider.a.p/blacklist.c.o src/libsider.a.p/chr.c.o src/libsider.a.p/cluster.c.o src/libsider.a.p/correlation.c.o src/libsider.a.p/db.c.o src/libsider.a.p/db_merge.c.o src/libsider.a.p/dbscan.c.o src/libsider.a.p/dedup.c.o src/libsider.a.p/exon.c.o src/libsider.a.p/fasta.c.o src/libsider.a.p/genotype.c.o src/libsider.a.p/gff.c.o src/libsider.a.p/gz.c.o src/libsider.a.p/hash.c.o src/libsider.a.p/ibitree.c.o src/libsider.a.p/io.c.o src/libsider.a.p/list.c.o src/libsider.a.p/log.c.o src/libsider.a.p/logger.c.o src/libsider.a.p/make_vcf.c.o src/libsider.a.p/merge_call.c.o src/libsider.a.p/process_sample.c.o src/libsider.a.p/retrocopy.c.o src/libsider.a.p/sam.c.o src/libsider.a.p/set.c.o src/libsider.a.p/str.c.o src/libsider.a.p/thpool.c.o src/libsider.a.p/utils.c.o src/libsider.a.p/vcf.c.o src/libsider.a.p/wrapper.c.o","[39/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_abnormal.c.o -MF tests/check_sider.p/check_sider_abnormal.c.o.d -o tests/check_sider.p/check_sider_abnormal.c.o -c ../tests/check_sider_abnormal.c","[40/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_bed.c.o -MF tests/check_sider.p/check_sider_bed.c.o.d -o tests/check_sider.p/check_sider_bed.c.o -c ../tests/check_sider_bed.c","[41/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_bitree.c.o -MF tests/check_sider.p/check_sider_bitree.c.o.d -o tests/check_sider.p/check_sider_bitree.c.o -c ../tests/check_sider_bitree.c","[42/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_array.c.o -MF tests/check_sider.p/check_sider_array.c.o.d -o tests/check_sider.p/check_sider_array.c.o -c ../tests/check_sider_array.c","[43/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_chr.c.o -MF tests/check_sider.p/check_sider_chr.c.o.d -o tests/check_sider.p/check_sider_chr.c.o -c ../tests/check_sider_chr.c","[44/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_blacklist.c.o -MF tests/check_sider.p/check_sider_blacklist.c.o.d -o tests/check_sider.p/check_sider_blacklist.c.o -c ../tests/check_sider_blacklist.c","[45/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_cluster.c.o -MF tests/check_sider.p/check_sider_cluster.c.o.d -o tests/check_sider.p/check_sider_cluster.c.o -c ../tests/check_sider_cluster.c","[46/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_correlation.c.o -MF tests/check_sider.p/check_sider_correlation.c.o.d -o tests/check_sider.p/check_sider_correlation.c.o -c ../tests/check_sider_correlation.c","[47/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_db_merge.c.o -MF tests/check_sider.p/check_sider_db_merge.c.o.d -o tests/check_sider.p/check_sider_db_merge.c.o -c ../tests/check_sider_db_merge.c","[48/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_db.c.o -MF tests/check_sider.p/check_sider_db.c.o.d -o tests/check_sider.p/check_sider_db.c.o -c ../tests/check_sider_db.c","[49/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_dbscan.c.o -MF tests/check_sider.p/check_sider_dbscan.c.o.d -o tests/check_sider.p/check_sider_dbscan.c.o -c ../tests/check_sider_dbscan.c","[50/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_dedup.c.o -MF tests/check_sider.p/check_sider_dedup.c.o.d -o tests/check_sider.p/check_sider_dedup.c.o -c ../tests/check_sider_dedup.c","[51/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_genotype.c.o -MF tests/check_sider.p/check_sider_genotype.c.o.d -o tests/check_sider.p/check_sider_genotype.c.o -c ../tests/check_sider_genotype.c","[52/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_fasta.c.o -MF tests/check_sider.p/check_sider_fasta.c.o.d -o tests/check_sider.p/check_sider_fasta.c.o -c ../tests/check_sider_fasta.c","[53/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_exon.c.o -MF tests/check_sider.p/check_sider_exon.c.o.d -o tests/check_sider.p/check_sider_exon.c.o -c ../tests/check_sider_exon.c","[54/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_gff.c.o -MF tests/check_sider.p/check_sider_gff.c.o.d -o tests/check_sider.p/check_sider_gff.c.o -c ../tests/check_sider_gff.c","[55/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_gz.c.o -MF tests/check_sider.p/check_sider_gz.c.o.d -o tests/check_sider.p/check_sider_gz.c.o -c ../tests/check_sider_gz.c","[56/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_ibitree.c.o -MF tests/check_sider.p/check_sider_ibitree.c.o.d -o tests/check_sider.p/check_sider_ibitree.c.o -c ../tests/check_sider_ibitree.c","[57/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_io.c.o -MF tests/check_sider.p/check_sider_io.c.o.d -o tests/check_sider.p/check_sider_io.c.o -c ../tests/check_sider_io.c","[58/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_process_sample.c.o -MF tests/check_sider.p/check_sider_process_sample.c.o.d -o tests/check_sider.p/check_sider_process_sample.c.o -c ../tests/check_sider_process_sample.c","[59/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_main.c.o -MF tests/check_sider.p/check_sider_main.c.o.d -o tests/check_sider.p/check_sider_main.c.o -c ../tests/check_sider_main.c","[60/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_hash.c.o -MF tests/check_sider.p/check_sider_hash.c.o.d -o tests/check_sider.p/check_sider_hash.c.o -c ../tests/check_sider_hash.c","[61/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_retrocopy.c.o -MF tests/check_sider.p/check_sider_retrocopy.c.o.d -o tests/check_sider.p/check_sider_retrocopy.c.o -c ../tests/check_sider_retrocopy.c","[62/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_list.c.o -MF tests/check_sider.p/check_sider_list.c.o.d -o tests/check_sider.p/check_sider_list.c.o -c ../tests/check_sider_list.c","[63/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_sam.c.o -MF tests/check_sider.p/check_sider_sam.c.o.d -o tests/check_sider.p/check_sider_sam.c.o -c ../tests/check_sider_sam.c","[64/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_vcf.c.o -MF tests/check_sider.p/check_sider_vcf.c.o.d -o tests/check_sider.p/check_sider_vcf.c.o -c ../tests/check_sider_vcf.c","[65/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_str.c.o -MF tests/check_sider.p/check_sider_str.c.o.d -o tests/check_sider.p/check_sider_str.c.o -c ../tests/check_sider_str.c","[66/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_set.c.o -MF tests/check_sider.p/check_sider_set.c.o.d -o tests/check_sider.p/check_sider_set.c.o -c ../tests/check_sider_set.c","[67/70] cc -o src/sider src/sider.p/main.c.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group src/libsider.a -pthread /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so -lm -ldl -Wl,--end-group","[68/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_utils.c.o -MF tests/check_sider.p/check_sider_utils.c.o.d -o tests/check_sider.p/check_sider_utils.c.o -c ../tests/check_sider_utils.c","[69/70] cc -Itests/check_sider.p -Itests -I../tests -I. -I.. -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -DHAVE_CONFIG_H -D_GNU_SOURCE -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -MD -MQ tests/check_sider.p/check_sider_wrapper.c.o -MF tests/check_sider.p/check_sider_wrapper.c.o.d -o tests/check_sider.p/check_sider_wrapper.c.o -c ../tests/check_sider_wrapper.c","../tests/check_sider_wrapper.c: In function ‘test_xfprintf_fn’:","../tests/check_sider_wrapper.c:281:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]"," 281 | fread (buf, sizeof (char), str_size, fp);"," | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~","../tests/check_sider_wrapper.c: In function ‘test_xfflush_fn’:","../tests/check_sider_wrapper.c:180:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]"," 180 | fread (buf, sizeof (char), str_size, fp);"," | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~","[70/70] cc -o tests/check_sider tests/check_sider.p/check_sider_abnormal.c.o tests/check_sider.p/check_sider_array.c.o tests/check_sider.p/check_sider_bed.c.o tests/check_sider.p/check_sider_bitree.c.o tests/check_sider.p/check_sider_blacklist.c.o tests/check_sider.p/check_sider_chr.c.o tests/check_sider.p/check_sider_cluster.c.o tests/check_sider.p/check_sider_correlation.c.o tests/check_sider.p/check_sider_db.c.o tests/check_sider.p/check_sider_db_merge.c.o tests/check_sider.p/check_sider_dbscan.c.o tests/check_sider.p/check_sider_dedup.c.o tests/check_sider.p/check_sider_exon.c.o tests/check_sider.p/check_sider_fasta.c.o tests/check_sider.p/check_sider_genotype.c.o tests/check_sider.p/check_sider_gff.c.o tests/check_sider.p/check_sider_gz.c.o tests/check_sider.p/check_sider_hash.c.o tests/check_sider.p/check_sider_ibitree.c.o tests/check_sider.p/check_sider_io.c.o tests/check_sider.p/check_sider_list.c.o tests/check_sider.p/check_sider_main.c.o tests/check_sider.p/check_sider_process_sample.c.o tests/check_sider.p/check_sider_retrocopy.c.o tests/check_sider.p/check_sider_sam.c.o tests/check_sider.p/check_sider_set.c.o tests/check_sider.p/check_sider_str.c.o tests/check_sider.p/check_sider_utils.c.o tests/check_sider.p/check_sider_vcf.c.o tests/check_sider.p/check_sider_wrapper.c.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group src/libsider.a -pthread /usr/lib/x86_64-linux-gnu/libsqlite3.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so -lm -ldl /usr/lib/x86_64-linux-gnu/libcheck_pic.a -lrt /usr/lib/x86_64-linux-gnu/libsubunit.so -Wl,--end-group"," dh_auto_test","\tcd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=4 meson test --verbose","ninja: Entering directory `/build/reproducible-path/sideretro-1.1.6/obj-x86_64-linux-gnu'","[1/65] Generating config.h with a custom command","1/1 sideRETRO:all RUNNING ",">>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=221 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/sideretro-1.1.6/obj-x86_64-linux-gnu/tests/check_sider","――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――","Running suite(s): ProcessSample","ok 1 - ../tests/check_sider_process_sample.c:Core:test_sider: Passed"," List","ok 2 - ../tests/check_sider_list.c:Core:test_list_new: Passed","ok 3 - ../tests/check_sider_list.c:Core:test_list_ins_prev: Passed","ok 4 - ../tests/check_sider_list.c:Core:test_list_ins_next: Passed","ok 5 - ../tests/check_sider_list.c:Core:test_list_ins_prev_link: Passed","ok 6 - ../tests/check_sider_list.c:Core:test_list_ins_next_link: Passed","ok 7 - ../tests/check_sider_list.c:Core:test_list_remove: Passed","ok 8 - ../tests/check_sider_list.c:Core:test_list_remove_link: Passed","ok 9 - ../tests/check_sider_list.c:Core:test_list_foreach: Passed"," Hash","ok 10 - ../tests/check_sider_hash.c:Core:test_hash_free: Passed","ok 11 - ../tests/check_sider_hash.c:Core:test_hash_insert: Passed","ok 12 - ../tests/check_sider_hash.c:Core:test_hash_lookup: Passed","ok 13 - ../tests/check_sider_hash.c:Core:test_hash_replace: Passed","ok 14 - ../tests/check_sider_hash.c:Core:test_hash_remove: Passed","ok 15 - ../tests/check_sider_hash.c:Core:test_hash_contains: Passed","ok 16 - ../tests/check_sider_hash.c:Core:test_hash_int: Passed","ok 17 - ../tests/check_sider_hash.c:Core:test_hash_direct: Passed","ok 18 - ../tests/check_sider_hash.c:Core:test_hash_many_insertions: Passed","ok 19 - ../tests/check_sider_hash.c:Misc:test_hash_foreach: Passed","ok 20 - ../tests/check_sider_hash.c:Misc:test_hash_iter: Passed","ok 21 - ../tests/check_sider_hash.c:Misc:test_hash_get_keys_as_list: Passed","ok 22 - ../tests/check_sider_hash.c:Misc:test_hash_get_values_as_list: Passed","ok 23 - ../tests/check_sider_hash.c:Misc:test_hash_get_keys_as_array: Passed","ok 24 - ../tests/check_sider_hash.c:Misc:test_hash_get_values_as_array: Passed"," Array","ok 25 - ../tests/check_sider_array.c:CoreFree:test_array: Passed","ok 26 - ../tests/check_sider_array.c:CoreFree:test_array_uniq: Passed","ok 27 - ../tests/check_sider_array.c:CoreFree:test_array_find_with_equal_fun: Passed","ok 28 - ../tests/check_sider_array.c:CoreNull:test_array_find: Passed","ok 29 - ../tests/check_sider_array.c:CoreNull:test_array_remove: Passed","ok 30 - ../tests/check_sider_array.c:CoreNull:test_array_remove_index: Passed","ok 31 - ../tests/check_sider_array.c:Free:test_array_no_free_segment: Passed"," Utils","ok 32 - ../tests/check_sider_utils.c:Core:test_fequal: Passed","ok 33 - ../tests/check_sider_utils.c:Core:test_equalstring: Passed","ok 34 - ../tests/check_sider_utils.c:Core:test_casequalstring: Passed","ok 35 - ../tests/check_sider_utils.c:Core:test_cmpstringp: Passed","ok 36 - ../tests/check_sider_utils.c:Core:test_casecmpstringp: Passed","ok 37 - ../tests/check_sider_utils.c:Core:test_chomp: Passed","ok 38 - ../tests/check_sider_utils.c:Core:test_trimc: Passed","ok 39 - ../tests/check_sider_utils.c:Core:test_trim: Passed","ok 40 - ../tests/check_sider_utils.c:Core:test_upper: Passed","ok 41 - ../tests/check_sider_utils.c:Core:test_lower: Passed","ok 42 - ../tests/check_sider_utils.c:Core:test_path_dir: Passed","ok 43 - ../tests/check_sider_utils.c:Core:test_path_file: Passed","ok 44 - ../tests/check_sider_utils.c:Core:test_which: Passed","ok 45 - ../tests/check_sider_utils.c:Core:test_exists: Passed","ok 46 - ../tests/check_sider_utils.c:Core:test_xstrdup_concat: Passed","ok 47 - ../tests/check_sider_utils.c:Core:test_xasprintf_concat: Passed","ok 48 - ../tests/check_sider_utils.c:Core:test_mkdir_p: Passed","ok 49 - ../tests/check_sider_utils.c:Core:test_setup_signal: Passed","ok 50 - ../tests/check_sider_utils.c:Core:test_buf_expand: Passed","ok 51 - ../tests/check_sider_utils.c:Core:test_entry_size: Passed"," SAM","ok 52 - ../tests/check_sider_sam.c:Core:test_sam_to_bam: Passed","ok 53 - ../tests/check_sider_sam.c:Core:test_sam_to_bam_fp: Passed","ok 54 - ../tests/check_sider_sam.c:Core:test_sam_test_sorted_order: Passed"," BiTree","ok 55 - ../tests/check_sider_bitree.c:Core:test_bitree: Passed"," IBiTree","ok 56 - ../tests/check_sider_ibitree.c:Core:test_ibitree_insert: Passed","ok 57 - ../tests/check_sider_ibitree.c:Core:test_ibitree_lookup: Passed","ok 58 - ../tests/check_sider_ibitree.c:Core:test_ibitree_lookup_frac: Passed","ok 59 - ../tests/check_sider_ibitree.c:Core:test_ibitree_lookup_either: Passed"," String","ok 60 - ../tests/check_sider_str.c:Core:test_string_new: Passed","ok 61 - ../tests/check_sider_str.c:Core:test_string_sized_new: Passed","ok 62 - ../tests/check_sider_str.c:Core:test_string_set: Passed","ok 63 - ../tests/check_sider_str.c:Core:test_string_concat: Passed","ok 64 - ../tests/check_sider_str.c:Core:test_string_printf: Passed","ok 65 - ../tests/check_sider_str.c:Core:test_string_concat_printf: Passed","ok 66 - ../tests/check_sider_str.c:Core:test_string_free: Passed","ok 67 - ../tests/check_sider_str.c:Core:test_string_clear: Passed"," DB","ok 68 - ../tests/check_sider_db.c:Core:test_db_open: Passed","ok 69 - ../tests/check_sider_db.c:Core:test_db_exec: Passed","ok 70 - ../tests/check_sider_db.c:Core:test_db_prepare: Passed","ok 71 - ../tests/check_sider_db.c:Core:test_db_schema: Passed","ok 72 - ../tests/check_sider_db.c:Abort:test_db_open_abort: Passed","ok 73 - ../tests/check_sider_db.c:Abort:test_db_close_abort: Passed","ok 74 - ../tests/check_sider_db.c:Abort:test_db_exec_abort: Passed","ok 75 - ../tests/check_sider_db.c:Abort:test_db_prepare_abort: Passed","ok 76 - ../tests/check_sider_db.c:Abort:test_db_step_abort: Passed","ok 77 - ../tests/check_sider_db.c:Abort:test_db_reset_abort: Passed","ok 78 - ../tests/check_sider_db.c:Abort:test_db_bind_int_abort: Passed","ok 79 - ../tests/check_sider_db.c:Abort:test_db_bind_int64_abort: Passed","ok 80 - ../tests/check_sider_db.c:Abort:test_db_bind_double_abort: Passed","ok 81 - ../tests/check_sider_db.c:Abort:test_db_bind_text_abort: Passed","ok 82 - ../tests/check_sider_db.c:Abort:test_db_column_int_abort: Passed","ok 83 - ../tests/check_sider_db.c:Abort:test_db_column_int64_abort: Passed","ok 84 - ../tests/check_sider_db.c:Abort:test_db_column_double_abort: Passed","ok 85 - ../tests/check_sider_db.c:Abort:test_db_column_text_abort: Passed"," Chr","ok 86 - ../tests/check_sider_chr.c:Core:test_chr_std_lookup: Passed"," Exon","ok 87 - ../tests/check_sider_exon.c:Core:test_exon_tree_index_dump: Passed","ok 88 - ../tests/check_sider_exon.c:Core:test_exon_tree_lookup_dump: Passed"," Abnormal","ok 89 - ../tests/check_sider_abnormal.c:Core:test_abnormal_filter_sorted: Passed","ok 90 - ../tests/check_sider_abnormal.c:Core:test_abnormal_filter_unsorted: Passed"," GFF","ok 91 - ../tests/check_sider_gff.c:Core:test_gff_header: Passed","ok 92 - ../tests/check_sider_gff.c:Core:test_gff_read: Passed","ok 93 - ../tests/check_sider_gff.c:Core:test_gff_filter: Passed","ok 94 - ../tests/check_sider_gff.c:Core:test_gff_looks_like_gff_file: Passed","ok 95 - ../tests/check_sider_gff.c:Abort:test_open_fatal: Passed","ok 96 - ../tests/check_sider_gff.c:Abort:test_seqname_fatal: Passed","ok 97 - ../tests/check_sider_gff.c:Abort:test_source_fatal: Passed","ok 98 - ../tests/check_sider_gff.c:Abort:test_feature_fatal: Passed","ok 99 - ../tests/check_sider_gff.c:Abort:test_start_fatal: Passed","ok 100 - ../tests/check_sider_gff.c:Abort:test_end_fatal: Passed","ok 101 - ../tests/check_sider_gff.c:Abort:test_score_fatal: Passed","ok 102 - ../tests/check_sider_gff.c:Abort:test_strand_fatal: Passed","ok 103 - ../tests/check_sider_gff.c:Abort:test_frame_fatal: Passed","ok 104 - ../tests/check_sider_gff.c:Abort:test_key_value_fatal: Passed","ok 105 - ../tests/check_sider_gff.c:Abort:test_close_fatal: Passed"," IO","ok 106 - ../tests/check_sider_io.c:Core:test_read_file_lines: Passed"," DBSCAN","ok 107 - ../tests/check_sider_dbscan.c:Core:test_dbscan: Passed"," Cluster","ok 108 - ../tests/check_sider_cluster.c:Core:test_cluster_without_genotype_support: Passed","ok 109 - ../tests/check_sider_cluster.c:Core:test_cluster_with_genotype_support: Passed"," Wrapper","ok 110 - ../tests/check_sider_wrapper.c:Core:test_xmalloc: Passed","ok 111 - ../tests/check_sider_wrapper.c:Core:test_xcalloc: Passed","ok 112 - ../tests/check_sider_wrapper.c:Core:test_xrealloc: Passed","ok 113 - ../tests/check_sider_wrapper.c:Core:test_xstrdup: Passed","ok 114 - ../tests/check_sider_wrapper.c:Core:test_xfree: Passed","ok 115 - ../tests/check_sider_wrapper.c:Core:test_xfopen: Passed","ok 116 - ../tests/check_sider_wrapper.c:Core:test_xfdopen: Passed","ok 117 - ../tests/check_sider_wrapper.c:Core:test_xfclose: Passed","ok 118 - ../tests/check_sider_wrapper.c:Core:test_xfflush: Passed","ok 119 - ../tests/check_sider_wrapper.c:Core:test_xpopen: Passed","ok 120 - ../tests/check_sider_wrapper.c:Core:test_xmkdir: Passed","ok 121 - ../tests/check_sider_wrapper.c:Core:test_xasprintf: Passed","ok 122 - ../tests/check_sider_wrapper.c:Core:test_xfprintf: Passed","ok 123 - ../tests/check_sider_wrapper.c:Core:test_xsigaction: Passed","ok 124 - ../tests/check_sider_wrapper.c:Abort:test_xfopen_rw_abort: Passed","ok 125 - ../tests/check_sider_wrapper.c:Abort:test_xfopen_w_abort: Passed","ok 126 - ../tests/check_sider_wrapper.c:Abort:test_xfopen_r_abort: Passed","ok 127 - ../tests/check_sider_wrapper.c:Abort:test_xfdopen_rw_abort: Passed","ok 128 - ../tests/check_sider_wrapper.c:Abort:test_xfdopen_w_abort: Passed","ok 129 - ../tests/check_sider_wrapper.c:Abort:test_xfdopen_r_abort: Passed","ok 130 - ../tests/check_sider_wrapper.c:Abort:test_xmkdir_abort: Passed","ok 131 - ../tests/check_sider_wrapper.c:Abort:test_xsigaction_abort: Passed","ok 132 - ../tests/check_sider_wrapper.c:Abort:test_xpopen_r_abort: Passed","ok 133 - ../tests/check_sider_wrapper.c:Abort:test_xpopen_w_abort: Passed"," DBMerge","not ok 134 - ../tests/check_sider_db_merge.c:Core:test_db_merge: Test timeout expired","not ok 135 - ../tests/check_sider_db_merge.c:Core:test_db_merge_in_line: Test timeout expired"," Set","ok 136 - ../tests/check_sider_set.c:Core:test_set_free: Passed","ok 137 - ../tests/check_sider_set.c:Core:test_set_insert: Passed","ok 138 - ../tests/check_sider_set.c:Core:test_set_remove: Passed","ok 139 - ../tests/check_sider_set.c:Core:test_set_union: Passed","ok 140 - ../tests/check_sider_set.c:Core:test_set_intersection: Passed","ok 141 - ../tests/check_sider_set.c:Core:test_set_difference: Passed","ok 142 - ../tests/check_sider_set.c:Core:test_set_is_subset: Passed","ok 143 - ../tests/check_sider_set.c:Core:test_set_is_equal: Passed","ok 144 - ../tests/check_sider_set.c:Core:test_set_is_member: Passed"," Correlation","ok 145 - ../tests/check_sider_correlation.c:Core:test_pearson: Passed","ok 146 - ../tests/check_sider_correlation.c:Core:test_spearman: Passed","ok 147 - ../tests/check_sider_correlation.c:Core:test_spearman_eq: Passed","ok 148 - ../tests/check_sider_correlation.c:Core:test_spearman_permutation_test: Passed"," BED","ok 149 - ../tests/check_sider_bed.c:Core:test_bed_header: Passed","ok 150 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 151 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 152 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 153 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 154 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 155 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 156 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 157 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 158 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 159 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 160 - ../tests/check_sider_bed.c:Abort:test_open_fatal: Passed","ok 161 - ../tests/check_sider_bed.c:Abort:test_chrom_fatal: Passed","ok 162 - ../tests/check_sider_bed.c:Abort:test_chrom_start_fatal: Passed","ok 163 - ../tests/check_sider_bed.c:Abort:test_chrom_end_fatal: Passed","ok 164 - ../tests/check_sider_bed.c:Abort:test_close_fatal: Passed"," Blacklist","ok 165 - ../tests/check_sider_blacklist.c:Core:test_blacklist_index_dump_from_gff: Passed","ok 166 - ../tests/check_sider_blacklist.c:Core:test_blacklist_index_dump_from_bed: Passed","ok 167 - ../tests/check_sider_blacklist.c:Core:test_blacklist_lookup: Passed"," Retrocopy","ok 168 - ../tests/check_sider_retrocopy.c:Core:test_retrocopy: Passed"," Dedup","sideRETRO:all time out (After 30 seconds)","――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――","1/1 sideRETRO:all TIMEOUT 30.01s killed by signal 15 SIGTERM","","","Summary of Failures:","","1/1 sideRETRO:all TIMEOUT 30.01s killed by signal 15 SIGTERM","","Ok: 0 ","Fail: 0 ","Timeout: 1 ","","Full log written to /build/reproducible-path/sideretro-1.1.6/obj-x86_64-linux-gnu/meson-logs/testlog.txt","\tcd obj-x86_64-linux-gnu && tail -v -n \\+0 meson-logs/testlog.txt","==> meson-logs/testlog.txt <==","Log of Meson test suite run on 2026-06-28T14:23:47.598712","","Inherited environment: DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_HOST_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_ARCH_LIBC=gnu DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_ARCH_BITS=64 DEB_BUILD_OPTIONS=parallel=4 DEB_HOST_ARCH=amd64 DEB_TARGET_ARCH_ENDIAN=little SOURCE_DATE_EPOCH=1782656306 DEB_HOST_ARCH_BITS=64 LANG=C.UTF-8 MAKEFLAGS='' DEB_TARGET_ARCH=amd64 DEB_HOST_GNU_CPU=x86_64 DEB_BUILD_ARCH_LIBC=gnu MFLAGS='' DEB_TARGET_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 LC_COLLATE=C.UTF-8 DEB_HOST_ARCH_OS=linux DEB_HOST_ARCH_CPU=amd64 MAKELEVEL=1 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH=amd64 DEB_HOST_ARCH_LIBC=gnu DEB_TARGET_ARCH_CPU=amd64 DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_ARCH_OS=linux LOGNAME=sbuild DEB_TARGET_MULTIARCH=x86_64-linux-gnu DEB_BUILD_GNU_CPU=x86_64 DEB_TARGET_ARCH_OS=linux USER=sbuild DEB_HOST_ARCH_ABI=base DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_ARCH_ABI=base LC_CTYPE=C.UTF-8 DEB_TARGET_GNU_CPU=x86_64 APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/build/reproducible-path/sideretro-1.1.6/debian/.debhelper/generated/_source/home DEB_RULES_REQUIRES_ROOT=no DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_HOST_ARCH_ENDIAN=little DEB_BUILD_MAINT_OPTIONS=hardening=+all SHELL=/bin/sh DH_INTERNAL_BUILDFLAGS=1 ASFLAGS='' ASFLAGS_FOR_BUILD='' CFLAGS='-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' CFLAGS_FOR_BUILD='-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' CPPFLAGS='-Wdate-time -D_FORTIFY_SOURCE=2' CPPFLAGS_FOR_BUILD='-Wdate-time -D_FORTIFY_SOURCE=2' CXXFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' CXXFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' DFLAGS=-frelease DFLAGS_FOR_BUILD=-frelease FCFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -fcf-protection' FCFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -fcf-protection' FFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -fcf-protection' FFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -fcf-protection' LDFLAGS='-Wl,-z,relro -Wl,-z,now' LDFLAGS_FOR_BUILD='-Wl,-z,relro -Wl,-z,now' OBJCFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' OBJCFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' OBJCXXFLAGS='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' OBJCXXFLAGS_FOR_BUILD='-g -O2 -ffile-prefix-map=/build/reproducible-path/sideretro-1.1.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' XDG_RUNTIME_DIR=/tmp/dh-xdg-rundir-euEsTGG4 DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=4 ","","==================================== 1/1 =====================================","test: sideRETRO:all","start time: 14:23:47","duration: 30.01s","result: killed by signal 15 SIGTERM","command: MESON_TEST_ITERATION=1 MALLOC_PERTURB_=221 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /build/reproducible-path/sideretro-1.1.6/obj-x86_64-linux-gnu/tests/check_sider","----------------------------------- stdout -----------------------------------","Running suite(s): ProcessSample","ok 1 - ../tests/check_sider_process_sample.c:Core:test_sider: Passed"," List","ok 2 - ../tests/check_sider_list.c:Core:test_list_new: Passed","ok 3 - ../tests/check_sider_list.c:Core:test_list_ins_prev: Passed","ok 4 - ../tests/check_sider_list.c:Core:test_list_ins_next: Passed","ok 5 - ../tests/check_sider_list.c:Core:test_list_ins_prev_link: Passed","ok 6 - ../tests/check_sider_list.c:Core:test_list_ins_next_link: Passed","ok 7 - ../tests/check_sider_list.c:Core:test_list_remove: Passed","ok 8 - ../tests/check_sider_list.c:Core:test_list_remove_link: Passed","ok 9 - ../tests/check_sider_list.c:Core:test_list_foreach: Passed"," Hash","ok 10 - ../tests/check_sider_hash.c:Core:test_hash_free: Passed","ok 11 - ../tests/check_sider_hash.c:Core:test_hash_insert: Passed","ok 12 - ../tests/check_sider_hash.c:Core:test_hash_lookup: Passed","ok 13 - ../tests/check_sider_hash.c:Core:test_hash_replace: Passed","ok 14 - ../tests/check_sider_hash.c:Core:test_hash_remove: Passed","ok 15 - ../tests/check_sider_hash.c:Core:test_hash_contains: Passed","ok 16 - ../tests/check_sider_hash.c:Core:test_hash_int: Passed","ok 17 - ../tests/check_sider_hash.c:Core:test_hash_direct: Passed","ok 18 - ../tests/check_sider_hash.c:Core:test_hash_many_insertions: Passed","ok 19 - ../tests/check_sider_hash.c:Misc:test_hash_foreach: Passed","ok 20 - ../tests/check_sider_hash.c:Misc:test_hash_iter: Passed","ok 21 - ../tests/check_sider_hash.c:Misc:test_hash_get_keys_as_list: Passed","ok 22 - ../tests/check_sider_hash.c:Misc:test_hash_get_values_as_list: Passed","ok 23 - ../tests/check_sider_hash.c:Misc:test_hash_get_keys_as_array: Passed","ok 24 - ../tests/check_sider_hash.c:Misc:test_hash_get_values_as_array: Passed"," Array","ok 25 - ../tests/check_sider_array.c:CoreFree:test_array: Passed","ok 26 - ../tests/check_sider_array.c:CoreFree:test_array_uniq: Passed","ok 27 - ../tests/check_sider_array.c:CoreFree:test_array_find_with_equal_fun: Passed","ok 28 - ../tests/check_sider_array.c:CoreNull:test_array_find: Passed","ok 29 - ../tests/check_sider_array.c:CoreNull:test_array_remove: Passed","ok 30 - ../tests/check_sider_array.c:CoreNull:test_array_remove_index: Passed","ok 31 - ../tests/check_sider_array.c:Free:test_array_no_free_segment: Passed"," Utils","ok 32 - ../tests/check_sider_utils.c:Core:test_fequal: Passed","ok 33 - ../tests/check_sider_utils.c:Core:test_equalstring: Passed","ok 34 - ../tests/check_sider_utils.c:Core:test_casequalstring: Passed","ok 35 - ../tests/check_sider_utils.c:Core:test_cmpstringp: Passed","ok 36 - ../tests/check_sider_utils.c:Core:test_casecmpstringp: Passed","ok 37 - ../tests/check_sider_utils.c:Core:test_chomp: Passed","ok 38 - ../tests/check_sider_utils.c:Core:test_trimc: Passed","ok 39 - ../tests/check_sider_utils.c:Core:test_trim: Passed","ok 40 - ../tests/check_sider_utils.c:Core:test_upper: Passed","ok 41 - ../tests/check_sider_utils.c:Core:test_lower: Passed","ok 42 - ../tests/check_sider_utils.c:Core:test_path_dir: Passed","ok 43 - ../tests/check_sider_utils.c:Core:test_path_file: Passed","ok 44 - ../tests/check_sider_utils.c:Core:test_which: Passed","ok 45 - ../tests/check_sider_utils.c:Core:test_exists: Passed","ok 46 - ../tests/check_sider_utils.c:Core:test_xstrdup_concat: Passed","ok 47 - ../tests/check_sider_utils.c:Core:test_xasprintf_concat: Passed","ok 48 - ../tests/check_sider_utils.c:Core:test_mkdir_p: Passed","ok 49 - ../tests/check_sider_utils.c:Core:test_setup_signal: Passed","ok 50 - ../tests/check_sider_utils.c:Core:test_buf_expand: Passed","ok 51 - ../tests/check_sider_utils.c:Core:test_entry_size: Passed"," SAM","ok 52 - ../tests/check_sider_sam.c:Core:test_sam_to_bam: Passed","ok 53 - ../tests/check_sider_sam.c:Core:test_sam_to_bam_fp: Passed","ok 54 - ../tests/check_sider_sam.c:Core:test_sam_test_sorted_order: Passed"," BiTree","ok 55 - ../tests/check_sider_bitree.c:Core:test_bitree: Passed"," IBiTree","ok 56 - ../tests/check_sider_ibitree.c:Core:test_ibitree_insert: Passed","ok 57 - ../tests/check_sider_ibitree.c:Core:test_ibitree_lookup: Passed","ok 58 - ../tests/check_sider_ibitree.c:Core:test_ibitree_lookup_frac: Passed","ok 59 - ../tests/check_sider_ibitree.c:Core:test_ibitree_lookup_either: Passed"," String","ok 60 - ../tests/check_sider_str.c:Core:test_string_new: Passed","ok 61 - ../tests/check_sider_str.c:Core:test_string_sized_new: Passed","ok 62 - ../tests/check_sider_str.c:Core:test_string_set: Passed","ok 63 - ../tests/check_sider_str.c:Core:test_string_concat: Passed","ok 64 - ../tests/check_sider_str.c:Core:test_string_printf: Passed","ok 65 - ../tests/check_sider_str.c:Core:test_string_concat_printf: Passed","ok 66 - ../tests/check_sider_str.c:Core:test_string_free: Passed","ok 67 - ../tests/check_sider_str.c:Core:test_string_clear: Passed"," DB","ok 68 - ../tests/check_sider_db.c:Core:test_db_open: Passed","ok 69 - ../tests/check_sider_db.c:Core:test_db_exec: Passed","ok 70 - ../tests/check_sider_db.c:Core:test_db_prepare: Passed","ok 71 - ../tests/check_sider_db.c:Core:test_db_schema: Passed","ok 72 - ../tests/check_sider_db.c:Abort:test_db_open_abort: Passed","ok 73 - ../tests/check_sider_db.c:Abort:test_db_close_abort: Passed","ok 74 - ../tests/check_sider_db.c:Abort:test_db_exec_abort: Passed","ok 75 - ../tests/check_sider_db.c:Abort:test_db_prepare_abort: Passed","ok 76 - ../tests/check_sider_db.c:Abort:test_db_step_abort: Passed","ok 77 - ../tests/check_sider_db.c:Abort:test_db_reset_abort: Passed","ok 78 - ../tests/check_sider_db.c:Abort:test_db_bind_int_abort: Passed","ok 79 - ../tests/check_sider_db.c:Abort:test_db_bind_int64_abort: Passed","ok 80 - ../tests/check_sider_db.c:Abort:test_db_bind_double_abort: Passed","ok 81 - ../tests/check_sider_db.c:Abort:test_db_bind_text_abort: Passed","ok 82 - ../tests/check_sider_db.c:Abort:test_db_column_int_abort: Passed","ok 83 - ../tests/check_sider_db.c:Abort:test_db_column_int64_abort: Passed","ok 84 - ../tests/check_sider_db.c:Abort:test_db_column_double_abort: Passed","ok 85 - ../tests/check_sider_db.c:Abort:test_db_column_text_abort: Passed"," Chr","ok 86 - ../tests/check_sider_chr.c:Core:test_chr_std_lookup: Passed"," Exon","ok 87 - ../tests/check_sider_exon.c:Core:test_exon_tree_index_dump: Passed","ok 88 - ../tests/check_sider_exon.c:Core:test_exon_tree_lookup_dump: Passed"," Abnormal","ok 89 - ../tests/check_sider_abnormal.c:Core:test_abnormal_filter_sorted: Passed","ok 90 - ../tests/check_sider_abnormal.c:Core:test_abnormal_filter_unsorted: Passed"," GFF","ok 91 - ../tests/check_sider_gff.c:Core:test_gff_header: Passed","ok 92 - ../tests/check_sider_gff.c:Core:test_gff_read: Passed","ok 93 - ../tests/check_sider_gff.c:Core:test_gff_filter: Passed","ok 94 - ../tests/check_sider_gff.c:Core:test_gff_looks_like_gff_file: Passed","ok 95 - ../tests/check_sider_gff.c:Abort:test_open_fatal: Passed","ok 96 - ../tests/check_sider_gff.c:Abort:test_seqname_fatal: Passed","ok 97 - ../tests/check_sider_gff.c:Abort:test_source_fatal: Passed","ok 98 - ../tests/check_sider_gff.c:Abort:test_feature_fatal: Passed","ok 99 - ../tests/check_sider_gff.c:Abort:test_start_fatal: Passed","ok 100 - ../tests/check_sider_gff.c:Abort:test_end_fatal: Passed","ok 101 - ../tests/check_sider_gff.c:Abort:test_score_fatal: Passed","ok 102 - ../tests/check_sider_gff.c:Abort:test_strand_fatal: Passed","ok 103 - ../tests/check_sider_gff.c:Abort:test_frame_fatal: Passed","ok 104 - ../tests/check_sider_gff.c:Abort:test_key_value_fatal: Passed","ok 105 - ../tests/check_sider_gff.c:Abort:test_close_fatal: Passed"," IO","ok 106 - ../tests/check_sider_io.c:Core:test_read_file_lines: Passed"," DBSCAN","ok 107 - ../tests/check_sider_dbscan.c:Core:test_dbscan: Passed"," Cluster","ok 108 - ../tests/check_sider_cluster.c:Core:test_cluster_without_genotype_support: Passed","ok 109 - ../tests/check_sider_cluster.c:Core:test_cluster_with_genotype_support: Passed"," Wrapper","ok 110 - ../tests/check_sider_wrapper.c:Core:test_xmalloc: Passed","ok 111 - ../tests/check_sider_wrapper.c:Core:test_xcalloc: Passed","ok 112 - ../tests/check_sider_wrapper.c:Core:test_xrealloc: Passed","ok 113 - ../tests/check_sider_wrapper.c:Core:test_xstrdup: Passed","ok 114 - ../tests/check_sider_wrapper.c:Core:test_xfree: Passed","ok 115 - ../tests/check_sider_wrapper.c:Core:test_xfopen: Passed","ok 116 - ../tests/check_sider_wrapper.c:Core:test_xfdopen: Passed","ok 117 - ../tests/check_sider_wrapper.c:Core:test_xfclose: Passed","ok 118 - ../tests/check_sider_wrapper.c:Core:test_xfflush: Passed","ok 119 - ../tests/check_sider_wrapper.c:Core:test_xpopen: Passed","ok 120 - ../tests/check_sider_wrapper.c:Core:test_xmkdir: Passed","ok 121 - ../tests/check_sider_wrapper.c:Core:test_xasprintf: Passed","ok 122 - ../tests/check_sider_wrapper.c:Core:test_xfprintf: Passed","ok 123 - ../tests/check_sider_wrapper.c:Core:test_xsigaction: Passed","ok 124 - ../tests/check_sider_wrapper.c:Abort:test_xfopen_rw_abort: Passed","ok 125 - ../tests/check_sider_wrapper.c:Abort:test_xfopen_w_abort: Passed","ok 126 - ../tests/check_sider_wrapper.c:Abort:test_xfopen_r_abort: Passed","ok 127 - ../tests/check_sider_wrapper.c:Abort:test_xfdopen_rw_abort: Passed","ok 128 - ../tests/check_sider_wrapper.c:Abort:test_xfdopen_w_abort: Passed","ok 129 - ../tests/check_sider_wrapper.c:Abort:test_xfdopen_r_abort: Passed","ok 130 - ../tests/check_sider_wrapper.c:Abort:test_xmkdir_abort: Passed","ok 131 - ../tests/check_sider_wrapper.c:Abort:test_xsigaction_abort: Passed","ok 132 - ../tests/check_sider_wrapper.c:Abort:test_xpopen_r_abort: Passed","ok 133 - ../tests/check_sider_wrapper.c:Abort:test_xpopen_w_abort: Passed"," DBMerge","not ok 134 - ../tests/check_sider_db_merge.c:Core:test_db_merge: Test timeout expired","not ok 135 - ../tests/check_sider_db_merge.c:Core:test_db_merge_in_line: Test timeout expired"," Set","ok 136 - ../tests/check_sider_set.c:Core:test_set_free: Passed","ok 137 - ../tests/check_sider_set.c:Core:test_set_insert: Passed","ok 138 - ../tests/check_sider_set.c:Core:test_set_remove: Passed","ok 139 - ../tests/check_sider_set.c:Core:test_set_union: Passed","ok 140 - ../tests/check_sider_set.c:Core:test_set_intersection: Passed","ok 141 - ../tests/check_sider_set.c:Core:test_set_difference: Passed","ok 142 - ../tests/check_sider_set.c:Core:test_set_is_subset: Passed","ok 143 - ../tests/check_sider_set.c:Core:test_set_is_equal: Passed","ok 144 - ../tests/check_sider_set.c:Core:test_set_is_member: Passed"," Correlation","ok 145 - ../tests/check_sider_correlation.c:Core:test_pearson: Passed","ok 146 - ../tests/check_sider_correlation.c:Core:test_spearman: Passed","ok 147 - ../tests/check_sider_correlation.c:Core:test_spearman_eq: Passed","ok 148 - ../tests/check_sider_correlation.c:Core:test_spearman_permutation_test: Passed"," BED","ok 149 - ../tests/check_sider_bed.c:Core:test_bed_header: Passed","ok 150 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 151 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 152 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 153 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 154 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 155 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 156 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 157 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 158 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 159 - ../tests/check_sider_bed.c:Core:test_beds: Passed","ok 160 - ../tests/check_sider_bed.c:Abort:test_open_fatal: Passed","ok 161 - ../tests/check_sider_bed.c:Abort:test_chrom_fatal: Passed","ok 162 - ../tests/check_sider_bed.c:Abort:test_chrom_start_fatal: Passed","ok 163 - ../tests/check_sider_bed.c:Abort:test_chrom_end_fatal: Passed","ok 164 - ../tests/check_sider_bed.c:Abort:test_close_fatal: Passed"," Blacklist","ok 165 - ../tests/check_sider_blacklist.c:Core:test_blacklist_index_dump_from_gff: Passed","ok 166 - ../tests/check_sider_blacklist.c:Core:test_blacklist_index_dump_from_bed: Passed","ok 167 - ../tests/check_sider_blacklist.c:Core:test_blacklist_lookup: Passed"," Retrocopy","ok 168 - ../tests/check_sider_retrocopy.c:Core:test_retrocopy: Passed"," Dedup","==============================================================================","","","Summary of Failures:","","1/1 sideRETRO:all TIMEOUT 30.01s killed by signal 15 SIGTERM","","Ok: 0 ","Fail: 0 ","Timeout: 1 ","dh_auto_test: error: cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=4 meson test --verbose returned exit code 1","make: *** [debian/rules:6: binary] Error 25","dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2","--------------------------------------------------------------------------------","Build finished at 2026-06-28T14:24:17Z","","Finished","--------"],"log_name":"build.log","match_lines":["not ok 134 - ../tests/check_sider_db_merge.c:Core:test_db_merge: Test timeout expired"],"start_line":1094,"title":"Build"},"is_admin":false,"lintian_result":null,"logs":{"build":{"description":"build","name":"build.log","url":"/lintian-fixes/c/sideretro/78e6644a-220b-49f9-8976-4648d26c4474/logs/build.log"},"codemod":{"description":"codemod","name":"codemod.log","url":"/lintian-fixes/c/sideretro/78e6644a-220b-49f9-8976-4648d26c4474/logs/codemod.log"},"worker":{"content":"[2026-06-28T14:13:45Z INFO janitor_worker] Opening branch at https://salsa.debian.org/med-team/sideretro.git\n[2026-06-28T14:16:02Z INFO janitor_worker] Cached branch URL http://janitor.debian.net/git/sideretro missing: http://tyr@janitor.debian.net/git/sideretro/\n[2026-06-28T14:16:02Z DEBUG janitor_worker] Workspace path: /srv/worker/output/1/janitor-worker-k6Fbc8/sideretro\n[2026-06-28T14:16:02Z DEBUG silver_platter::workspace] Creating sprout from git+ssh://git@salsa.debian.org/med-team/sideretro.git\n 93% (162/174)\nTotal 214 (delta 47), reused 182 (delta 31), pack-reused 0 (from 0)\nNothing to delete.\n[2026-06-28T14:18:20Z DEBUG silver_platter::workspace] Fetching colocated branches: {}\n[2026-06-28T14:18:20Z INFO janitor_worker] Workspace ready - starting.\n[2026-06-28T14:18:20Z INFO janitor_worker::debian] Running [\"lintian-brush\"]\n[2026-06-28T14:18:20Z DEBUG debian_analyzer::detect_gbp_dch] Branch history analysis: changelog_only: 3, other_only: 0, mixed: 4, dch_references: 0, unreleased_references: 4\nfound 47 deltas to reuse\n[2026-06-28T14:18:28Z INFO ognibuild::debian::fix_build] Using fixers: [PgBuildExtOutOfDateControlFixer, MissingConfigureFixer, MissingAutomakeInputFixer, MissingConfigStatusInputFixer, MissingPerlFileFixer, DebcargoUnacceptablePredicateFixer, DebcargoUnacceptableComparatorFixer, RetryAptFetchFailure, PackageDependencyFixer]\n[2026-06-28T14:18:28Z DEBUG ognibuild::debian::build] Adding dummy changelog entry 1.1.6-4~jan+lint1 for build\n[2026-06-28T14:18:28Z DEBUG ognibuild::debian::build] Writing build log to /srv/worker/output/1/janitor-worker-k6Fbc8/build.log\n[2026-06-28T14:18:28Z INFO ognibuild::debian::build] Building debian packages, running sbuild --chroot-mode=unshare --no-clean-source -A -s -v -d sid.\n[2026-06-28T14:24:19Z WARN buildlog_consultant::sbuild] Unknown line in summary: --------------------------------------------------------------------------------\n \n[2026-06-28T14:24:19Z WARN buildlog_consultant::sbuild] Unknown line in summary: Finished at 2026-06-28T14:24:17Z\n \n[2026-06-28T14:24:19Z WARN buildlog_consultant::sbuild] Unknown line in summary: Build needed 00:05:48, 12312k disk space\n \n[2026-06-28T14:24:19Z WARN buildlog_consultant::sbuild] Unknown key in summary: E\n[2026-06-28T14:24:19Z WARN buildlog_consultant::sbuild] Unknown key in summary: brz\n[2026-06-28T14:24:19Z DEBUG buildlog_consultant::common] Regex backtracking limit exceeded for pattern '.*.go:[0-9]+:[0-9]+: (?!note:).*' on line (length: 1864)\n[2026-06-28T14:24:19Z DEBUG buildlog_consultant::common] Found match against not ok [0-9]+ .* on \"not ok 134 - ../tests/check_sider_db_merge.c:Core:test_db_merge: Test timeout expired\\n\" (line 385)\n[2026-06-28T14:24:19Z WARN ognibuild::debian::fix_build] Build failed with unidentified error. Giving up.\n","description":"worker","name":"worker.log","url":"/lintian-fixes/c/sideretro/78e6644a-220b-49f9-8976-4648d26c4474/logs/worker.log"}},"my_review":null,"other_reviews":[],"primary_log":"worker","publish_blockers":{"backoff":{"details":{"attempt_count":0,"next_try_time":"2026-06-28T14:24:19.738248Z"},"result":true},"change_set":{"details":{"change_set_id":"78e6644a-220b-49f9-8976-4648d26c4474","change_set_state":"working"},"result":false},"command":{"details":{"actual":"DEB_UPDATE_CHANGELOG=auto lintian-brush","correct":"DEB_UPDATE_CHANGELOG=auto lintian-brush"},"result":true},"inactive":{"details":{"inactive":false},"result":true},"previous_mp":{"details":[],"result":true},"propose_rate_limit":{"details":{"bucket":"debian-med-packaging@lists.alioth.debian.org"},"result":true},"publish_status":{"details":{"reviews":{},"status":"rejected"},"result":false},"success":{"details":{"result_code":"unidentified"},"result":false}},"publish_history":[],"queue_position":21559,"result":{"applied":[{"certainty":"certain","description":"Update standards version to 4.7.4, no changes needed.\n\nUpgrade checklist verified:\n 4.7.3 → 4.7.4:\n * Package is not in non-free-firmware","fixed_lintian_issues":[{"info":"4.7.3 (released 2025-12-23) (current is 4.7.4.1)","package":null,"package_type":"source","tag":"out-of-date-standards-version"}],"fixer_name":"out-of-date-standards-version","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:f90c1e8c165c459e5621bd0c5d39e54dc0468edd","summary":"Update standards version to 4.7.4, no changes needed."}],"changelog_behaviour":{"explanation":"Assuming changelog should be updated","update":true},"failed":{}},"result_code":"unidentified","resume_from":"{build,build}","reviews":[],"revision":"git-v1:f90c1e8c165c459e5621bd0c5d39e54dc0468edd","run":{"branch_url":"git+ssh://git@salsa.debian.org/med-team/sideretro.git","build_version":null,"change_set":"78e6644a-220b-49f9-8976-4648d26c4474","codebase":"sideretro","command":"DEB_UPDATE_CHANGELOG=auto lintian-brush","context":"\"debian-watch-does-not-check-openpgp-signature\"","debian_build_distribution":null,"debian_build_version":null,"description":"Unidentified error: ","duration_seconds":635,"failure_stage":"{build,build}","failure_transient":null,"finish_time":"2026-06-28T14:24:19.738248Z","id":"78e6644a-220b-49f9-8976-4648d26c4474","logfilenames":["worker.log","codemod.log","build.log"],"main_branch_revision":"git-v1:b2f0a41951179b80a6a5d47fc65bcdb8bdbd5bf0","publish_status":"rejected","result":{"applied":[{"certainty":"certain","description":"Update standards version to 4.7.4, no changes needed.\n\nUpgrade checklist verified:\n 4.7.3 → 4.7.4:\n * Package is not in non-free-firmware","fixed_lintian_issues":[{"info":"4.7.3 (released 2025-12-23) (current is 4.7.4.1)","package":null,"package_type":"source","tag":"out-of-date-standards-version"}],"fixer_name":"out-of-date-standards-version","overridden_lintian_issues":[],"patch_name":null,"revision_id":"git-v1:f90c1e8c165c459e5621bd0c5d39e54dc0468edd","summary":"Update standards version to 4.7.4, no changes needed."}],"changelog_behaviour":{"explanation":"Assuming changelog should be updated","update":true},"failed":{}},"result_branches":[{"absorbed":false,"base_revision":"git-v1:b2f0a41951179b80a6a5d47fc65bcdb8bdbd5bf0","remote_name":"master","revision":"git-v1:f90c1e8c165c459e5621bd0c5d39e54dc0468edd","role":"main"}],"result_code":"unidentified","result_tags":[],"revision":"git-v1:f90c1e8c165c459e5621bd0c5d39e54dc0468edd","start_time":"2026-06-28T14:13:44.038513Z","subpath":"","suite":"lintian-fixes","target_branch_url":null,"vcs_type":"git","worker":"tyr"},"run_id":"78e6644a-220b-49f9-8976-4648d26c4474","success_probability":0.4,"suite":"lintian-fixes","total_previous_runs":5,"unchanged_run":{"branch_url":"https://salsa.debian.org/med-team/sideretro.git/","build_version":"1.1.6-3~jan+control1","change_set":"ccabe02f-0609-41ba-96c4-ed34207b7245","codebase":"sideretro","command":"brz up '--revision=git-v1:b2f0a41951179b80a6a5d47fc65bcdb8bdbd5bf0'","context":null,"debian_build_distribution":"sid","debian_build_version":"1.1.6-3~jan+control1","description":"No change build","failure_stage":null,"failure_transient":null,"finish_time":"2026-05-13T15:06:20.972018Z","id":"fe636560-1fc3-4f51-8c3d-76e60c0d13a0","logfilenames":["worker.log","build.log","codemod.log"],"main_branch_revision":"git-v1:b2f0a41951179b80a6a5d47fc65bcdb8bdbd5bf0","publish_status":"unknown","result_branches":[],"result_code":"success","result_tags":[],"revision":"git-v1:b2f0a41951179b80a6a5d47fc65bcdb8bdbd5bf0","start_time":"2026-05-13T15:03:06.587774Z","subpath":"","suite":"control","target_branch_url":null,"vcs_type":"git","worker":"osuosl32-amd64"},"utcnow":"2026-07-06T02:27:55.892963049+00:00","vcs_type":"git","vcs_url":"git+ssh://git@salsa.debian.org/med-team/sideretro.git","version":"0.0.0","worker_log_name":"worker.log","worker_name":"tyr"}