Package: src:pigx-rnaseq Version: 0.1.1-2 Severity: serious Tags: forky sid ftbfs User: [email protected] Usertags: ftbfs-nocheck-profile
Dear maintainer: During a rebuild of all packages in unstable using the nocheck build profile, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202512/ A wiki page discussing how to reproduce bugs in this category and possible solutions is available here: https://wiki.debian.org/qa.debian.org/FTBFS/nocheck (It's a wiki, so you are welcome to contribute) About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:pigx-rnaseq, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] configure: Using /bin/gunzip as gunzip executable. configure: Using /bin/sed as sed executable. configure: Using /bin/bash as bash executable. checking for snakemake... no configure: error: Could not find snakemake. tail -v -n \+0 config.log ==> config.log <== This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by PiGx_rnaseq configure 0.1.1, which was generated by GNU Autoconf 2.72. Invocation command line was $ ./configure --build=x86_64-linux-gnu --prefix=/usr '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules '--libdir=${prefix}/lib/x86_64-linux-gnu' --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking GUNZIP=/bin/gunzip SED=/bin/sed ## --------- ## ## Platform. ## ## --------- ## hostname = r7a-large-1765302271 uname -m = x86_64 uname -r = 6.12.57+deb13-cloud-amd64 uname -s = Linux uname -v = #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = x86_64 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /usr/local/sbin/ PATH: /usr/local/bin/ PATH: /usr/sbin/ PATH: /usr/bin/ PATH: /sbin/ PATH: /bin/ PATH: /usr/games/ ## ----------- ## ## Core tests. ## ## ----------- ## configure:1795: looking for aux files: missing install-sh configure:1808: trying ./build-aux/ configure:1837: ./build-aux/missing found configure:1819: ./build-aux/install-sh found configure:1969: checking for a BSD-compatible install configure:2043: result: /usr/bin/install -c configure:2054: checking whether sleep supports fractional seconds configure:2070: result: yes configure:2073: checking filesystem timestamp resolution configure:2208: result: 0.01 configure:2213: checking whether build environment is sane configure:2258: result: yes configure:2429: checking for a race-free mkdir -p configure:2472: result: /usr/bin/mkdir -p configure:2479: checking for gawk configure:2515: result: no configure:2479: checking for mawk configure:2500: found /usr/bin/mawk configure:2512: result: mawk configure:2523: checking whether make sets $(MAKE) configure:2547: result: yes configure:2573: checking whether make supports nested variables configure:2592: result: yes configure:2606: checking xargs -n works configure:2622: result: yes configure:2697: checking how to create a pax tar archive configure:2708: tar --version tar (GNU tar) 1.35 Copyright (C) 2023 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Written by John Gilmore and Jay Fenlason. configure:2711: $? = 0 configure:2751: tardir=conftest.dir && eval tar --format=posix -chf - "$tardir" >conftest.tar configure:2754: $? = 0 configure:2758: tar -xf - <conftest.tar configure:2761: $? = 0 configure:2763: cat conftest.dir/file GrepMe configure:2766: $? = 0 configure:2781: result: gnutar configure:2812: checking for a sed that does not truncate output configure:2884: result: /bin/sed configure:2927: checking for a Python interpreter with version >= 3.5 configure:2945: python -c import sys # split strings by '.' and convert to numeric. Append some zeros # because we need at least 4 digits for the hex conversion. # map returns an iterator in Python 3.0 and a list in 2.x minver = list(map(int, '3.5'.split('.'))) + [0, 0, 0] minverhex = 0 # xrange is not present in Python 3.0 and range returns an iterator for i in list(range(0, 4)): minverhex = (minverhex << 8) + minver[i] sys.exit(sys.hexversion < minverhex) ./configure: line 2946: python: command not found configure:2948: $? = 127 configure:2945: python3 -c import sys # split strings by '.' and convert to numeric. Append some zeros # because we need at least 4 digits for the hex conversion. # map returns an iterator in Python 3.0 and a list in 2.x minver = list(map(int, '3.5'.split('.'))) + [0, 0, 0] minverhex = 0 # xrange is not present in Python 3.0 and range returns an iterator for i in list(range(0, 4)): minverhex = (minverhex << 8) + minver[i] sys.exit(sys.hexversion < minverhex) configure:2948: $? = 0 configure:2956: result: python3 configure:2964: checking for python3 configure:2987: found /usr/bin/python3 configure:3000: result: /usr/bin/python3 configure:3017: checking for python3 version configure:3026: result: 3.13 configure:3031: checking for python3 platform configure:3040: result: linux configure:3103: checking for GNU default python3 prefix configure:3105: result: ${prefix} configure:3173: checking for GNU default python3 exec_prefix configure:3175: result: ${exec_prefix} configure:3222: checking for python3 script directory (pythondir) configure:3262: result: ${PYTHON_PREFIX}/lib/python3.13/site-packages configure:3270: checking for python3 extension module directory (pyexecdir) configure:3310: result: ${PYTHON_EXEC_PREFIX}/lib/python3.13/site-packages configure:3333: checking python3 module: yaml configure:3338: result: yes configure:3410: Using /bin/gunzip as gunzip executable. configure:3467: Using /bin/sed as sed executable. configure:3524: Using /bin/bash as bash executable. configure:3532: checking for snakemake configure:3569: result: no configure:3577: error: Could not find snakemake. ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_env_BAMCOVERAGE_set= ac_cv_env_BAMCOVERAGE_value= ac_cv_env_FASTP_set= ac_cv_env_FASTP_value= ac_cv_env_GNUBASH_set=set ac_cv_env_GNUBASH_value=/bin/bash ac_cv_env_GUNZIP_set=set ac_cv_env_GUNZIP_value=/bin/gunzip ac_cv_env_HISAT2_BUILD_set= ac_cv_env_HISAT2_BUILD_value= ac_cv_env_HISAT2_set= ac_cv_env_HISAT2_value= ac_cv_env_MEGADEPTH_set= ac_cv_env_MEGADEPTH_value= ac_cv_env_MULTIQC_set= ac_cv_env_MULTIQC_value= ac_cv_env_PANDOC_set= ac_cv_env_PANDOC_value= ac_cv_env_PYTHONPATH_set= ac_cv_env_PYTHONPATH_value= ac_cv_env_PYTHON_set= ac_cv_env_PYTHON_value= ac_cv_env_RSCRIPT_set= ac_cv_env_RSCRIPT_value= ac_cv_env_R_LIBS_SITE_set= ac_cv_env_R_LIBS_SITE_value= ac_cv_env_R_set= ac_cv_env_R_value= ac_cv_env_SALMON_set=set ac_cv_env_SALMON_value=/usr/bin/salmon ac_cv_env_SAMTOOLS_set= ac_cv_env_SAMTOOLS_value= ac_cv_env_SED_set=set ac_cv_env_SED_value=/bin/sed ac_cv_env_SNAKEMAKE_set= ac_cv_env_SNAKEMAKE_value= ac_cv_env_STAR_set=set ac_cv_env_STAR_value=/usr/bin/STAR ac_cv_env_build_alias_set=set ac_cv_env_build_alias_value=x86_64-linux-gnu ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_path_PYTHON=/usr/bin/python3 ac_cv_path_SED=/bin/sed ac_cv_path_SNAKEMAKE=no ac_cv_path_install='/usr/bin/install -c' ac_cv_path_mkdir=/usr/bin/mkdir ac_cv_prog_AWK=mawk ac_cv_prog_make_make_set=yes am_cv_filesystem_timestamp_resolution=0.01 am_cv_make_support_nested_variables=yes am_cv_pathless_PYTHON=python3 am_cv_prog_tar_pax=gnutar am_cv_python_platform=linux am_cv_python_pyexecdir='${PYTHON_EXEC_PREFIX}/lib/python3.13/site-packages' am_cv_python_pythondir='${PYTHON_PREFIX}/lib/python3.13/site-packages' am_cv_python_version=3.13 am_cv_sleep_fractional_seconds=yes am_cv_xargs_n_works=yes ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} '\''/<<PKGBUILDDIR>>/build-aux/missing'\'' aclocal-1.18' AMTAR='$${TAR-tar}' AM_BACKSLASH='\' AM_DEFAULT_V='' AM_DEFAULT_VERBOSITY='0' AM_V='' AUTOCONF='${SHELL} '\''/<<PKGBUILDDIR>>/build-aux/missing'\'' autoconf' AUTOHEADER='${SHELL} '\''/<<PKGBUILDDIR>>/build-aux/missing'\'' autoheader' AUTOMAKE='${SHELL} '\''/<<PKGBUILDDIR>>/build-aux/missing'\'' automake-1.18' AWK='mawk' BAMCOVERAGE='' CSCOPE='cscope' CTAGS='ctags' CYGPATH_W='echo' DEFS='' ECHO_C='' ECHO_N='-n' ECHO_T='' ETAGS='etags' FASTP='' GNUBASH='/bin/bash' GUNZIP='/bin/gunzip' HISAT2='' HISAT2_BUILD='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LIBOBJS='' LIBS='' LTLIBOBJS='' MAKEINFO='${SHELL} '\''/<<PKGBUILDDIR>>/build-aux/missing'\'' makeinfo' MEGADEPTH='' MKDIR_P='/usr/bin/mkdir -p' MULTIQC='' PACKAGE='pigx_rnaseq' PACKAGE_BUGREPORT='' PACKAGE_NAME='PiGx_rnaseq' PACKAGE_STRING='PiGx_rnaseq 0.1.1' PACKAGE_TARNAME='pigx_rnaseq' PACKAGE_URL='' PACKAGE_VERSION='0.1.1' PANDOC='' PATH_SEPARATOR=':' PYTHON='/usr/bin/python3' PYTHONPATH='' PYTHON_EXEC_PREFIX='${exec_prefix}' PYTHON_PLATFORM='linux' PYTHON_PREFIX='${prefix}' PYTHON_VERSION='3.13' R='' RSCRIPT='' R_LIBS_SITE='' SALMON='/usr/bin/salmon' SAMTOOLS='' SED='/bin/sed' SET_MAKE='' SHELL='/bin/bash' SNAKEMAKE='no' STAR='/usr/bin/STAR' STRIP='' VERSION='0.1.1' am__isrc='' am__leading_dot='.' am__rm_f_notfound='' am__tar='tar --format=posix -chf - "$$tardir"' am__untar='tar -xf -' am__xargs_n='xargs -n' bindir='${exec_prefix}/bin' build_alias='x86_64-linux-gnu' capture_environment='' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' host_alias='' htmldir='${docdir}' includedir='${prefix}/include' infodir='${prefix}/share/info' install_sh='${SHELL} /<<PKGBUILDDIR>>/build-aux/install-sh' libdir='${prefix}/lib/x86_64-linux-gnu' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='/var' mandir='${prefix}/share/man' mkdir_p='$(MKDIR_P)' oldincludedir='/usr/include' pdfdir='${docdir}' pkgpyexecdir='${pyexecdir}/pigx_rnaseq' pkgpythondir='${pythondir}/pigx_rnaseq' prefix='/usr' program_transform_name='s,x,x,' psdir='${docdir}' pyexecdir='${PYTHON_EXEC_PREFIX}/lib/python3.13/site-packages' pythondir='${PYTHON_PREFIX}/lib/python3.13/site-packages' runstatedir='/run' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='/etc' target_alias='' ## ------------------- ## ## File substitutions. ## ## ------------------- ## PIPELINE_META='' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "PiGx_rnaseq" #define PACKAGE_TARNAME "pigx_rnaseq" #define PACKAGE_VERSION "0.1.1" #define PACKAGE_STRING "PiGx_rnaseq 0.1.1" #define PACKAGE_BUGREPORT "" #define PACKAGE_URL "" #define PACKAGE "pigx_rnaseq" #define VERSION "0.1.1" configure: exit 1 dh_auto_configure: error: ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking GUNZIP=/bin/gunzip SED=/bin/sed returned exit code 1 make[1]: *** [debian/rules:19: override_dh_auto_configure] Error 25 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:12: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 --------------------------------------------------------------------------------
