[Debian-med-packaging] Bug#1122310: pigx-rnaseq: FTBFS with the nocheck build profile

Tue Dec 9 23:12:28 GMT 2025

Package: src:pigx-rnaseq
Version: 0.1.1-2
Severity: serious
Tags: forky sid ftbfs
User: debian-qa at lists.debian.org
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
--------------------------------------------------------------------------------