Your message dated Wed, 10 Dec 2025 11:35:25 +0000
with message-id <[email protected]>
and subject line Bug#1122310: fixed in pigx-rnaseq 0.1.1-3
has caused the Debian Bug report #1122310,
regarding pigx-rnaseq: FTBFS with the nocheck build profile
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1122310: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1122310
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: pigx-rnaseq
Source-Version: 0.1.1-3
Done: Santiago Vila <[email protected]>
We believe that the bug you reported is fixed in the latest version of
pigx-rnaseq, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Santiago Vila <[email protected]> (supplier of updated pigx-rnaseq package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 10 Dec 2025 11:40:00 +0100
Source: pigx-rnaseq
Architecture: source
Version: 0.1.1-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Santiago Vila <[email protected]>
Closes: 1122310
Changes:
pigx-rnaseq (0.1.1-3) unstable; urgency=medium
.
* Team upload.
* d/control: Drop <!nocheck> from several BD. Closes: #1122310.
* d/control: Drop "Rules-Requires-Root: no" (default).
* d/control: Drop "Priority: optional" (default).
* d/rules: Drop DH_VERBOSE, leftover from first release.
Checksums-Sha1:
6350920e5c980dfaf436ae2dd02133f2c7b5d666 2355 pigx-rnaseq_0.1.1-3.dsc
d0985956ed933420241f3b0eaa1d200223cabc0c 15576
pigx-rnaseq_0.1.1-3.debian.tar.xz
77c1ecc9f43d10ff26e0756d047985e38957c0dd 26433
pigx-rnaseq_0.1.1-3_source.buildinfo
Checksums-Sha256:
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pigx-rnaseq_0.1.1-3.dsc
8915ac04152a95775b22773ca33002b533a59302ed34e0eb0c001dbf3f0192c4 15576
pigx-rnaseq_0.1.1-3.debian.tar.xz
84ded84283acc6385c4bbf528613be0b9f05a80107fb83293f50556502d74655 26433
pigx-rnaseq_0.1.1-3_source.buildinfo
Files:
bc64c48d093670c310b93e38babd83fd 2355 science optional pigx-rnaseq_0.1.1-3.dsc
b627f298814d3c5dfaf57e7c37f85b6a 15576 science optional
pigx-rnaseq_0.1.1-3.debian.tar.xz
61b8c19282fa13c641dee73b3739f45a 26433 science optional
pigx-rnaseq_0.1.1-3_source.buildinfo
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