Package: src:psortb
Version: 3.0.6+dfsg-3
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp -a psort/bin/psort psort/bin/psort.debsave
dh_auto_configure
/usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now"
External Module XML::RPC, XML Based RPC client, is not installed on this
computer.
The XML::RPC in PSortb needs it for making calls to remote PSortb servers, if
you don't plan to do this, ignore this warning
We think we've found blastall, please enter the path if this isn't correct
[/usr/bin/] /usr/bin/
We think we've found pfscan, please enter the path if this isn't correct
[/usr/bin/] /usr/bin/
Where do you plan to install the psort configuration files? [/usr/local/psortb]
/usr/local/psortb
Checking if your kit is complete...
Looks good
hmmer was not found in the dynamic linker path, is there somewhere else we
should check? [/usr/local/lib64] /usr/local/lib64
We're still not finding hmmer either in your dynamic linker path
(/etc/ld.so.conf) or
in /usr/local/lib64.
Do you want to continue anyways? [Y/n] [Y] Y
squid was not found in the dynamic linker path, is there somewhere else we
should check? [/usr/local/lib64] /usr/local/lib64
We're still not finding squid either in your dynamic linker path
(/etc/ld.so.conf) or
in /usr/local/lib64.
Do you want to continue anyways? [Y/n] [Y] Y
Checking if your kit is complete...
Looks good
Writing MYMETA.yml and MYMETA.json
svmloc was not found in the dynamic linker path, is there somewhere else we
should check? [/usr/local/lib64] /usr/local/lib64
We're still not finding svmloc either in your dynamic linker path
(/etc/ld.so.conf) or
in /usr/local/lib64.
Do you want to continue anyways? [Y/n] [Y] Y
Checking if your kit is complete...
Looks good
Writing MYMETA.yml and MYMETA.json
modhmm was not found in the dynamic linker path, is there somewhere else we
should check? [/usr/local/lib64] /usr/local/lib64
We're still not finding modhmm either in your dynamic linker path
(/etc/ld.so.conf) or
in /usr/local/lib64.
Do you want to continue anyways? [Y/n] [Y] Y
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Bio::Tools::PSort
Writing MYMETA.yml and MYMETA.json
Updating psort/bin/psort with path hints
Making sclblast databases
Building a new DB, current time: 05/05/2024 12:55:03
New DB name: /<<PKGBUILDDIR>>/psort/conf/analysis/sclblast/gramneg/sclblast
New DB title: sclblast
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Error: NCBI C++ Exception:
T0 "c++/include/corelib/ncbidiag.hpp", line 2490: Error:
(CSeqIdException::eFormat) ncbi::objects::CSeq_id::Set() - Malformatted ID
15596049[Extracellular]
Program failed, try executing the command manually.
Building a new DB, current time: 05/05/2024 12:55:04
New DB name: /<<PKGBUILDDIR>>/psort/conf/analysis/sclblast/grampos/sclblast
New DB title: sclblast
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
BLAST Database creation error: Error: Duplicate seq_ids are found:
LCL|145559529
Program failed, try executing the command manually.
Building a new DB, current time: 05/05/2024 12:55:04
New DB name: /<<PKGBUILDDIR>>/psort/conf/analysis/sclblast/archaea/sclblast
New DB title: sclblast
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
FASTA-Reader: Ignoring invalid residues at position(s): On line 46049: 38
FASTA-Reader: Ignoring invalid residues at position(s): On line 87237: 23
FASTA-Reader: Title ends with at least 50 valid amino acid characters. Was the
sequence accidentally put in the title line?
FASTA-Reader: Ignoring invalid residues at position(s): On line 87252: 4
FASTA-Reader: Ignoring invalid residues at position(s): On line 87263: 8
BLAST Database creation error: Error: Duplicate seq_ids are found:
LCL|15596641
Program failed, try executing the command manually.
Ready for make, next steps you must run:
$ make
$ make test
$ make install
RECOMMENDED:
cp -r psort /usr/local/psortb
PSortb will then be available at /usr/local/psortb/bin/psort or in your path
depending on your configuration
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# hack around the issue that configure injects wrong root dir /usr/local/psortb
mv psort/bin/psort.debsave psort/bin/psort
dh_auto_build
make -j2
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>/algorithm-hmm'
cp lib/Bio/Tools/PSort/Report/Formatter/normal.pm
blib/lib/Bio/Tools/PSort/Report/Formatter/normal.pm
cp lib/Bio/Tools/PSort/Report/Formatter/terse.pm
blib/lib/Bio/Tools/PSort/Report/Formatter/terse.pm
cp lib/Bio/Tools/Motif.pm blib/lib/Bio/Tools/Motif.pm
cp lib/Bio/Tools/PSort/Module/AnalysisI.pm
blib/lib/Bio/Tools/PSort/Module/AnalysisI.pm
cp lib/Bio/Tools/PSort/Report/Formatter/html.pm
blib/lib/Bio/Tools/PSort/Report/Formatter/html.pm
cp lib/Bio/Tools/PSort/Module/Motif.pm blib/lib/Bio/Tools/PSort/Module/Motif.pm
cp lib/Bio/Tools/PSort/Module/Bayesian.pm
blib/lib/Bio/Tools/PSort/Module/Bayesian.pm
cp lib/Bio/Tools/PSort/Module/OutputI.pm
blib/lib/Bio/Tools/PSort/Module/OutputI.pm
cp lib/Bio/Tools/PSort/Report/Result.pm
blib/lib/Bio/Tools/PSort/Report/Result.pm
cp lib/Bio/Tools/PSort/Report/Formatter.pm
blib/lib/Bio/Tools/PSort/Report/Formatter.pm
cp lib/Bio/Tools/PSort/Module/ModHMM.pm
blib/lib/Bio/Tools/PSort/Module/ModHMM.pm
cp lib/Bio/Tools/PSort/Module/SVMLocApache.pm
blib/lib/Bio/Tools/PSort/Module/SVMLocApache.pm
cp lib/Bio/Tools/PSort/Module/InputI.pm
blib/lib/Bio/Tools/PSort/Module/InputI.pm
cp lib/Bio/Tools/PSort/Report.pm blib/lib/Bio/Tools/PSort/Report.pm
cp lib/Bio/Tools/PSort/Profile.pm blib/lib/Bio/Tools/PSort/Profile.pm
cp lib/Bio/Tools/PSort/Module/OMPMotif.pm
blib/lib/Bio/Tools/PSort/Module/OMPMotif.pm
cp lib/Bio/Tools/PSort/Module/SVMLoc.pm
blib/lib/Bio/Tools/PSort/Module/SVMLoc.pm
cp lib/Bio/Tools/PSort/Constants.pm blib/lib/Bio/Tools/PSort/Constants.pm
cp lib/Bio/Tools/PSort/Pathway.pm blib/lib/Bio/Tools/PSort/Pathway.pm
cp lib/Bio/Tools/PSort/ModuleI.pm blib/lib/Bio/Tools/PSort/ModuleI.pm
cp lib/Bio/Tools/PSort/Module/Signal.pm
blib/lib/Bio/Tools/PSort/Module/Signal.pm
cp lib/Bio/Tools/PSort/Profile/Match.pm
blib/lib/Bio/Tools/PSort/Profile/Match.pm
cp lib/Bio/Tools/PSort/Module/Rules.pm blib/lib/Bio/Tools/PSort/Module/Rules.pm
cp lib/Bio/Tools/PSort/Module/Profile.pm
blib/lib/Bio/Tools/PSort/Module/Profile.pm
cp lib/Bio/Tools/PSort.pm blib/lib/Bio/Tools/PSort.pm
cp lib/Bio/Tools/PSort/Install.pm blib/lib/Bio/Tools/PSort/Install.pm
cp lib/Bio/Tools/Motif/Pattern.pm blib/lib/Bio/Tools/Motif/Pattern.pm
cp lib/Bio/Tools/Motif/Match.pm blib/lib/Bio/Tools/Motif/Match.pm
cp lib/Bio/Tools/PSort/Report/Formatter/long.pm
blib/lib/Bio/Tools/PSort/Report/Formatter/long.pm
cp lib/Bio/Tools/PSort/Module/HMMTOP.pm
blib/lib/Bio/Tools/PSort/Module/HMMTOP.pm
cp lib/Bio/Tools/PSort/Module/SCLBlast.pm
blib/lib/Bio/Tools/PSort/Module/SCLBlast.pm
cp lib/Bio/Tools/PSort/Module/Null.pm blib/lib/Bio/Tools/PSort/Module/Null.pm
cp lib/Bio/Tools/Signal.pm blib/lib/Bio/Tools/Signal.pm
cp lib/Bio/Tools/Run/SCLBlastLocal.pm blib/lib/Bio/Tools/Run/SCLBlastLocal.pm
cp lib/Bio/Tools/SVMLoc.pm blib/lib/Bio/Tools/SVMLoc.pm
cp lib/Bio/Tools/Run/SCLBlast/Hit.pm blib/lib/Bio/Tools/Run/SCLBlast/Hit.pm
cp lib/Bio/Tools/Run/HMMTOP.pm blib/lib/Bio/Tools/Run/HMMTOP.pm
cp lib/Bio/Tools/PSort/XMLRPC/Client.pm
blib/lib/Bio/Tools/PSort/XMLRPC/Client.pm
cp lib/Bio/Tools/Signal/Report.pm blib/lib/Bio/Tools/Signal/Report.pm
cp lib/Bio/Tools/Run/SCLBlast/Report.pm
blib/lib/Bio/Tools/Run/SCLBlast/Report.pm
cp lib/Bio/Tools/Run/HMMTOP/Helix.pm blib/lib/Bio/Tools/Run/HMMTOP/Helix.pm
cp lib/Bio/Tools/Run/HMMTOP/Report.pm blib/lib/Bio/Tools/Run/HMMTOP/Report.pm
cp lib/Bio/Tools/Run/SCLBlast.pm blib/lib/Bio/Tools/Run/SCLBlast.pm
Running Mkbootstrap for HMM ()
chmod 644 "HMM.bs"
"/usr/bin/perl" "/usr/share/perl/5.38.2/ExtUtils/xsubpp" -C++ -typemap
'/usr/share/perl/5.38/ExtUtils/typemap' -typemap '/<<PKGBUILDDIR>>/algorithm-hmm/typemap' HMM.xs >
HMM.xsc
cp lib/Algorithm/HMM/Report.pm ../blib/lib/Algorithm/HMM/Report.pm
cp lib/Algorithm/HMM.pm ../blib/lib/Algorithm/HMM.pm
AutoSplitting ../blib/lib/Algorithm/HMM.pm (../blib/lib/auto/Algorithm/HMM)
cp lib/Algorithm/HMM/Hit/Domain.pm ../blib/lib/Algorithm/HMM/Hit/Domain.pm
cp lib/Algorithm/HMM/Hit.pm ../blib/lib/Algorithm/HMM/Hit.pm
cp lib/Algorithm/HMM/Hit/Global.pm ../blib/lib/Algorithm/HMM/Hit/Global.pm
g++ -c -Isrc/include `pkg-config --cflags libsquid` `pkg-config --cflags libhmmer2` -D_REENTRANT -D_GNU_SOURCE -DDEBIAN
-fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.38/CORE"
hmm-binding.cpp
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
Please specify prototyping behavior for HMM.xs (see perlxs manual)
mv HMM.xsc HMM.c
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs
../blib/arch/auto/Algorithm/HMM/HMM.bs 644
g++ -c -Isrc/include `pkg-config --cflags libsquid` `pkg-config --cflags libhmmer2` -D_REENTRANT -D_GNU_SOURCE -DDEBIAN
-fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.38/CORE"
HMM.c
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
hmm-binding.cpp: In member function ‘HMMReport* HMM::search(char*)’:
hmm-binding.cpp:136:71: warning: ISO C++ forbids converting a string constant
to ‘char*’ [-Wwrite-strings]
136 | PostprocessSignificantHit(ghit, dhit, trace, model, dseq, seqlen,
"SEQ",
|
^~~~~
rm -f ../blib/arch/auto/Algorithm/HMM/HMM.so
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro
-Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong HMM.o hmm-binding.o -o
../blib/arch/auto/Algorithm/HMM/HMM.so \
-lm -lpthread -lstdc++ -lhmmer -lsquid \
chmod 755 ../blib/arch/auto/Algorithm/HMM/HMM.so
Manifying 5 pod documents
make[3]: Leaving directory '/<<PKGBUILDDIR>>/algorithm-hmm'
make[3]: Entering directory '/<<PKGBUILDDIR>>/bio-tools-psort-svmloc'
Running Mkbootstrap for SVMLoc ()
chmod 644 "SVMLoc.bs"
"/usr/bin/perl" "/usr/share/perl/5.38.2/ExtUtils/xsubpp" -C++ -typemap
'/usr/share/perl/5.38/ExtUtils/typemap' -typemap '/<<PKGBUILDDIR>>/bio-tools-psort-svmloc/typemap'
SVMLoc.xs > SVMLoc.xsc
cp lib/Bio/Tools/PSort/SVMLoc.pm ../blib/lib/Bio/Tools/PSort/SVMLoc.pm
AutoSplitting ../blib/lib/Bio/Tools/PSort/SVMLoc.pm
(../blib/lib/auto/Bio/Tools/PSort/SVMLoc)
cp lib/Bio/Tools/PSort/SVMLoc/DataSet.pm
../blib/lib/Bio/Tools/PSort/SVMLoc/DataSet.pm
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SVMLoc.bs
../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.bs 644
Please specify prototyping behavior for SVMLoc.xs (see perlxs manual)
mv SVMLoc.xsc SVMLoc.c
g++ -c -Wall -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\"
-DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.38/CORE" SVMLoc.c
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
rm -f ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro
-Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong SVMLoc.o -o
../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so \
-lsvmloc -lm -lsvm -lstdc++ \
chmod 755 ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so
Manifying 2 pod documents
make[3]: Leaving directory '/<<PKGBUILDDIR>>/bio-tools-psort-svmloc'
make[3]: Entering directory '/<<PKGBUILDDIR>>/bio-tools-psort-modhmm'
Running Mkbootstrap for ModHMM ()
chmod 644 "ModHMM.bs"
"/usr/bin/perl" "/usr/share/perl/5.38.2/ExtUtils/xsubpp" -typemap
'/usr/share/perl/5.38/ExtUtils/typemap' -typemap '/<<PKGBUILDDIR>>/bio-tools-psort-modhmm/typemap'
modhmm.xs > modhmm.xsc
cp lib/Bio/Tools/PSort/ModHMM.pm ../blib/lib/Bio/Tools/PSort/ModHMM.pm
AutoSplitting ../blib/lib/Bio/Tools/PSort/ModHMM.pm
(../blib/lib/auto/Bio/Tools/PSort/ModHMM)
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC
"-I/usr/lib/x86_64-linux-gnu/perl/5.38/CORE" binding.c
binding.c: In function ‘helix_DESTROY’:
binding.c:52:13: error: implicit declaration of function ‘free’
[-Werror=implicit-function-declaration]
52 | free(hSites->helix);
| ^~~~
binding.c:4:1: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
3 | #include "modhmm0.92b/structs.h"
+++ |+#include <stdlib.h>
4 |
binding.c:52:13: warning: incompatible implicit declaration of built-in
function ‘free’ [-Wbuiltin-declaration-mismatch]
52 | free(hSites->helix);
| ^~~~
binding.c:52:13: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
binding.c:55:9: warning: incompatible implicit declaration of built-in function
‘free’ [-Wbuiltin-declaration-mismatch]
55 | free(hSites);
| ^~~~
binding.c:55:9: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
cc1: some warnings being treated as errors
make[3]: *** [Makefile:329: binding.o] Error 1
make[3]: *** Waiting for unfinished jobs....
mv modhmm.xsc modhmm.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/bio-tools-psort-modhmm'
make[2]: *** [Makefile:590: subdirs] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j2 returned exit code 2
make[1]: *** [debian/rules:25: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:10: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202405/
About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large from AWS, using sbuild and a
reduced chroot with only build-essential packages.
If you could not 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 affects, so that this is still visible in the BTS web
page for this package.
Thanks.
