Bug #123058 for bioperl-run: Undeclared dependency IPC::Run

Sat Sep 16 01:56:39 2017 SREZIC [...] cpan.org - Ticket created

Subject:

Undeclared dependency IPC::Run

t/SABlastPlus.t fails if IPC::Run is not installed: ... # Failed test 'use Bio::Tools::Run::StandAloneBlastPlus;' # at t/SABlastPlus.t line 15. # Tried to use 'Bio::Tools::Run::StandAloneBlastPlus'. # Error: Can't locate IPC/Run.pm in @INC (you may need to install the IPC::Run module) (@INC contains: ../../.. ../../../.. ../lib ... .) at /tmpfs/.cpan-build-cpansand/2017091521/BioPerl-Run-1.007002-Y3ZYcq/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm line 417. # BEGIN failed--compilation aborted at /tmpfs/.cpan-build-cpansand/2017091521/BioPerl-Run-1.007002-Y3ZYcq/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm line 417. # Compilation failed in require at /tmpfs/.cpan-build-cpansand/2017091521/BioPerl-Run-1.007002-Y3ZYcq/blib/lib/Bio/Tools/Run/BlastPlus.pm line 84. # BEGIN failed--compilation aborted at /tmpfs/.cpan-build-cpansand/2017091521/BioPerl-Run-1.007002-Y3ZYcq/blib/lib/Bio/Tools/Run/BlastPlus.pm line 84. # Compilation failed in require at /tmpfs/.cpan-build-cpansand/2017091521/BioPerl-Run-1.007002-Y3ZYcq/blib/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm line 179. # BEGIN failed--compilation aborted at /tmpfs/.cpan-build-cpansand/2017091521/BioPerl-Run-1.007002-Y3ZYcq/blib/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm line 179. # Compilation failed in require at /tmpfs/.cpan-build-cpansand/2017091521/BioPerl-Run-1.007002-Y3ZYcq/blib/lib/Bio/Tools/Run/StandAloneBlastPlus.pm line 427. # BEGIN failed--compilation aborted at /tmpfs/.cpan-build-cpansand/2017091521/BioPerl-Run-1.007002-Y3ZYcq/blib/lib/Bio/Tools/Run/StandAloneBlastPlus.pm line 427. # Compilation failed in require at t/SABlastPlus.t line 15. # BEGIN failed--compilation aborted at t/SABlastPlus.t line 15. # Failed test 'use Bio::Tools::Run::WrapperBase::CommandExts;' # at t/SABlastPlus.t line 17. # Tried to use 'Bio::Tools::Run::WrapperBase::CommandExts'. # Error: Attempt to reload Bio/Tools/Run/WrapperBase/CommandExts.pm aborted. # Compilation failed in require at t/SABlastPlus.t line 17. # BEGIN failed--compilation aborted at t/SABlastPlus.t line 17. Can't locate object method "new" via package "Bio::Tools::Run::BlastPlus" at t/SABlastPlus.t line 21. # Looks like your test exited with 255 just after 3. t/SABlastPlus.t ............... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 72/73 subtests ...

Sat Sep 16 11:38:59 2017 cjfields [...] uiuc.edu - Correspondence added

Fixed on github: https://github.com/bioperl/bioperl-run/commit/d2485a029710683b80218dbe459695ca472eb56f Thanks! On Sat Sep 16 00:56:39 2017, SREZIC wrote: Show quoted text

> t/SABlastPlus.t fails if IPC::Run is not installed: > > ... > # Failed test 'use Bio::Tools::Run::StandAloneBlastPlus;' > # at t/SABlastPlus.t line 15. > # Tried to use 'Bio::Tools::Run::StandAloneBlastPlus'. > # Error: Can't locate IPC/Run.pm in @INC (you may need to install > the IPC::Run module) (@INC contains: ../../.. ../../../.. ../lib ... > .) at /tmpfs/.cpan-build-cpansand/2017091521/BioPerl-Run-1.007002- > Y3ZYcq/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm line 417. > # BEGIN failed--compilation aborted at /tmpfs/.cpan-build- > cpansand/2017091521/BioPerl-Run-1.007002- > Y3ZYcq/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm line 417. > # Compilation failed in require at /tmpfs/.cpan-build- > cpansand/2017091521/BioPerl-Run-1.007002- > Y3ZYcq/blib/lib/Bio/Tools/Run/BlastPlus.pm line 84. > # BEGIN failed--compilation aborted at /tmpfs/.cpan-build- > cpansand/2017091521/BioPerl-Run-1.007002- > Y3ZYcq/blib/lib/Bio/Tools/Run/BlastPlus.pm line 84. > # Compilation failed in require at /tmpfs/.cpan-build- > cpansand/2017091521/BioPerl-Run-1.007002- > Y3ZYcq/blib/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm line > 179. > # BEGIN failed--compilation aborted at /tmpfs/.cpan-build- > cpansand/2017091521/BioPerl-Run-1.007002- > Y3ZYcq/blib/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm line > 179. > # Compilation failed in require at /tmpfs/.cpan-build- > cpansand/2017091521/BioPerl-Run-1.007002- > Y3ZYcq/blib/lib/Bio/Tools/Run/StandAloneBlastPlus.pm line 427. > # BEGIN failed--compilation aborted at /tmpfs/.cpan-build- > cpansand/2017091521/BioPerl-Run-1.007002- > Y3ZYcq/blib/lib/Bio/Tools/Run/StandAloneBlastPlus.pm line 427. > # Compilation failed in require at t/SABlastPlus.t line 15. > # BEGIN failed--compilation aborted at t/SABlastPlus.t line 15. > > # Failed test 'use Bio::Tools::Run::WrapperBase::CommandExts;' > # at t/SABlastPlus.t line 17. > # Tried to use 'Bio::Tools::Run::WrapperBase::CommandExts'. > # Error: Attempt to reload > Bio/Tools/Run/WrapperBase/CommandExts.pm aborted. > # Compilation failed in require at t/SABlastPlus.t line 17. > # BEGIN failed--compilation aborted at t/SABlastPlus.t line 17. > Can't locate object method "new" via package > "Bio::Tools::Run::BlastPlus" at t/SABlastPlus.t line 21. > # Looks like your test exited with 255 just after 3. > t/SABlastPlus.t ............... > Dubious, test returned 255 (wstat 65280, 0xff00) > Failed 72/73 subtests > ...

Sat Sep 16 11:39:00 2017 The RT System itself - Status changed from 'new' to 'open'

Sat Sep 16 11:39:01 2017 cjfields [...] uiuc.edu - Status changed from 'open' to 'resolved'

Sat Mar 31 19:44:08 2018 jkeenan [...] cpan.org - Correspondence added

On Sat Sep 16 11:38:59 2017, cjfields wrote: Show quoted text

> Fixed on github: https://github.com/bioperl/bioperl- > run/commit/d2485a029710683b80218dbe459695ca472eb56f > > Thanks! > > On Sat Sep 16 00:56:39 2017, SREZIC wrote:

> > t/SABlastPlus.t fails if IPC::Run is not installed: > > > > ... > > # Failed test 'use Bio::Tools::Run::StandAloneBlastPlus;' > > # at t/SABlastPlus.t line 15. > > # Tried to use 'Bio::Tools::Run::StandAloneBlastPlus'. > > # Error: Can't locate IPC/Run.pm in @INC (you may need to > > install > > the IPC::Run module) (@INC contains: ../../.. ../../../.. ../lib ... > > .) at /tmpfs/.cpan-build-cpansand/2017091521/BioPerl-Run-1.007002- > > Y3ZYcq/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm line 417. > > # BEGIN failed--compilation aborted at /tmpfs/.cpan-build- > > cpansand/2017091521/BioPerl-Run-1.007002- > > Y3ZYcq/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm line 417. > > # Compilation failed in require at /tmpfs/.cpan-build- > > cpansand/2017091521/BioPerl-Run-1.007002- > > Y3ZYcq/blib/lib/Bio/Tools/Run/BlastPlus.pm line 84. > > # BEGIN failed--compilation aborted at /tmpfs/.cpan-build- > > cpansand/2017091521/BioPerl-Run-1.007002- > > Y3ZYcq/blib/lib/Bio/Tools/Run/BlastPlus.pm line 84. > > # Compilation failed in require at /tmpfs/.cpan-build- > > cpansand/2017091521/BioPerl-Run-1.007002- > > Y3ZYcq/blib/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm > > line > > 179. > > # BEGIN failed--compilation aborted at /tmpfs/.cpan-build- > > cpansand/2017091521/BioPerl-Run-1.007002- > > Y3ZYcq/blib/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm > > line > > 179. > > # Compilation failed in require at /tmpfs/.cpan-build- > > cpansand/2017091521/BioPerl-Run-1.007002- > > Y3ZYcq/blib/lib/Bio/Tools/Run/StandAloneBlastPlus.pm line 427. > > # BEGIN failed--compilation aborted at /tmpfs/.cpan-build- > > cpansand/2017091521/BioPerl-Run-1.007002- > > Y3ZYcq/blib/lib/Bio/Tools/Run/StandAloneBlastPlus.pm line 427. > > # Compilation failed in require at t/SABlastPlus.t line 15. > > # BEGIN failed--compilation aborted at t/SABlastPlus.t line 15. > > > > # Failed test 'use Bio::Tools::Run::WrapperBase::CommandExts;' > > # at t/SABlastPlus.t line 17. > > # Tried to use 'Bio::Tools::Run::WrapperBase::CommandExts'. > > # Error: Attempt to reload > > Bio/Tools/Run/WrapperBase/CommandExts.pm aborted. > > # Compilation failed in require at t/SABlastPlus.t line 17. > > # BEGIN failed--compilation aborted at t/SABlastPlus.t line 17. > > Can't locate object method "new" via package > > "Bio::Tools::Run::BlastPlus" at t/SABlastPlus.t line 21. > > # Looks like your test exited with 255 just after 3. > > t/SABlastPlus.t ............... > > Dubious, test returned 255 (wstat 65280, 0xff00) > > Failed 72/73 subtests > > ...

I believe this ticket was changed to Resolved status prematurely. The ticket was closed on Sep 16 2017, but the last CPAN release preceded that by two days. In any event, I encountered this problem today when I attempted to install bioperl-run (version 1.007002) against perl-5.27.10 on FreeBSD-11.0 using 'cpanm' as the installer. This was attempted as part of a larger effort to determine the readiness of a selected subset of CPAN distributions for the upcoming release of perl-5.28.0. Attached please find an excerpt from the cpanm build.log file as well as the relevant 'perl -V' output. Please advise. Thank you very much. Jim Keenan

Subject:

CJFIELDS.BioPerl-Run-1.007002.log.txt

Message body is not shown because it is too large.

Subject:

freebsd-11.0.perl-5.27.10_V.txt

Summary of my perl5 (revision 5 version 27 subversion 10) configuration: Platform: osname=freebsd osvers=11.0-release-p1 archname=amd64-freebsd-thread-multi uname='freebsd kid51-freebsd-11-install-3 11.0-release-p1 freebsd 11.0-release-p1 #0 r306420: thu sep 29 01:43:23 utc 2016 root@releng2.nyi.freebsd.org:usrobjusrsrcsysgeneric amd64 ' config_args='-des -Dusedevel -Duseithreads -Doptimize=-O2 -pipe -fstack-protector -fno-strict-aliasing -Uversiononly -Dman1dir=none -Dman3dir=none -Dprefix=/home/jkeenan/prep528/testing/perl-5.27.10' hint=recommended useposix=true d_sigaction=define useithreads=define usemultiplicity=define use64bitint=define use64bitall=define uselongdouble=undef usemymalloc=n default_inc_excludes_dot=define bincompat5005=undef Compiler: cc='cc' ccflags ='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_FORTIFY_SOURCE=2' optimize='-O2 -pipe -fstack-protector -fno-strict-aliasing' cppflags='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include' ccversion='' gccversion='4.2.1 Compatible FreeBSD Clang 3.8.0 (tags/RELEASE_380/final 262564)' gccosandvers='' intsize=4 longsize=8 ptrsize=8 doublesize=8 byteorder=12345678 doublekind=3 d_longlong=define longlongsize=8 d_longdbl=define longdblsize=16 longdblkind=3 ivtype='long' ivsize=8 nvtype='double' nvsize=8 Off_t='off_t' lseeksize=8 alignbytes=8 prototype=define Linker and Libraries: ld='cc' ldflags ='-pthread -Wl,-E -fstack-protector-strong -L/usr/local/lib' libpth=/usr/lib /usr/local/lib /usr/bin/../lib/clang/3.8.0/lib /usr/lib libs=-lpthread -lgdbm -lm -lcrypt -lutil perllibs=-lpthread -lm -lcrypt -lutil libc= so=so useshrplib=false libperl=libperl.a gnulibc_version='' Dynamic Linking: dlsrc=dl_dlopen.xs dlext=so d_dlsymun=undef ccdlflags=' ' cccdlflags='-DPIC -fPIC' lddlflags='-shared -L/usr/local/lib -fstack-protector-strong' Characteristics of this binary (from libperl): Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS PERL_COPY_ON_WRITE PERL_DONT_CREATE_GVSV PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP PERL_OP_PARENT PERL_PRESERVE_IVUV PERL_USE_DEVEL USE_64_BIT_ALL USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE USE_LOCALE_NUMERIC USE_LOCALE_TIME USE_PERLIO USE_PERL_ATOF USE_REENTRANT_API Built under freebsd Compiled at Mar 21 2018 12:59:59 %ENV: PERL2DIR="/home/jkeenan/gitwork/perl2" PERL_WORKDIR="/home/jkeenan/gitwork/perl" @INC: lib/5.27.10/amd64-freebsd-thread-multi lib/5.27.10 lib /home/jkeenan/prep528/testing/perl-5.27.10/lib/site_perl/5.27.10/amd64-freebsd-thread-multi /home/jkeenan/prep528/testing/perl-5.27.10/lib/site_perl/5.27.10 /home/jkeenan/prep528/testing/perl-5.27.10/lib/5.27.10/amd64-freebsd-thread-multi /home/jkeenan/prep528/testing/perl-5.27.10/lib/5.27.10

Sat Mar 31 19:44:09 2018 jkeenan [...] cpan.org - Status changed from 'resolved' to 'open'