BioPerl-Run v1.007003 Perl 5 v5.24.1 x86_64-linux

Status

Pass

From

Slaven Rezić (SREZIC)

Dist

BioPerl-Run v1.007003

Platform

Perl 5 v5.24.1 x86_64-linux

Date

2019-02-08 20:09:37

ID

75cec0ac-2bdd-11e9-aa26-9fe1c07ade3c

This distribution has been tested as part of the CPAN Testers
project, supporting the Perl programming language.  See
http://wiki.cpantesters.org/ for more information or email
questions to cpan-testers-discuss@perl.org


--
Dear Christopher Fields,

This is a computer-generated report for BioPerl-Run-1.007003
on perl 5.24.1, created by CPAN-Reporter-1.2018.

Thank you for uploading your work to CPAN.  Congratulations!
All tests were successful.

Sections of this report:

    * Tester comments
    * Program output
    * Prerequisites
    * Environment and other context

------------------------------
TESTER COMMENTS
------------------------------

Additional comments from tester:

none provided

------------------------------
PROGRAM OUTPUT
------------------------------

Output from './Build test':

# Required executable for Bio::Tools::Run::Alignment::Amap is not present
t/Amap.t ...................... ok
t/AnalysisFactory_soap.t ...... skipped: Network tests have not been requested
t/Analysis_soap.t ............. skipped: Network tests have not been requested
# Required executable for Bio::Tools::Run::BEDTools is not present
t/BEDTools.t .................. ok
# Required executable for Bio::Tools::Run::Alignment::Blat is not present
t/Blat.t ...................... ok
# Required executable for Bio::Tools::Run::Coil is not present
t/Coil.t ...................... ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present
t/Consense.t .................. ok
# Required executable for Bio::Tools::Run::Alignment::DBA is not present
t/DBA.t ....................... ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present
t/DrawGram.t .................. ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present
t/DrawTree.t .................. ok
t/EMBOSS.t .................... ok
t/Ensembl.t ................... skipped: Network tests have not been requested
# You need at least version 1.2 of JDK to run eponine
t/Eponine.t ................... ok
# Required executable for Bio::Tools::Run::Alignment::Exonerate is not present
t/Exonerate.t ................. ok
# Required executable for Bio::Tools::Run::Phylo::FastTree is not present
t/FastTree.t .................. ok
# Required executable for Bio::Tools::Run::FootPrinter is not present
t/FootPrinter.t ............... ok
# Required environment variable $GENEMARK_MODELS is not set
t/Genemark.hmm.prokaryotic.t .. ok
# Required executable for Bio::Tools::Run::Genewise is not present
t/Genewise.t .................. ok
# Required environment variable $GENSCANDIR is not set
t/Genscan.t ................... ok
# Required executable for Bio::Tools::Run::Phylo::Gerp is not present
t/Gerp.t ...................... ok
# Required executable for Bio::Tools::Run::Glimmer is not present
t/Glimmer2.t .................. ok
# Required executable for Bio::Tools::Run::Glimmer is not present
t/Glimmer3.t .................. ok
# Required executable for Bio::Tools::Run::Hmmer is not present
t/Hmmer.t ..................... ok
# Required executable for Bio::Tools::Run::Phylo::Hyphy::REL is not present
t/Hyphy.t ..................... ok
# Required executable for Bio::Tools::Run::Infernal is not present
t/Infernal.t .................. ok
# Required executable for Bio::Tools::Run::Alignment::Kalign is not present
t/Kalign.t .................... ok
# Required executable for Bio::Tools::Run::Phylo::LVB is not present
t/LVB.t ....................... ok
# Required executable for Bio::Tools::Run::Alignment::Lagan is not present
t/Lagan.t ..................... ok
# Required executable for Bio::Tools::Run::Alignment::MAFFT is not present
t/MAFFT.t ..................... ok
# Required executable for Bio::Tools::Run::MCS is not present
t/MCS.t ....................... ok
# Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
t/MSAProbs.t .................. ok
# Required executable for Bio::Tools::Run::Match is not present
t/Match.t ..................... ok
# Required executable for Bio::Tools::Run::Mdust is not present
t/Mdust.t ..................... ok
# Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
t/Molphy.t .................... ok
# Required executable for Bio::Tools::Run::Alignment::Muscle is not present
t/Muscle.t .................... ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
t/Neighbor.t .................. ok
# Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present
t/Njtree.t .................... ok
# Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present
t/Pal2Nal.t ................... ok
# Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
t/PhastCons.t ................. ok
# Required executable for Bio::Tools::Run::Phylo::Phyml is not present
t/Phyml.t ..................... ok
# Required executable for Bio::Tools::Run::Primate is not present
t/Primate.t ................... ok
# Required executable for Bio::Tools::Run::Primer3 is not present
t/Primer3.t ................... ok
# Required executable for Bio::Tools::Run::Prints is not present
t/Prints.t .................... ok
# Required executable for Bio::Tools::Run::Alignment::Probalign is not present
t/Probalign.t ................. ok
# Required executable for Bio::Tools::Run::Alignment::Probcons is not present
t/Probcons.t .................. ok
# Required executable for Bio::Tools::Run::Profile is not present
t/Profile.t ................... ok
# Required executable for Bio::Tools::Run::Promoterwise is not present
t/Promoterwise.t .............. ok
t/ProtDist.t .................. ok
t/ProtPars.t .................. ok
# Required executable for Bio::Tools::Run::Pseudowise is not present
t/Pseudowise.t ................ ok
# Required executable for Bio::Tools::Run::Phylo::QuickTree is not present
t/QuickTree.t ................. ok
# Required executable for Bio::Tools::Run::Phylo::Raxml is not present
t/Raxml.t ..................... ok
# Required executable for Bio::Tools::Run::RepeatMasker is not present
t/RepeatMasker.t .............. ok
# Required executable for Bio::Tools::Run::BlastPlus is not present
t/SABlastPlus.t ............... ok
# Required executable for Bio::Tools::Run::Phylo::SLR is not present
t/SLR.t ....................... ok
# Required executable for Bio::Tools::Run::Samtools is not present
t/Samtools.t .................. ok
# Required executable for Bio::Tools::Run::Seg is not present
t/Seg.t ....................... ok
# Required executable for Bio::Tools::Run::Phylo::Semphy is not present
t/Semphy.t .................... ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present
t/SeqBoot.t ................... ok
# Required executable for Bio::Tools::Run::Signalp is not present
t/Signalp.t ................... ok
# Required executable for Bio::Tools::Run::Alignment::Sim4 is not present
t/Sim4.t ...................... ok
# Required executable for Bio::Tools::Run::Simprot is not present
t/Simprot.t ................... ok
t/SoapEU-function.t ........... skipped: Valid email not provided; required for tests
# NCBI SOAP EUtilities API no longer supported as of 2015, modules are deprecated and will be removed in a future release
t/SoapEU-unit.t ............... ok
# Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
t/StandAloneFasta.t ........... ok
# Required executable for Bio::Tools::Run::Tmhmm is not present
t/Tmhmm.t ..................... ok
t/TribeMCL.t .................. ok
t/Vista.t ..................... ok
# Required executable for Bio::Tools::Run::Alignment::Gmap is not present
t/gmap-run.t .................. ok
# Required executable for Bio::Tools::Run::tRNAscanSE is not present
t/tRNAscanSE.t ................ ok
All tests successful.
Files=70, Tests=2205, 10 wallclock secs ( 0.22 usr  0.43 sys +  7.60 cusr  1.83 csys = 10.08 CPU)
Result: PASS

------------------------------
PREREQUISITES
------------------------------

Prerequisite modules loaded:

requires:

    Module             Need     Have    
    ------------------ -------- --------
    Bio::Root::Root    0        1.007001
    Bio::Root::Version 1.007000 1.007001
    perl               v5.6.1   5.024001

build_requires:

    Module             Need     Have    
    ------------------ -------- --------
    Bio::Root::Test    0        0       
    Bio::Root::Version 1.007000 1.007001

configure_requires:

    Module             Need     Have    
    ------------------ -------- --------
    Module::Build      0.42     0.4224  


------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------

Environment variables:

    LANG = C
    PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/cpansand/bin/linux-gnu:/home/cpansand/bin/sh:/home/cpansand/bin:/usr/games:/home/cpansand/devel:/home/eserte/src/srezic-misc/scripts
    PERL5LIB = /home/cpansand/.cpan/build/2019020820/FFI-Platypus-0.81_04-3/blib/arch:/home/cpansand/.cpan/build/2019020820/FFI-Platypus-0.81_04-3/blib/lib
    PERL5OPT = 
    PERL5_CPANPLUS_IS_RUNNING = 17408
    PERL5_CPAN_IS_RUNNING = 17408
    PERL5_CPAN_IS_RUNNING_IN_RECURSION = 11954,17408
    PERLDOC = -MPod::Perldoc::ToTextOverstrike
    PERL_BATCH = yes
    PERL_CANARY_STABILITY_NOPROMPT = 1
    PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2019020819/cpanreporter_000_config.ini
    PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
    PERL_USE_UNSAFE_INC = 1
    SHELL = /usr/bin/zsh
    TERM = screen
    TMPDIR = /var/tmp/cpansmoker-1023/2019020819

Perl special variables (and OS-specific diagnostics, for MSWin32):

    $^X = /opt/perl-5.24.1/bin/perl
    $UID/$EUID = 1023 / 1023
    $GID = 1023 1023
    $EGID = 1023 1023

Perl module toolchain versions installed:

    Module              Have    
    ------------------- --------
    CPAN                2.16    
    CPAN::Meta          2.150010
    Cwd                 3.75    
    ExtUtils::CBuilder  0.280230
    ExtUtils::Command   7.34    
    ExtUtils::Install   2.14    
    ExtUtils::MakeMaker 7.34    
    ExtUtils::Manifest  1.70    
    ExtUtils::ParseXS   3.31    
    File::Spec          3.75    
    JSON                4.01    
    JSON::PP            2.97001 
    Module::Build       0.4224  
    Module::Signature   0.83    
    Parse::CPAN::Meta   2.150010
    Test::Harness       3.42    
    Test::More          1.302140
    YAML                1.26    
    YAML::Syck          1.30    
    version             0.9923  


--

Summary of my perl5 (revision 5 version 24 subversion 1) configuration:
   
  Platform:
    osname=linux, osvers=4.9.0-3-amd64, archname=x86_64-linux
    uname='linux debian9 4.9.0-3-amd64 #1 smp debian 4.9.30-2+deb9u1 (2017-06-18) x86_64 gnulinux '
    config_args='-ds -e -Dprefix=/opt/perl-5.24.1 -Dcf_email=srezic@cpan.org'
    hint=recommended, useposix=true, d_sigaction=define
    useithreads=undef, usemultiplicity=undef
    use64bitint=define, use64bitall=define, uselongdouble=undef
    usemymalloc=n, bincompat5005=undef
  Compiler:
    cc='cc', ccflags ='-fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
    optimize='-O2',
    cppflags='-fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
    ccversion='', gccversion='6.3.0 20170516', 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 =' -fstack-protector-strong -L/usr/local/lib'
    libpth=/usr/local/lib /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed /usr/include/x86_64-linux-gnu /usr/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib
    libs=-lpthread -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc -lgdbm_compat
    perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
    libc=libc-2.24.so, so=so, useshrplib=false, libperl=libperl.a
    gnulibc_version='2.24'
  Dynamic Linking:
    dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
    cccdlflags='-fPIC', lddlflags='-shared -O2 -L/usr/local/lib -fstack-protector-strong'


Characteristics of this binary (from libperl): 
  Compile-time options: HAS_TIMES PERLIO_LAYERS PERL_COPY_ON_WRITE
                        PERL_DONT_CREATE_GVSV
                        PERL_HASH_FUNC_ONE_AT_A_TIME_HARD PERL_MALLOC_WRAP
                        PERL_PRESERVE_IVUV USE_64_BIT_ALL USE_64_BIT_INT
                        USE_LARGE_FILES USE_LOCALE USE_LOCALE_COLLATE
                        USE_LOCALE_CTYPE USE_LOCALE_NUMERIC USE_LOCALE_TIME
                        USE_PERLIO USE_PERL_ATOF
  Built under linux
  Compiled at Jun 23 2017 20:31:37
  %ENV:
    PERL5LIB="/home/cpansand/.cpan/build/2019020820/FFI-Platypus-0.81_04-3/blib/arch:/home/cpansand/.cpan/build/2019020820/FFI-Platypus-0.81_04-3/blib/lib"
    PERL5OPT=""
    PERL5_CPANPLUS_IS_RUNNING="17408"
    PERL5_CPAN_IS_RUNNING="17408"
    PERL5_CPAN_IS_RUNNING_IN_RECURSION="11954,17408"
    PERLDOC="-MPod::Perldoc::ToTextOverstrike"
    PERL_BATCH="yes"
    PERL_CANARY_STABILITY_NOPROMPT="1"
    PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2019020819/cpanreporter_000_config.ini"
    PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
    PERL_USE_UNSAFE_INC="1"
  @INC:
    /home/cpansand/.cpan/build/2019020820/FFI-Platypus-0.81_04-3/blib/arch
    /home/cpansand/.cpan/build/2019020820/FFI-Platypus-0.81_04-3/blib/lib
    /opt/perl-5.24.1/lib/site_perl/5.24.1/x86_64-linux
    /opt/perl-5.24.1/lib/site_perl/5.24.1
    /opt/perl-5.24.1/lib/5.24.1/x86_64-linux
    /opt/perl-5.24.1/lib/5.24.1
    .