Bio_AssemblyImprovement v1.160490 Perl 5 v5.27.5 x86_64-linux

Status
Pass
From
Slaven Rezić (SREZIC)
Dist
Bio_AssemblyImprovement v1.160490
Platform
Perl 5 v5.27.5 x86_64-linux
Date
2017-10-27 15:28:21
ID
7731dbec-bb2b-11e7-b25d-961adb110bc2
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 Andrew Page,

This is a computer-generated report for Bio_AssemblyImprovement-1.160490
on perl 5.27.5, 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 '/usr/bin/make test':

PERL_DL_NONLAZY=1 "/opt/perl-5.27.5/bin/perl5.27.5" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Abacas/*.t t/AdapterRemoval/Trimmomatic/*.t t/Assemble/SGA/*.t t/Circlator/*.t t/DigitalNormalisation/Khmer/*.t t/FillGaps/*.t t/IvaQC/*.t t/Overall/*.t t/PrepareForSubmission/*.t t/PrimerRemoval/*.t t/Quiver/*.t t/Scaffold/*.t t/Util/*.t t/Validate/*.t
t/Abacas/Iterative.t .................... ok
t/Abacas/Main.t ......................... ok
t/AdapterRemoval/Trimmomatic/Main.t ..... ok
t/Assemble/SGA/IndexAndCorrectReads.t ... ok
t/Assemble/SGA/Main.t ................... ok
t/Assemble/SGA/PreprocessReads.t ........ ok
t/Circlator/Main.t ...................... ok
t/DigitalNormalisation/Khmer/Main.t ..... ok
t/FillGaps/GapFillerConfig.t ............ ok
t/FillGaps/Iterative.t .................. ok
Traceback (most recent call last):
  File "/home/cpansand/.cpan/build/2017102715/Bio_AssemblyImprovement-1.160490-0/t/dummy_iva_qc_script_raise_error.py", line 7, in <module>
    raise Error ('Could not run iva_qc check - ignore error message')
__main__.Error: Could not run iva_qc check - ignore error message
Error running iva_qc with: /home/cpansand/.cpan/build/2017102715/Bio_AssemblyImprovement-1.160490-0/t/dummy_iva_qc_script_raise_error.py -f /home/cpansand/.cpan/build/2017102715/Bio_AssemblyImprovement-1.160490-0/t/data/forward.fastq -r /home/cpansand/.cpan/build/2017102715/Bio_AssemblyImprovement-1.160490-0/t/data/reverse.fastq --ref_db /home/cpansand/.cpan/build/2017102715/Bio_AssemblyImprovement-1.160490-0/t/data/database /home/cpansand/.cpan/build/2017102715/Bio_AssemblyImprovement-1.160490-0/t/data/contigs.fa test_iva_qc 
t/IvaQC/Main.t .......................... ok
t/Overall/CheckAllModulesCompile.t ...... ok
t/PrepareForSubmission/RenameContigs.t .. ok
t/PrimerRemoval/Main.t .................. ok
t/Quiver/Main.t ......................... ok
t/requires_external.t ................... ok
t/Scaffold/Descaffold.t ................. ok
t/Scaffold/Iterative.t .................. ok
t/Scaffold/PreprocessInputFiles.t ....... ok
t/Scaffold/SSpaceConfig.t ............... ok
t/Util/FastaTools.t ..................... ok
t/Util/FastqTools.t ..................... ok
t/Util/OrderContigsByLength.t ........... ok
/home/cpansand/.cpan/build/2017102715/Bio_AssemblyImprovement-1.160490-0/t/does_not_exist.pl does not exist. Using default: /home/cpansand/.cpan/build/2017102715/Bio_AssemblyImprovement-1.160490-0/t/dummy_gap_filler_script.pl at lib/Bio/AssemblyImprovement/Validate/Executable.pm line 29.
t/Validate/Executable.t ................. ok
All tests successful.
Files=24, Tests=246,  6 wallclock secs ( 0.04 usr  0.10 sys +  4.29 cusr  1.19 csys =  5.62 CPU)
Result: PASS

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

Prerequisite modules loaded:

requires:

    Module                 Need Have    
    ---------------------- ---- --------
    Bio::SeqIO             0    1.007002
    Cwd                    0    3.62    
    File::Basename         0    2.85    
    File::Copy             0    2.32    
    File::Path             2.07 2.15    
    File::Spec             0    3.62    
    File::Temp             0    0.2304  
    File::Which            0    1.22    
    Getopt::Long           0    2.5     
    Getopt::Std            0    1.12    
    IO::Compress::Gzip     0    2.074   
    IO::Uncompress::Gunzip 0    2.074   
    lib                    0    0.64    
    Moose                  0    2.2006  
    Moose::Role            0    2.2006  
    POSIX                  0    1.78    
    Statistics::Lite       0    3.62    
    strict                 0    1.11    
    Switch                 0    2.17    
    warnings               0    1.37    

build_requires:

    Module                 Need Have    
    ---------------------- ---- --------
    Env::Path              0    0.19    
    ExtUtils::MakeMaker    0    7.30    
    File::Slurp            0    9999.19 
    Test::File::Contents   0    0.23    
    Test::Most             0    0.35    

configure_requires:

    Module                 Need Have    
    ---------------------- ---- --------
    ExtUtils::MakeMaker    0    7.30    


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

Environment variables:

    LANG = C
    LC_ALL = de_DE.UTF-8
    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 = 
    PERL5OPT = 
    PERL5_CPANPLUS_IS_RUNNING = 32357
    PERL5_CPAN_IS_RUNNING = 32357
    PERL5_CPAN_IS_RUNNING_IN_RECURSION = 29283,32357
    PERLDOC = -MPod::Perldoc::ToTextOverstrike
    PERL_BATCH = yes
    PERL_CANARY_STABILITY_NOPROMPT = 1
    PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2017102712/cpanreporter_000_config.ini
    PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
    PERL_PARALLEL_SMOKER = yes
    PERL_USE_UNSAFE_INC = 1
    SHELL = /usr/bin/zsh
    TERM = screen
    TMPDIR = /var/tmp/cpansmoker-1023/2017102712

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

    $^X = /opt/perl-5.27.5/bin/perl5.27.5
    $UID/$EUID = 1023 / 1023
    $GID = 1023 1023
    $EGID = 1023 1023

Perl module toolchain versions installed:

    Module              Have    
    ------------------- --------
    CPAN                2.16    
    CPAN::Meta          2.150010
    Cwd                 3.62    
    ExtUtils::CBuilder  0.280226
    ExtUtils::Command   7.30    
    ExtUtils::Install   2.14    
    ExtUtils::MakeMaker 7.30    
    ExtUtils::Manifest  1.70    
    ExtUtils::ParseXS   3.35    
    File::Spec          3.62    
    JSON                2.94    
    JSON::PP            2.94    
    Module::Build       0.4224  
    Module::Signature   0.81    
    Parse::CPAN::Meta   2.150010
    Test::Harness       3.39    
    Test::More          1.302106
    YAML                1.23    
    YAML::Syck          1.30    
    version             0.9918  


--

Summary of my perl5 (revision 5 version 27 subversion 5) 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+deb9u5 (2017-09-19) x86_64 gnulinux '
    config_args='-ds -e -Dprefix=/opt/perl-5.27.5 -Dusedevel -Dusemallocwrap=no -Dcf_email=srezic@cpan.org'
    hint=recommended
    useposix=true
    d_sigaction=define
    useithreads=undef
    usemultiplicity=undef
    use64bitint=define
    use64bitall=define
    uselongdouble=undef
    usemymalloc=n
    default_inc_excludes_dot=define
    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 -D_FORTIFY_SOURCE=2'
    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_OP_PARENT
    PERL_PRESERVE_IVUV
    PERL_USE_DEVEL
    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 Oct 25 2017 16:03:52
  %ENV:
    PERL5LIB=""
    PERL5OPT=""
    PERL5_CPANPLUS_IS_RUNNING="32357"
    PERL5_CPAN_IS_RUNNING="32357"
    PERL5_CPAN_IS_RUNNING_IN_RECURSION="29283,32357"
    PERLDOC="-MPod::Perldoc::ToTextOverstrike"
    PERL_BATCH="yes"
    PERL_CANARY_STABILITY_NOPROMPT="1"
    PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2017102712/cpanreporter_000_config.ini"
    PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
    PERL_PARALLEL_SMOKER="yes"
    PERL_USE_UNSAFE_INC="1"
  @INC:
    /opt/perl-5.27.5/lib/site_perl/5.27.5/x86_64-linux
    /opt/perl-5.27.5/lib/site_perl/5.27.5
    /opt/perl-5.27.5/lib/5.27.5/x86_64-linux
    /opt/perl-5.27.5/lib/5.27.5
    .