Bio_AssemblyImprovement v1.160490 Perl 5 v5.28.0 OpenBSD.amd64-openbsd-thread-multi

Status
Fail
From
Alceu Rodrigues de Freitas Junior
Dist
Bio_AssemblyImprovement v1.160490
Platform
Perl 5 v5.28.0 OpenBSD.amd64-openbsd-thread-multi
Date
2018-07-04 04:48:34
ID
821b2ffc-7f45-11e8-a300-999fc19b7f86
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 5.28.0, created by CPAN-Reporter-1.2018.

Thank you for uploading your work to CPAN.  However, there was a problem
testing your distribution.

If you think this report is invalid, please consult the CPAN Testers Wiki
for suggestions on how to avoid getting FAIL reports for missing library
or binary dependencies, unsupported operating systems, and so on:

http://wiki.cpantesters.org/wiki/CPANAuthorNotes

Sections of this report:

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

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

Additional comments from tester:

this report is from an automated smoke testing program
and was not reviewed by a human for accuracy

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

Output from '/usr/bin/make test':

PERL_DL_NONLAZY=1 "/home/vegeta/perl5/perlbrew/perls/perl-blead/bin/perl5.28.0" "-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
Useless use of concatenation (.) or string in void context at lib/Bio/AssemblyImprovement/Abacas/Main.pm line 33.
t/Abacas/Iterative.t .................... ok
Useless use of concatenation (.) or string in void context at lib/Bio/AssemblyImprovement/Abacas/Main.pm line 33.
t/Abacas/Main.t ......................... ok
Can't exec "java": No such file or directory at lib/Bio/AssemblyImprovement/AdapterRemoval/Trimmomatic/Main.pm line 44.
Error running Trimmomatic with:
java -Xmx1000m -jar t/DummyTrimmomatic.jar PE -threads 1 t/data/trimmo_reads_1.fastq t/data/trimmo_reads_2.fastq trimmed.paired_1.fastq trimmed.unpaired_1.fastq trimmed.paired_2.fastq trimmed.unpaired_2.fastq ILLUMINACLIP:/mnt/cpan_build_dir/vegeta/Bio_AssemblyImprovement-1.160490-0/t/data/trimmo_adapters.fasta:2:10:7:1 MINLEN:50 at lib/Bio/AssemblyImprovement/AdapterRemoval/Trimmomatic/Main.pm line 45.
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 2 just after 2.
t/AdapterRemoval/Trimmomatic/Main.t ..... 
Dubious, test returned 2 (wstat 512, 0x200)
All 2 subtests passed 
t/Assemble/SGA/IndexAndCorrectReads.t ... ok
t/Assemble/SGA/Main.t ................... ok
t/Assemble/SGA/PreprocessReads.t ........ ok
t/Circlator/Main.t ...................... ok
gzip failed: input file '/mnt/cpan_build_dir/vegeta/Bio_AssemblyImprovement-1.160490-0/variable_length.fastq.keep' does not exist
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 2 just after 2.
t/DigitalNormalisation/Khmer/Main.t ..... 
Dubious, test returned 2 (wstat 512, 0x200)
All 2 subtests passed 
t/FillGaps/GapFillerConfig.t ............ ok
t/FillGaps/Iterative.t .................. ok
Can't exec "/mnt/cpan_build_dir/vegeta/Bio_AssemblyImprovement-1.160490-0/t/dummy_iva_qc_script_raise_error.py": No such file or directory at lib/Bio/AssemblyImprovement/IvaQC/Main.pm line 48.
Error running iva_qc with: /mnt/cpan_build_dir/vegeta/Bio_AssemblyImprovement-1.160490-0/t/dummy_iva_qc_script_raise_error.py -f /mnt/cpan_build_dir/vegeta/Bio_AssemblyImprovement-1.160490-0/t/data/forward.fastq -r /mnt/cpan_build_dir/vegeta/Bio_AssemblyImprovement-1.160490-0/t/data/reverse.fastq --ref_db /mnt/cpan_build_dir/vegeta/Bio_AssemblyImprovement-1.160490-0/t/data/database /mnt/cpan_build_dir/vegeta/Bio_AssemblyImprovement-1.160490-0/t/data/contigs.fa test_iva_qc 
t/IvaQC/Main.t .......................... ok
Useless use of concatenation (.) or string in void context at lib/Bio/AssemblyImprovement/Abacas/Main.pm line 33, <$modules> line 2.
t/Overall/CheckAllModulesCompile.t ...... ok
t/PrepareForSubmission/RenameContigs.t .. ok

#   Failed test 'Results file exists in expected location'
#   at t/PrimerRemoval/Main.t line 39.

#   Failed test 'Results file exists in expected location'
#   at t/PrimerRemoval/Main.t line 39.
# Looks like you failed 2 tests of 6.
t/PrimerRemoval/Main.t .................. 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/6 subtests 
t/Quiver/Main.t ......................... ok

#   Failed test 'java in PATH'
#   at t/requires_external.t line 8.
# Looks like you failed 1 test of 1.
t/requires_external.t ................... 
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/1 subtests 
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
/mnt/cpan_build_dir/vegeta/Bio_AssemblyImprovement-1.160490-0/t/does_not_exist.pl does not exist. Using default: /mnt/cpan_build_dir/vegeta/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

Test Summary Report
-------------------
t/AdapterRemoval/Trimmomatic/Main.t   (Wstat: 512 Tests: 2 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
t/DigitalNormalisation/Khmer/Main.t   (Wstat: 512 Tests: 2 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
t/PrimerRemoval/Main.t                (Wstat: 512 Tests: 6 Failed: 2)
  Failed tests:  5-6
  Non-zero exit status: 2
t/requires_external.t                 (Wstat: 256 Tests: 1 Failed: 1)
  Failed test:  1
  Non-zero exit status: 1
Files=24, Tests=239, 20 wallclock secs ( 0.09 usr  0.20 sys + 11.67 cusr  6.28 csys = 18.24 CPU)
Result: FAIL
Failed 4/24 test programs. 3/239 subtests failed.
*** Error 255 in /mnt/cpan_build_dir/vegeta/Bio_AssemblyImprovement-1.160490-0 (Makefile:1003 'test_dynamic')

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

Prerequisite modules loaded:

requires:

    Module                 Need Have    
    ---------------------- ---- --------
    Bio::SeqIO             0    1.007002
    Cwd                    0    3.74    
    File::Basename         0    2.85    
    File::Copy             0    2.33    
    File::Path             2.07 2.15    
    File::Spec             0    3.74    
    File::Temp             0    0.2306  
    File::Which            0    1.22    
    Getopt::Long           0    2.5     
    Getopt::Std            0    1.12    
    IO::Compress::Gzip     0    2.081   
    IO::Uncompress::Gunzip 0    2.081   
    lib                    0    0.64    
    Moose                  0    2.2011  
    Moose::Role            0    2.2011  
    POSIX                  0    1.84    
    Statistics::Lite       0    3.62    
    strict                 0    1.11    
    Switch                 0    2.17    
    warnings               0    1.42    

build_requires:

    Module                 Need Have    
    ---------------------- ---- --------
    Env::Path              0    0.19    
    ExtUtils::MakeMaker    0    7.34    
    File::Slurp            0    9999.19 
    Test::File::Contents   0    0.23    
    Test::Most             0    0.35    

configure_requires:

    Module                 Need Have    
    ---------------------- ---- --------
    ExtUtils::MakeMaker    0    7.34    


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

Environment variables:

    AUTOMATED_TESTING = 1
    DBD_MYSQL_TESTDB = test
    DBD_MYSQL_TESTHOST = localhost
    DBD_MYSQL_TESTPASSWORD = 
    DBD_MYSQL_TESTPORT = 3306
    DBD_MYSQL_TESTUSER = vegeta
    EXTENDED_TESTING = 1
    PATH = /home/vegeta/perl5/perlbrew/bin:/home/vegeta/perl5/perlbrew/perls/perl-blead/bin:/home/vegeta/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/X11R6/bin:/usr/local/bin:/usr/local/sbin
    PERL5LIB = 
    PERL5OPT = 
    PERL5_CPANPLUS_IS_RUNNING = 36016
    PERL5_CPAN_IS_RUNNING = 36016
    PERL5_CPAN_IS_RUNNING_IN_RECURSION = 17366,36016
    PERLBREW_HOME = /home/vegeta/.perlbrew
    PERLBREW_MANPATH = /home/vegeta/perl5/perlbrew/perls/perl-blead/man
    PERLBREW_PATH = /home/vegeta/perl5/perlbrew/bin:/home/vegeta/perl5/perlbrew/perls/perl-blead/bin
    PERLBREW_PERL = perl-blead
    PERLBREW_ROOT = /home/vegeta/perl5/perlbrew
    PERLBREW_SHELLRC_VERSION = 0.83
    PERLBREW_VERSION = 0.83
    PERL_CR_SMOKER_CURRENT = Bio_AssemblyImprovement-1.160490
    PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
    PERL_MM_USE_DEFAULT = 1
    SHELL = /usr/local/bin/bash
    TERM = xterm

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

    $^X = /home/vegeta/perl5/perlbrew/perls/perl-blead/bin/perl5.28.0
    $UID/$EUID = 1001 / 1001
    $GID = 999 999 1001
    $EGID = 999 999 1001

Perl module toolchain versions installed:

    Module              Have    
    ------------------- --------
    CPAN                2.16    
    CPAN::Meta          2.150010
    Cwd                 3.74    
    ExtUtils::CBuilder  0.280230
    ExtUtils::Command   7.34    
    ExtUtils::Install   2.14    
    ExtUtils::MakeMaker 7.34    
    ExtUtils::Manifest  1.71    
    ExtUtils::ParseXS   3.35    
    File::Spec          3.74    
    JSON                2.97001 
    JSON::PP            2.97001 
    Module::Build       0.4224  
    Module::Signature   0.81    
    Parse::CPAN::Meta   2.150010
    Test::Harness       3.42    
    Test::More          1.302136
    YAML                1.26    
    YAML::Syck          n/a     
    version             0.9924  


--

Summary of my perl5 (revision 5 version 28 subversion 0) configuration:
  Snapshot of: 197e7984e9f640254af80f8553707bad217f3814
  Platform:
    osname=openbsd
    osvers=6.3
    archname=OpenBSD.amd64-openbsd-thread-multi
    uname='openbsd cpan-smoker-openbsd 6.3 generic.mp#107 amd64 '
    config_args='-de -Dprefix=/home/vegeta/perl5/perlbrew/perls/perl-blead -Dman1dir=none -Dman3dir=none -Duse64bitall -Dusemultiplicity -Duse64bitint -Dusethreads -Dusedevel -Aeval:scriptdir=/home/vegeta/perl5/perlbrew/perls/perl-blead/bin'
    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 ='-pthread -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_FORTIFY_SOURCE=2'
    optimize='-O2'
    cppflags='-pthread -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
    ccversion=''
    gccversion='4.2.1 Compatible OpenBSD Clang 5.0.1 (tags/RELEASE_501/final)'
    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
    libs=-lpthread -lm -lutil -lc
    perllibs=-lpthread -lm -lutil -lc
    libc=/usr/lib/libc.so.92.3
    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 -fPIC  -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
  Locally applied patches:
    Devel::PatchPerl 1.48
  Built under openbsd
  Compiled at Jun 10 2018 14:27:57
  %ENV:
    PERL5LIB=""
    PERL5OPT=""
    PERL5_CPANPLUS_IS_RUNNING="36016"
    PERL5_CPAN_IS_RUNNING="36016"
    PERL5_CPAN_IS_RUNNING_IN_RECURSION="17366,36016"
    PERLBREW_HOME="/home/vegeta/.perlbrew"
    PERLBREW_MANPATH="/home/vegeta/perl5/perlbrew/perls/perl-blead/man"
    PERLBREW_PATH="/home/vegeta/perl5/perlbrew/bin:/home/vegeta/perl5/perlbrew/perls/perl-blead/bin"
    PERLBREW_PERL="perl-blead"
    PERLBREW_ROOT="/home/vegeta/perl5/perlbrew"
    PERLBREW_SHELLRC_VERSION="0.83"
    PERLBREW_VERSION="0.83"
    PERL_CR_SMOKER_CURRENT="Bio_AssemblyImprovement-1.160490"
    PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
    PERL_MM_USE_DEFAULT="1"
  @INC:
    /home/vegeta/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.28.0/OpenBSD.amd64-openbsd-thread-multi
    /home/vegeta/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.28.0
    /home/vegeta/perl5/perlbrew/perls/perl-blead/lib/5.28.0/OpenBSD.amd64-openbsd-thread-multi
    /home/vegeta/perl5/perlbrew/perls/perl-blead/lib/5.28.0