Bio-Tools-Run-Alignment-TCoffee v1.7.2 Perl 5 v5.24.3 RC1 x86_64-linux

Status
Fail
From
Slaven Rezić (SREZIC)
Dist
Bio-Tools-Run-Alignment-TCoffee v1.7.2
Platform
Perl 5 v5.24.3 RC1 x86_64-linux
Date
2017-09-15T16:32:08
ID
6ad5bca6-9a33-11e7-bb01-ae9681bcf4a8
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 carandraug,

This is a computer-generated report for Bio-Tools-Run-Alignment-TCoffee-1.7.2
on perl 5.24.3, 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:

none provided

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

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

PERL_DL_NONLAZY=1 "/opt/perl-5.24.3-RC1/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/00-compile.t ........... ok
t/author-eol.t ........... skipped: these tests are for testing by the author
t/author-mojibake.t ...... skipped: these tests are for testing by the author
t/author-no-tabs.t ....... skipped: these tests are for testing by the author
t/author-pod-coverage.t .. skipped: these tests are for testing by the author
t/author-pod-syntax.t .... skipped: these tests are for testing by the author

#   Failed test 't_coffee 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 

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Cannot find executable for t_coffee. path="t_coffee"
STACK: Error::throw
STACK: Bio::Root::Root::throw /opt/perl-5.24.3-RC1/lib/site_perl/5.24.3/Bio/Root/Root.pm:447
STACK: Bio::Tools::Run::WrapperBase::executable /opt/perl-5.24.3-RC1/lib/site_perl/5.24.3/Bio/Tools/Run/WrapperBase.pm:340
STACK: Bio::Tools::Run::Alignment::TCoffee::version /home/cpansand/.cpan/build/2017091506/Bio-Tools-Run-Alignment-TCoffee-1.7.2-0/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:123
STACK: t/TCoffee.t:47
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 2 just after 3.
t/TCoffee.t .............. 
Dubious, test returned 2 (wstat 512, 0x200)
All 3 subtests passed 

Test Summary Report
-------------------
t/requires_external.t  (Wstat: 256 Tests: 1 Failed: 1)
  Failed test:  1
  Non-zero exit status: 1
t/TCoffee.t            (Wstat: 512 Tests: 3 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
Files=8, Tests=6,  1 wallclock secs ( 0.03 usr  0.02 sys +  0.26 cusr  0.04 csys =  0.35 CPU)
Result: FAIL
Failed 2/8 test programs. 1/6 subtests failed.
Makefile:897: die Regel für Ziel „test_dynamic“ scheiterte
make: *** [test_dynamic] Fehler 2

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

Prerequisite modules loaded:

requires:

    Module                            Need  Have    
    --------------------------------- ----- --------
    Bio::AlignIO                      0     0       
    Bio::Factory::ApplicationFactoryI 0     0       
    Bio::Installer::Generic           0     0       
    Bio::Root::IO                     0     0       
    Bio::Root::Root                   0     1.007002
    Bio::Seq                          0     0       
    Bio::SeqIO                        0     0       
    Bio::SimpleAlign                  0     0       
    Bio::Tools::Run::WrapperBase      0     1.007002
    Cwd                               0     3.62    
    perl                              5.006 5.024003
    strict                            0     1.11    
    utf8                              0     1.19    
    vars                              0     1.03    
    warnings                          0     1.36    

build_requires:

    Module                            Need  Have    
    --------------------------------- ----- --------
    blib                              1.01  1.06    
    Env::Path                         0.18  0.19    
    ExtUtils::MakeMaker               0     7.30    
    File::Spec                        0     3.62    
    IO::Handle                        0     1.36    
    IPC::Open3                        0     1.20    
    Test::Exception                   0     0.43    
    Test::More                        0     1.302096
    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 = 18066
    PERL5_CPAN_IS_RUNNING = 18066
    PERL5_CPAN_IS_RUNNING_IN_RECURSION = 13867,18066
    PERLDOC = -MPod::Perldoc::ToTextOverstrike
    PERL_BATCH = yes
    PERL_CANARY_STABILITY_NOPROMPT = 1
    PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2017091415/cpanreporter_001_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-1023/2017091415

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

    $^X = /opt/perl-5.24.3-RC1/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                 3.62    
    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          1.302096
    YAML                1.23    
    YAML::Syck          1.30    
    version             0.9918  


--

Summary of my perl5 (revision 5 version 24 subversion 3) 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+deb9u3 (2017-08-06) x86_64 gnulinux '
    config_args='-ds -e -Dprefix=/opt/perl-5.24.3-RC1 -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
  Locally applied patches:
	RC1
  Built under linux
  Compiled at Sep 10 2017 16:04:31
  %ENV:
    PERL5LIB=""
    PERL5OPT=""
    PERL5_CPANPLUS_IS_RUNNING="18066"
    PERL5_CPAN_IS_RUNNING="18066"
    PERL5_CPAN_IS_RUNNING_IN_RECURSION="13867,18066"
    PERLDOC="-MPod::Perldoc::ToTextOverstrike"
    PERL_BATCH="yes"
    PERL_CANARY_STABILITY_NOPROMPT="1"
    PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2017091415/cpanreporter_001_config.ini"
    PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
    PERL_PARALLEL_SMOKER="yes"
    PERL_USE_UNSAFE_INC="1"
  @INC:
    /opt/perl-5.24.3-RC1/lib/site_perl/5.24.3/x86_64-linux
    /opt/perl-5.24.3-RC1/lib/site_perl/5.24.3
    /opt/perl-5.24.3-RC1/lib/5.24.3/x86_64-linux
    /opt/perl-5.24.3-RC1/lib/5.24.3
    .