Bio-Tools-Run-Alignment-TCoffee v1.7.2 Perl 5 v5.26.0 i86pc-solaris-thread-multi

Status
Fail
From
Serguei Trouchelle (STRO)
Dist
Bio-Tools-Run-Alignment-TCoffee v1.7.2
Platform
Perl 5 v5.26.0 i86pc-solaris-thread-multi
Date
2017-09-22T09:23:00
ID
a1062a56-9f77-11e7-ac3c-c4adf83032b5
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 5.26.0, 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/stro/perl/5.26.0t/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 /home/stro/perl/5.26.0t/lib/site_perl/5.26.0/Bio/Root/Root.pm:447
STACK: Bio::Tools::Run::WrapperBase::executable /home/stro/perl/5.26.0t/lib/site_perl/5.26.0/Bio/Tools/Run/WrapperBase.pm:340
STACK: Bio::Tools::Run::Alignment::TCoffee::version /home/stro/cpan/build/5.26.0t/build/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 ( 0.04 usr  0.02 sys +  0.55 cusr  0.12 csys =  0.73 CPU)
Result: FAIL
Failed 2/8 test programs. 1/6 subtests failed.
*** Error code 2
make: Fatal error: Command failed for target `test_dynamic'

------------------------------
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     1.007002
    Bio::Tools::Run::WrapperBase      0     0       
    Cwd                               0     3.67    
    perl                              5.006 5.026000
    strict                            0     1.11    
    utf8                              0     1.19    
    vars                              0     1.03    
    warnings                          0     1.37    

build_requires:

    Module                            Need  Have    
    --------------------------------- ----- --------
    blib                              1.01  1.06    
    Env::Path                         0.18  0.19    
    ExtUtils::MakeMaker               0     7.24    
    File::Spec                        0     3.67    
    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     7.24    


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

Environment variables:

    AUTOMATED_TESTING = 1
    LANG = en_US.UTF-8
    PATH = /usr/gnu/bin:/usr/bin:/usr/sbin:/sbin:/usr/sfw/bin:
    PERL5LIB = 
    PERL5OPT = 
    PERL5_CPANPLUS_IS_RUNNING = 28074
    PERL5_CPAN_IS_RUNNING = 28074
    PERL5_CPAN_IS_RUNNING_IN_RECURSION = 24236,28074
    PERL_CR_SMOKER_CURRENT = Bio-Tools-Run-Alignment-TCoffee-1.7.2
    PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
    PERL_MM_USE_DEFAULT = 1
    PERL_USE_UNSAFE_INC = 1
    SHELL = /bin/bash
    TERM = xterm-256color

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

    $^X = /home/stro/perl/5.26.0t/bin/perl
    $UID/$EUID = 101 / 101
    $GID = 10 10
    $EGID = 10 10

Perl module toolchain versions installed:

    Module              Have      
    ------------------- ----------
    CPAN                2.18      
    CPAN::Meta          2.150010  
    Cwd                 3.67      
    ExtUtils::CBuilder  0.280225  
    ExtUtils::Command   7.24      
    ExtUtils::Install   2.04      
    ExtUtils::MakeMaker 7.24      
    ExtUtils::Manifest  1.70      
    ExtUtils::ParseXS   3.34      
    File::Spec          3.67      
    JSON                2.94      
    JSON::PP            2.27400_02
    Module::Build       0.4224    
    Module::Signature   n/a       
    Parse::CPAN::Meta   2.150010  
    Test::Harness       3.38      
    Test::More          1.302096  
    YAML                1.23      
    YAML::Syck          1.30      
    version             0.9917    


--

Summary of my perl5 (revision 5 version 26 subversion 0) configuration:
   
  Platform:
    osname=solaris
    osvers=2.11
    archname=i86pc-solaris-thread-multi
    uname='sunos vm-openindiana-001 5.11 illumos-ed992b0aac i86pc i386 i86pc solaris '
    config_args=''
    hint=recommended
    useposix=true
    d_sigaction=define
    useithreads=define
    usemultiplicity=define
    use64bitint=undef
    use64bitall=undef
    uselongdouble=undef
    usemymalloc=n
    default_inc_excludes_dot=define
    bincompat5005=undef
  Compiler:
    cc='/opt/SUNWspro/bin/cc'
    ccflags ='-D_REENTRANT -I/usr/gnu/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPERL_USE_SAFE_PUTENV'
    optimize='-O'
    cppflags='-D_REENTRANT -I/usr/gnu/include'
    ccversion='Sun C 5.10 SunOS_i386 2009/06/03'
    gccversion=''
    gccosandvers=''
    intsize=4
    longsize=4
    ptrsize=4
    doublesize=8
    byteorder=1234
    doublekind=3
    d_longlong=define
    longlongsize=8
    d_longdbl=define
    longdblsize=12
    longdblkind=3
    ivtype='long'
    ivsize=4
    nvtype='double'
    nvsize=8
    Off_t='off_t'
    lseeksize=8
    alignbytes=4
    prototype=define
  Linker and Libraries:
    ld='/opt/SUNWspro/bin/cc'
    ldflags =' -L/usr/lib -L/usr/ccs/lib -L/opt/sunstudio12.1/prod/lib -L/lib -L/usr/gnu/lib '
    libpth=/usr/lib /usr/ccs/lib /opt/sunstudio12.1/prod/lib /lib /usr/gnu/lib
    libs=-lpthread -lsocket -lnsl -lgdbm -ldb -ldl -lm -lc
    perllibs=-lpthread -lsocket -lnsl -ldl -lm -lc
    libc=/lib/libc.so
    so=so
    useshrplib=true
    libperl=libperl.so
    gnulibc_version=''
  Dynamic Linking:
    dlsrc=dl_dlopen.xs
    dlext=so
    d_dlsymun=undef
    ccdlflags='  -R /home/stro/perl/5.26.0t/lib/5.26.0/i86pc-solaris-thread-multi/CORE'
    cccdlflags='-KPIC'
    lddlflags='-G -L/usr/lib -L/usr/ccs/lib -L/opt/sunstudio12.1/prod/lib -L/lib -L/usr/gnu/lib'


Characteristics of this binary (from libperl): 
  Compile-time options:
    HAS_TIMES
    MULTIPLICITY
    PERLIO_LAYERS
    PERL_COPY_ON_WRITE
    PERL_DONT_CREATE_GVSV
    PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
    PERL_IMPLICIT_CONTEXT
    PERL_MALLOC_WRAP
    PERL_OP_PARENT
    PERL_PRESERVE_IVUV
    PERL_USE_SAFE_PUTENV
    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 solaris
  Compiled at Sep 18 2017 00:57:02
  %ENV:
    PERL5LIB=""
    PERL5OPT=""
    PERL5_CPANPLUS_IS_RUNNING="28074"
    PERL5_CPAN_IS_RUNNING="28074"
    PERL5_CPAN_IS_RUNNING_IN_RECURSION="24236,28074"
    PERL_CR_SMOKER_CURRENT="Bio-Tools-Run-Alignment-TCoffee-1.7.2"
    PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
    PERL_MM_USE_DEFAULT="1"
    PERL_USE_UNSAFE_INC="1"
  @INC:
    /home/stro/perl/5.26.0t/lib/site_perl/5.26.0/i86pc-solaris-thread-multi
    /home/stro/perl/5.26.0t/lib/site_perl/5.26.0
    /home/stro/perl/5.26.0t/lib/5.26.0/i86pc-solaris-thread-multi
    /home/stro/perl/5.26.0t/lib/5.26.0
    .