Bio-Tools-Run-Alignment-TCoffee v1.7.2 Perl 5 v5.22.2 darwin-thread-multi-2level

Status
Fail
From
Nigel Horne
Dist
Bio-Tools-Run-Alignment-TCoffee v1.7.2
Platform
Perl 5 v5.22.2 darwin-thread-multi-2level
Date
2017-11-07T07:26:40
ID
ff991f18-c38c-11e7-9bef-e555db1c1d4b
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 5.22.2, 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 '/sw/bin/make test':

PERL_DL_NONLAZY=1 "/Users/hornenj/perl5/perlbrew/perls/perl-5.22.2/bin/perl5.22.2" "-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 /Users/hornenj/.cpan/build/BioPerl-1.007002-6/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Tools::Run::WrapperBase::executable /Users/hornenj/.cpan/build/BioPerl-Run-1.007002-2/blib/lib/Bio/Tools/Run/WrapperBase.pm:340
STACK: Bio::Tools::Run::Alignment::TCoffee::version /Users/hornenj/.cpan/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 ( 0.02 usr  0.01 sys +  0.34 cusr  0.11 csys =  0.48 CPU)
Result: FAIL
Failed 2/8 test programs. 1/6 subtests failed.
make: *** [Makefile:896: test_dynamic] Error 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     1.007002
    Bio::SeqIO                        0     0       
    Bio::SimpleAlign                  0     0       
    Bio::Tools::Run::WrapperBase      0     0       
    Cwd                               0     3.62    
    perl                              5.006 5.022002
    strict                            0     1.09    
    utf8                              0     1.17    
    vars                              0     1.03    
    warnings                          0     1.34    

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     1.35    
    IPC::Open3                        0     1.18    
    Test::Exception                   0     0.43    
    Test::More                        0     1.302106
    Test::Most                        0     0.35    

configure_requires:

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


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

Environment variables:

    AUTOMATED_TESTING = 1
    LANG = en_US.UTF-8
    LC_ALL = POSIX
    PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.22.2/bin:/Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.26.1-thread/bin:/Users/hornenj/bin:/usr/bin:/bin:/usr/X11R6/bin:/sw/bin
    PERL5LIB = /Users/hornenj/.cpan/build/Env-Path-0.19-12/blib/arch:/Users/hornenj/.cpan/build/Env-Path-0.19-12/blib/lib:/Users/hornenj/.cpan/build/BioPerl-Run-1.007002-2/blib/arch:/Users/hornenj/.cpan/build/BioPerl-Run-1.007002-2/blib/lib:/Users/hornenj/.cpan/build/BioPerl-1.007002-6/blib/arch:/Users/hornenj/.cpan/build/BioPerl-1.007002-6/blib/lib:/Users/hornenj/.cpan/build/Data-Stag-0.14-6/blib/arch:/Users/hornenj/.cpan/build/Data-Stag-0.14-6/blib/lib
    PERL5OPT = 
    PERL5_CPANPLUS_IS_RUNNING = 11849
    PERL5_CPAN_IS_RUNNING = 11849
    PERL5_MINISMOKEBOX = 0.68
    PERLBREW_BASHRC_VERSION = 0.80
    PERLBREW_HOME = /Users/hornenj/.perlbrew
    PERLBREW_LIB = 
    PERLBREW_MANPATH = /Users/hornenj/perl5/perlbrew/perls/perl-5.22.2/man
    PERLBREW_PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.22.2/bin
    PERLBREW_PERL = perl-5.22.2
    PERLBREW_ROOT = /Users/hornenj/perl5/perlbrew
    PERLBREW_VERSION = 0.80
    PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
    PERL_LOCAL_LIB_ROOT = 
    PERL_MM_USE_DEFAULT = 1
    SHELL = /bin/bash
    TERM = xterm-256color
    TMPDIR = /var/folders/pz/pd7y1qjs6s3cbk170cw50fjc000c61/T/

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

    $^X = /Users/hornenj/perl5/perlbrew/perls/perl-5.22.2/bin/perl5.22.2
    $UID/$EUID = 12481 / 12481
    $GID = 14 14 5344 37191 527 12 62 204 399 206 37223 241 223
    $EGID = 14 14 5344 37191 527 12 62 204 399 206 37223 241 223

Perl module toolchain versions installed:

    Module              Have    
    ------------------- --------
    CPAN                2.16    
    CPAN::Meta          2.150010
    Cwd                 3.62    
    ExtUtils::CBuilder  0.280224
    ExtUtils::Command   7.30    
    ExtUtils::Install   2.06    
    ExtUtils::MakeMaker 7.30    
    ExtUtils::Manifest  1.70    
    ExtUtils::ParseXS   3.30    
    File::Spec          3.62    
    JSON                2.93    
    JSON::PP            2.27400 
    Module::Build       0.4220  
    Module::Signature   0.79    
    Parse::CPAN::Meta   2.150010
    Test::Harness       3.36    
    Test::More          1.302106
    YAML                1.23    
    YAML::Syck          1.30    
    version             0.9917  


--

Summary of my perl5 (revision 5 version 22 subversion 2) configuration:
   
  Platform:
    osname=darwin, osvers=14.5.0, archname=darwin-thread-multi-2level
    uname='darwin ncbimac2027 14.5.0 darwin kernel version 14.5.0: mon jan 11 18:48:35 pst 2016; root:xnu-2782.50.2~1release_x86_64 x86_64 '
    config_args='-de -Dprefix=/Users/hornenj/perl5/perlbrew/perls/perl-5.22.2 -Duseithreads -Dusemultiplicity -Dusedevel -Accflags=-O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -msse2 -msse -mmmx -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fassociative-math -Acc=cc -Aeval:scriptdir=/Users/hornenj/perl5/perlbrew/perls/perl-5.22.2/bin'
    hint=recommended, useposix=true, d_sigaction=define
    useithreads=define, usemultiplicity=define
    use64bitint=define, use64bitall=define, uselongdouble=undef
    usemymalloc=n, bincompat5005=undef
  Compiler:
    cc=' cc', ccflags ='-fno-common -DPERL_DARWIN -O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -msse2 -msse -mmmx -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fassociative-math -fno-strict-aliasing -fstack-protector-strong -I/usr/local/include',
    optimize='-O3',
    cppflags='-fno-common -DPERL_DARWIN -O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -msse2 -msse -mmmx -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fassociative-math -fno-strict-aliasing -fstack-protector-strong -I/usr/local/include'
    ccversion='', gccversion='4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)', 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='env MACOSX_DEPLOYMENT_TARGET=10.3 cc', ldflags =' -fstack-protector-strong -L/usr/local/lib'
    libpth=/usr/local/lib /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/7.0.2/lib /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib /usr/lib
    libs=-lpthread -ldbm -ldl -lm -lutil -lc
    perllibs=-lpthread -ldl -lm -lutil -lc
    libc=, so=dylib, useshrplib=false, libperl=libperl.a
    gnulibc_version=''
  Dynamic Linking:
    dlsrc=dl_dlopen.xs, dlext=bundle, d_dlsymun=undef, ccdlflags=' '
    cccdlflags=' ', lddlflags=' -bundle -undefined dynamic_lookup -L/usr/local/lib -fstack-protector-strong'


Characteristics of this binary (from libperl): 
  Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
                        PERL_DONT_CREATE_GVSV
                        PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
                        PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
                        PERL_NEW_COPY_ON_WRITE 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 1.30
  Built under darwin
  Compiled at May  2 2016 08:59:06
  %ENV:
    PERL5LIB="/Users/hornenj/.cpan/build/Env-Path-0.19-12/blib/arch:/Users/hornenj/.cpan/build/Env-Path-0.19-12/blib/lib:/Users/hornenj/.cpan/build/BioPerl-Run-1.007002-2/blib/arch:/Users/hornenj/.cpan/build/BioPerl-Run-1.007002-2/blib/lib:/Users/hornenj/.cpan/build/BioPerl-1.007002-6/blib/arch:/Users/hornenj/.cpan/build/BioPerl-1.007002-6/blib/lib:/Users/hornenj/.cpan/build/Data-Stag-0.14-6/blib/arch:/Users/hornenj/.cpan/build/Data-Stag-0.14-6/blib/lib"
    PERL5OPT=""
    PERL5_CPANPLUS_IS_RUNNING="11849"
    PERL5_CPAN_IS_RUNNING="11849"
    PERL5_MINISMOKEBOX="0.68"
    PERLBREW_BASHRC_VERSION="0.80"
    PERLBREW_HOME="/Users/hornenj/.perlbrew"
    PERLBREW_LIB=""
    PERLBREW_MANPATH="/Users/hornenj/perl5/perlbrew/perls/perl-5.22.2/man"
    PERLBREW_PATH="/Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.22.2/bin"
    PERLBREW_PERL="perl-5.22.2"
    PERLBREW_ROOT="/Users/hornenj/perl5/perlbrew"
    PERLBREW_VERSION="0.80"
    PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
    PERL_LOCAL_LIB_ROOT=""
    PERL_MM_USE_DEFAULT="1"
  @INC:
    /Users/hornenj/.cpan/build/Env-Path-0.19-12/blib/arch
    /Users/hornenj/.cpan/build/Env-Path-0.19-12/blib/lib
    /Users/hornenj/.cpan/build/BioPerl-Run-1.007002-2/blib/arch
    /Users/hornenj/.cpan/build/BioPerl-Run-1.007002-2/blib/lib
    /Users/hornenj/.cpan/build/BioPerl-1.007002-6/blib/arch
    /Users/hornenj/.cpan/build/BioPerl-1.007002-6/blib/lib
    /Users/hornenj/.cpan/build/Data-Stag-0.14-6/blib/arch
    /Users/hornenj/.cpan/build/Data-Stag-0.14-6/blib/lib
    /Users/hornenj/perl5/perlbrew/perls/perl-5.22.2/lib/site_perl/5.22.2/darwin-thread-multi-2level
    /Users/hornenj/perl5/perlbrew/perls/perl-5.22.2/lib/site_perl/5.22.2
    /Users/hornenj/perl5/perlbrew/perls/perl-5.22.2/lib/5.22.2/darwin-thread-multi-2level
    /Users/hornenj/perl5/perlbrew/perls/perl-5.22.2/lib/5.22.2
    .