Bio-ViennaNGS vv0.18 Perl 5 v5.14.2 x86_64-linux-gnu-thread-multi
- Status
- Pass
- From
- NONAME
- Dist
-
Bio-ViennaNGS vv0.18
- Platform
- Perl 5 v5.14.2 x86_64-linux-gnu-thread-multi
- Date
- 2018-03-13 17:15:00
- ID
- 0f96111a-26e2-11e8-ac87-bd0fd8caa0cc
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 MTW,
This is a computer-generated report for Bio-ViennaNGS-v0.18
on perl 5.14.2, created by App::cpanminus::reporter 0.13 (1.5015).
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 '':
Building and testing Bio-ViennaNGS-v0.18.0
cp share/data2/MIOS.bed12 blib/lib/auto/share/dist/Bio-ViennaNGS/data2/MIOS.bed12
cp share/template-TrackHub/trackDb.txt blib/lib/auto/share/dist/Bio-ViennaNGS/template-TrackHub/trackDb.txt
cp share/data1/NC_000913.3.30k.fa blib/lib/auto/share/dist/Bio-ViennaNGS/data1/NC_000913.3.30k.fa
cp share/template-TrackHub/description.html blib/lib/auto/share/dist/Bio-ViennaNGS/template-TrackHub/description.html
cp share/data1/NC_000913.3.30k.gff blib/lib/auto/share/dist/Bio-ViennaNGS/data1/NC_000913.3.30k.gff
cp share/data3/all_DENVG_5UTR.fa blib/lib/auto/share/dist/Bio-ViennaNGS/data3/all_DENVG_5UTR.fa
cp share/template-AssemblyHub/trackDb.txt blib/lib/auto/share/dist/Bio-ViennaNGS/template-AssemblyHub/trackDb.txt
cp share/data1/NC_000913.3.chrom.sizes blib/lib/auto/share/dist/Bio-ViennaNGS/data1/NC_000913.3.chrom.sizes
cp share/template-TrackHub/hub.txt blib/lib/auto/share/dist/Bio-ViennaNGS/template-TrackHub/hub.txt
cp share/data1/SRR794848.8k.bam blib/lib/auto/share/dist/Bio-ViennaNGS/data1/SRR794848.8k.bam
cp share/template-AssemblyHub/genome.txt blib/lib/auto/share/dist/Bio-ViennaNGS/template-AssemblyHub/genome.txt
cp share/template-TrackHub/genome.txt blib/lib/auto/share/dist/Bio-ViennaNGS/template-TrackHub/genome.txt
cp share/data1/NC_000913.CDS.bed6 blib/lib/auto/share/dist/Bio-ViennaNGS/data1/NC_000913.CDS.bed6
cp share/template-AssemblyHub/hub.txt blib/lib/auto/share/dist/Bio-ViennaNGS/template-AssemblyHub/hub.txt
cp share/data1/NC_000913.CDS.bed blib/lib/auto/share/dist/Bio-ViennaNGS/data1/NC_000913.CDS.bed
cp share/template-AssemblyHub/groups.txt blib/lib/auto/share/dist/Bio-ViennaNGS/template-AssemblyHub/groups.txt
cp share/template-AssemblyHub/description.html blib/lib/auto/share/dist/Bio-ViennaNGS/template-AssemblyHub/description.html
cp share/data2/MIOS_sj.bed blib/lib/auto/share/dist/Bio-ViennaNGS/data2/MIOS_sj.bed
cp lib/Bio/ViennaNGS/FeatureChain.pm blib/lib/Bio/ViennaNGS/FeatureChain.pm
cp lib/Bio/ViennaNGS/BedGraphEntry.pm blib/lib/Bio/ViennaNGS/BedGraphEntry.pm
cp lib/Bio/ViennaNGS/Bam.pm blib/lib/Bio/ViennaNGS/Bam.pm
cp lib/Bio/ViennaNGS/SpliceJunc.pm blib/lib/Bio/ViennaNGS/SpliceJunc.pm
cp lib/Bio/ViennaNGS/Subtypes.pm blib/lib/Bio/ViennaNGS/Subtypes.pm
cp lib/Bio/ViennaNGS/Peak.pm blib/lib/Bio/ViennaNGS/Peak.pm
cp lib/Bio/ViennaNGS/FeatureInterval.pm blib/lib/Bio/ViennaNGS/FeatureInterval.pm
cp lib/Bio/ViennaNGS/ExtFeature.pm blib/lib/Bio/ViennaNGS/ExtFeature.pm
cp lib/Bio/ViennaNGS/Util.pm blib/lib/Bio/ViennaNGS/Util.pm
cp lib/Bio/ViennaNGS/Expression.pm blib/lib/Bio/ViennaNGS/Expression.pm
cp lib/Bio/ViennaNGS/Feature.pm blib/lib/Bio/ViennaNGS/Feature.pm
cp lib/Bio/ViennaNGS.pm blib/lib/Bio/ViennaNGS.pm
cp lib/Bio/ViennaNGS/AnnoC.pm blib/lib/Bio/ViennaNGS/AnnoC.pm
cp lib/Bio/ViennaNGS/FeatureIO.pm blib/lib/Bio/ViennaNGS/FeatureIO.pm
cp lib/Bio/ViennaNGS/FeatureLine.pm blib/lib/Bio/ViennaNGS/FeatureLine.pm
cp lib/Bio/ViennaNGS/Tutorial.pm blib/lib/Bio/ViennaNGS/Tutorial.pm
cp lib/Bio/ViennaNGS/Bed.pm blib/lib/Bio/ViennaNGS/Bed.pm
cp lib/Bio/ViennaNGS/UCSC.pm blib/lib/Bio/ViennaNGS/UCSC.pm
cp lib/Bio/ViennaNGS/Fasta.pm blib/lib/Bio/ViennaNGS/Fasta.pm
cp lib/Bio/ViennaNGS/MinimalFeature.pm blib/lib/Bio/ViennaNGS/MinimalFeature.pm
cp scripts/bam_split.pl blib/script/bam_split.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bam_split.pl
cp scripts/kmer_analysis.pl blib/script/kmer_analysis.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/kmer_analysis.pl
cp scripts/fasta_subgrep.pl blib/script/fasta_subgrep.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/fasta_subgrep.pl
cp scripts/bed62bed12.pl blib/script/bed62bed12.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bed62bed12.pl
cp scripts/splice_site_summary.pl blib/script/splice_site_summary.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/splice_site_summary.pl
cp scripts/trim_fastq.pl blib/script/trim_fastq.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/trim_fastq.pl
cp scripts/newUCSCdb.pl blib/script/newUCSCdb.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/newUCSCdb.pl
cp scripts/track_hub_constructor.pl blib/script/track_hub_constructor.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/track_hub_constructor.pl
cp scripts/gff2bed.pl blib/script/gff2bed.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/gff2bed.pl
cp scripts/normalize_multicov.pl blib/script/normalize_multicov.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/normalize_multicov.pl
cp scripts/bam_to_bigwig.pl blib/script/bam_to_bigwig.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bam_to_bigwig.pl
cp scripts/bam_uniq.pl blib/script/bam_uniq.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bam_uniq.pl
cp scripts/bed2bedGraph.pl blib/script/bed2bedGraph.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bed2bedGraph.pl
cp scripts/bed2nt2aa.pl blib/script/bed2nt2aa.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bed2nt2aa.pl
cp scripts/fasta_multigrep.pl blib/script/fasta_multigrep.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/fasta_multigrep.pl
cp scripts/sj_visualizer.pl blib/script/sj_visualizer.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/sj_visualizer.pl
cp scripts/fasta_regex.pl blib/script/fasta_regex.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/fasta_regex.pl
cp scripts/rnaseq_peakfinder.pl blib/script/rnaseq_peakfinder.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/rnaseq_peakfinder.pl
cp scripts/Tutorial_pipeline03.pl blib/script/Tutorial_pipeline03.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/Tutorial_pipeline03.pl
cp scripts/assembly_hub_constructor.pl blib/script/assembly_hub_constructor.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/assembly_hub_constructor.pl
Manifying 19 pod documents
Manifying 17 pod documents
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/data2/MIOS.bed12 (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/template-TrackHub/trackDb.txt (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/data1/NC_000913.3.30k.fa (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/template-TrackHub/description.html (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/data1/NC_000913.3.30k.gff (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/data3/all_DENVG_5UTR.fa (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/template-AssemblyHub/trackDb.txt (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/data1/NC_000913.3.chrom.sizes (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/template-TrackHub/hub.txt (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/data1/SRR794848.8k.bam (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/template-AssemblyHub/genome.txt (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/template-TrackHub/genome.txt (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/data1/NC_000913.CDS.bed6 (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/template-AssemblyHub/hub.txt (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/data1/NC_000913.CDS.bed (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/template-AssemblyHub/groups.txt (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/template-AssemblyHub/description.html (unchanged)
Skip blib/lib/auto/share/dist/Bio-ViennaNGS/data2/MIOS_sj.bed (unchanged)
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/00-prereq.t ............ skipped: Test::Prereq required to test dependencies
# Test Bio::ViennaNGS v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::AnnoC v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::Bam v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::Bed v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::BedGraphEntry v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::Expression v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::ExtFeature v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::Fasta v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::Feature v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::FeatureChain v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::FeatureLine v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::FeatureInterval v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::FeatureIO v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::MinimalFeature v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::Peak v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::SpliceJunc v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::Subtypes v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::Tutorial v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::UCSC v0.18, Perl 5.014002, /usr/bin/perl
# Test Bio::ViennaNGS::Util v0.18, Perl 5.014002, /usr/bin/perl
t/01-load.t .............. ok
t/02-thirdparty.t ........ ok
t/04-UCSC-TrackHub.t ..... ok
t/05-UCSC-AssemblyHub.t .. ok
t/06-SpliceJunc.t ........ ok
t/07-FeatureIO.t ......... ok
t/08-FeatureInterval.t ... ok
t/09-MinimalFeature.t .... ok
t/10-Features.t .......... ok
t/11-BedGraphEntry.t ..... ok
All tests successful.
Files=11, Tests=179, 4 wallclock secs ( 0.08 usr 0.02 sys + 3.06 cusr 0.42 csys = 3.58 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
No requirements found
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = C
LANGUAGE = en_US:en
LC_ALL = en_US.UTF-8
PATH = /opt/local/bin:/opt/local/sbin:/home/mtw/.local/bin:/home/mtw/bin/x86_64:/usr/bin:/usr/bin/X11:/bin:/usr/sbin:/sbin:/home/mtw/Perl:/usr/local/bin:/home/mtw/perl5/bin:/usr/local/perl5/bin/
PERL5LIB = /home/mtw/Perl/MyModules/Bio-ViennaNGS/lib/:/home/mtw/perl5/lib/perl5:/home/mtw/.local/lib/perl5/site_perl/5.12.4
PERL_MB_OPT = --install_base /home/mtw/perl5
PERL_MM_OPT = INSTALL_BASE=/home/mtw/perl5
SHELL = /bin/tcsh
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
EGID = 1000 24 25 29 30 33 44 46 104 107 109 126 1000
EUID = 1000
EXECUTABLE_NAME = /usr/bin/perl
GID = 1000 24 25 29 30 33 44 46 104 107 109 126 1000
UID = 1000
Perl module toolchain versions installed:
Module Have
------------------- ---------
CPAN 1.9600_01
CPAN::Meta 2.120351
Cwd 3.36
ExtUtils::CBuilder 0.280205
ExtUtils::Command 1.17
ExtUtils::Install 1.56
ExtUtils::MakeMaker 7.04
ExtUtils::Manifest 1.65
ExtUtils::ParseXS 2.2210
File::Spec 3.33
JSON 2.53
JSON::PP 2.27203
Module::Build 0.4001
Module::Signature 0.68
Parse::CPAN::Meta 1.4405
Test::Harness 3.35
Test::More 1.001014
YAML 0.81
YAML::Syck 1.20
version 0.88
--
Summary of my perl5 (revision 5 version 14 subversion 2) configuration:
Platform:
osname=linux, osvers=4.9.0-2-amd64, archname=x86_64-linux-gnu-thread-multi
uname='linux tatooine 4.9.0-2-amd64 #1 smp debian 4.9.13-1 (2017-02-27) x86_64 gnulinux '
config_args='-Dusethreads -Duselargefiles -Dccflags=-DDEBIAN -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Dldflags= -Wl,-z,relro -Dlddlflags=-shared -Wl,-z,relro -Dcccdlflags=-fPIC -Darchname=x86_64-linux-gnu -Dprefix=/usr -Dprivlib=/usr/share/perl/5.14 -Darchlib=/usr/lib/perl/5.14 -Dvendorprefix=/usr -Dvendorlib=/usr/share/perl5 -Dvendorarch=/usr/lib/perl5 -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl/5.14.2 -Dsitearch=/usr/local/lib/perl/5.14.2 -Dman1dir=/usr/share/man/man1 -Dman3dir=/usr/share/man/man3 -Dsiteman1dir=/usr/local/man/man1 -Dsiteman3dir=/usr/local/man/man3 -Dusesitecustomize -Duse64bitint -Dman1ext=1 -Dman3ext=3perl -Dpager=/usr/bin/sensible-pager -Uafs -Ud_csh -Ud_ualarm -Uusesfio -Uusenm -Ui_libutil -DDEBUGGING=-g -Doptimize=-O2 -Duseshrplib -Dlibperl=libperl.so.5.14.2 -des'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2 -g',
cppflags='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include'
ccversion='', gccversion='4.7.2', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
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 -L/usr/local/lib'
libpth=/usr/local/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib /usr/lib
libs=-lgdbm -lgdbm_compat -ldb -ldl -lm -lpthread -lc -lcrypt
perllibs=-ldl -lm -lpthread -lc -lcrypt
libc=, so=so, useshrplib=true, libperl=libperl.so.5.14.2
gnulibc_version='2.13'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV USE_64_BIT_ALL USE_64_BIT_INT
USE_ITHREADS USE_LARGE_FILES USE_PERLIO USE_PERL_ATOF
USE_REENTRANT_API USE_SITECUSTOMIZE
Locally applied patches:
DEBPKG:debian/arm_thread_stress_timeout - http://bugs.debian.org/501970 Raise the timeout of ext/threads/shared/t/stress.t to accommodate slower build hosts
DEBPKG:debian/cpan_definstalldirs - Provide a sensible INSTALLDIRS default for modules installed from CPAN.
DEBPKG:debian/db_file_ver - http://bugs.debian.org/340047 Remove overly restrictive DB_File version check.
DEBPKG:debian/doc_info - Replace generic man(1) instructions with Debian-specific information.
DEBPKG:debian/enc2xs_inc - http://bugs.debian.org/290336 Tweak enc2xs to follow symlinks and ignore missing @INC directories.
DEBPKG:debian/errno_ver - http://bugs.debian.org/343351 Remove Errno version check due to upgrade problems with long-running processes.
DEBPKG:debian/libperl_embed_doc - http://bugs.debian.org/186778 Note that libperl-dev package is required for embedded linking
DEBPKG:fixes/respect_umask - Respect umask during installation
DEBPKG:debian/writable_site_dirs - Set umask approproately for site install directories
DEBPKG:debian/extutils_set_libperl_path - EU:MM: Set location of libperl.a to /usr/lib
DEBPKG:debian/no_packlist_perllocal - Don't install .packlist or perllocal.pod for perl or vendor
DEBPKG:debian/prefix_changes - Fiddle with *PREFIX and variables written to the makefile
DEBPKG:debian/fakeroot - Postpone LD_LIBRARY_PATH evaluation to the binary targets.
DEBPKG:debian/instmodsh_doc - Debian policy doesn't install .packlist files for core or vendor.
DEBPKG:debian/ld_run_path - Remove standard libs from LD_RUN_PATH as per Debian policy.
DEBPKG:debian/libnet_config_path - Set location of libnet.cfg to /etc/perl/Net as /usr may not be writable.
DEBPKG:debian/m68k_thread_stress - http://bugs.debian.org/517938 http://bugs.debian.org/495826 Disable some threads tests on m68k for now due to missing TLS.
DEBPKG:debian/mod_paths - Tweak @INC ordering for Debian
DEBPKG:debian/module_build_man_extensions - http://bugs.debian.org/479460 Adjust Module::Build manual page extensions for the Debian Perl policy
DEBPKG:debian/prune_libs - http://bugs.debian.org/128355 Prune the list of libraries wanted to what we actually need.
DEBPKG:fixes/net_smtp_docs - [rt.cpan.org #36038] http://bugs.debian.org/100195 Document the Net::SMTP 'Port' option
DEBPKG:debian/perlivp - http://bugs.debian.org/510895 Make perlivp skip include directories in /usr/local
DEBPKG:debian/cpanplus_definstalldirs - http://bugs.debian.org/533707 Configure CPANPLUS to use the site directories by default.
DEBPKG:debian/cpanplus_config_path - Save local versions of CPANPLUS::Config::System into /etc/perl.
DEBPKG:debian/deprecate-with-apt - http://bugs.debian.org/580034 Point users to Debian packages of deprecated core modules
DEBPKG:fixes/hurd-ccflags - [a190e64] http://bugs.debian.org/587901 [perl #92244] Make hints/gnu.sh append to $ccflags rather than overriding them
DEBPKG:debian/squelch-locale-warnings - http://bugs.debian.org/508764 Squelch locale warnings in Debian package maintainer scripts
DEBPKG:debian/skip-upstream-git-tests - Skip tests specific to the upstream Git repository
DEBPKG:fixes/extutils-cbuilder-cflags - [011e8fb] http://bugs.debian.org/624460 [perl #89478] Append CFLAGS and LDFLAGS to their Config.pm counterparts in EU::CBuilder
DEBPKG:fixes/module-build-home-directory - http://bugs.debian.org/624850 [rt.cpan.org #67893] Fix failing tilde test when run under a UID without a passwd entry
DEBPKG:debian/patchlevel - http://bugs.debian.org/567489 List packaged patches for 5.14.2-21+deb7u5 in patchlevel.h
DEBPKG:fixes/h2ph-multiarch - [e7ec705] http://bugs.debian.org/625808 [perl #90122] Make h2ph correctly search gcc include directories
DEBPKG:fixes/index-tainting - [3b36395] http://bugs.debian.org/291450 [perl #64804] RT 64804: tainting with index() of a constant
DEBPKG:fixes/document_makemaker_ccflags - http://bugs.debian.org/628522 [rt.cpan.org #68613] Document that CCFLAGS should include $Config{ccflags}
DEBPKG:fixes/sys-syslog-socket-timeout-kfreebsd.patch - http://bugs.debian.org/627821 [rt.cpan.org #69997] Use a socket timeout on GNU/kFreeBSD to catch ICMP port unreachable messages
DEBPKG:fixes/hurd-hints - http://bugs.debian.org/636609 Improve general GNU hints, needed for GNU/Hurd.
DEBPKG:fixes/pod_fixes - [7698aed] http://bugs.debian.org/637816 Fix typos in several pod/perl*.pod files
DEBPKG:debian/find_html2text - http://bugs.debian.org/640479 Configure CPAN::Distribution with correct name of html2text
DEBPKG:fixes/digest_eval_hole - http://bugs.debian.org/644108 Close the eval "require $module" security hole in Digest->new($algorithm)
DEBPKG:fixes/hurd-ndbm - [f0d0a20] [perl #102680] http://bugs.debian.org/645989 Add GNU/Hurd hints for NDBM_File
DEBPKG:fixes/sysconf.t-posix - [8040185] [perl #102888] http://bugs.debian.org/646016 Fix hang in ext/POSIX/t/sysconf.t on GNU/Hurd
DEBPKG:fixes/hurd-largefile - [1fda587] [perl #103014] http://bugs.debian.org/645790 enable LFS on GNU/Hurd
DEBPKG:debian/hurd_test_todo_syslog - http://bugs.debian.org/650093 Disable failing GNU/Hurd tests in cpan/Sys-Syslog/t/syslog.t
DEBPKG:fixes/hurd_skip_itimer_virtual - [rt.cpan.org #72754] http://bugs.debian.org/650094 Skip interval timer tests in Time::HiRes on GNU/Hurd
DEBPKG:debian/hurd_test_skip_sigdispatch - http://bugs.debian.org/650188 Disable failing GNU/Hurd tests op/sigdispatch.t
DEBPKG:debian/hurd_test_skip_stack - http://bugs.debian.org/650175 Disable failing GNU/Hurd tests dist/threads/t/stack.t
DEBPKG:debian/hurd_test_skip_pipe - http://bugs.debian.org/650187 Disable failing GNU/Hurd tests io/pipe.t
DEBPKG:debian/hurd_test_skip_io_pipe - http://bugs.debian.org/650096 Disable failing GNU/Hurd tests dist/IO/t/io_pipe.t
DEBPKG:fixes/manpage_name_CPAN - http://bugs.debian.org/650448 [rt.cpan.org #73396] cpan/CPAN: add NAME headings in modules with POD
DEBPKG:fixes/manpage_name_CPANPLUS - http://bugs.debian.org/650450 [rt.cpan.org #73398] cpan/CPANPLUS: add NAME headings in modules with POD
DEBPKG:fixes/manpage_name_Test-Harness - http://bugs.debian.org/650451 [rt.cpan.org #73399] cpan/Test-Harness: add NAME headings in modules with POD
DEBPKG:fixes/manpage_name_Term-UI - http://bugs.debian.org/650452 [rt.cpan.org #73400] cpan/Term-UI: add NAME headings in modules with POD
DEBPKG:fixes/podlators_ae_ligature_fallback - http://bugs.debian.org/652851 Fix the ASCII fallback string for AE
DEBPKG:fixes/fsf_postal_address - [de89470] Update references to the FSF's postal address
DEBPKG:fixes/cpan_module_pod_fixes - [perl #106870] [rt.cpan.org #73447] [rt.cpan.org #73446] Fix POD formatting in Term-Cap and Pod-Parser
DEBPKG:fixes/cgi_no_shellwords_pl - Use Text::ParseWords instead of shellwords.pl
DEBPKG:fixes/path_max_fallback - [perl #109262] http://bugs.debian.org/656869 Don't use _POSIX_PATH_MAX as a fallback PATH_MAX
DEBPKG:debian/makemaker-pasthru - http://bugs.debian.org/660195 [rt.cpan.org #28632] Make EU::MM pass LD through to recursive Makefile.PL invocations
DEBPKG:fixes/propagate_tainted_errors.patch - http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=663158 [perl #111654] properly propagate tainted errors
DEBPKG:debian/perl5db-x-terminal-emulator.patch - http://bugs.debian.org/668490 Invoke x-terminal-emulator rather than xterm in perl5db.pl
DEBPKG:fixes/socket_cache_propagate - http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=659075 [rt.cpan.org #61577] [perl #112736] sockdomain and socktype undef on newly accepted sockets
DEBPKG:fixes/ipc_open3 - [perl #114454] http://bugs.debian.org/683894 IPC::Open3::open3(..., '-') broken
DEBPKG:fixes/string_repeat_overrun - http://bugs.debian.org/689314 [b675304] avoid calling memset with a negative count
DEBPKG:debian/cpan-missing-site-dirs - http://bugs.debian.org/688842 Fix CPAN::FirstTime defaults with nonexisting site dirs if a parent is writable
DEBPKG:fixes/kfreebsd-overrides - http://bugs.debian.org/689713 [perl #115324] [7dc6565] Remove unnecessary overrides in gnukfreebsd and gnuknetbsd hints.
DEBPKG:fixes/tainted-smartmatch - [be88a5c] http://bugs.debian.org/690571 [perl #93590] $tainted ~~ [...] failing
DEBPKG:fixes/regexp-matching-starter - [6e634c5] http://bugs.debian.org/690975 [perl #101710] Regression with /i, latin1 chars.
DEBPKG:fixes/regexp-matching-fold - [399fb9c] http://bugs.debian.org/690976 regexec.c: Fix "\x{FB01}\x{FB00}" =~ /ff/i
DEBPKG:fixes/regexp-matching-opposite-case - [dc91d5a] http://bugs.debian.org/690979 [perl #101970] /[[:lower:]]/i matches upper case
DEBPKG:fixes/reading-glob-copy-handle - [fd1564b] http://bugs.debian.org/629363 [perl #92258] <$fh> hangs on a glob copy
DEBPKG:fixes/smartmatch-rhs-precedence - http://bugs.debian.org/691102 [011be0b] Enforce Any ~~ Object smartmatch precedence
DEBPKG:fixes/perlcheat-update - http://bugs.debian.org/691112 [ab0ae0a] Update PerlCheat to 5.14
DEBPKG:fixes/cgi-cr-escaping - http://bugs.debian.org/693420 CR escaping for P3P and Set-Cookie headers
DEBPKG:fixes/maketext-code-execution - [1735f6f] http://bugs.debian.org/695224 Fix misparsing of maketext strings.
DEBPKG:fixes/storable-security-warning - [664f237] http://bugs.debian.org/695223 add a note about security concerns in Storable
DEBPKG:fixes/digest-sha-doublefree - [rt.cpan.org #82655] http://bugs.debian.org/698172 [a8c6ff7] Fix a double-free bug in Digest::SHA
DEBPKG:fixes/64bitint-signedness-wraparound - http://bugs.debian.org/698320 [94e529c] Avoid wraparound when casting unsigned size_t to signed ssize_t.
DEBPKG:fixes/stdin-sigchld - http://bugs.debian.org/700171 [perl #116621] [be48bbe] add a couple missing LEAVEs in perlio_async_run()
DEBPKG:fixes/hsplit-rehash - [d59e31f] http://bugs.debian.org/702296 Prevent premature hsplit() calls, and only trigger REHASH after hsplit()
DEBPKG:fixes/encode-memleak - http://bugs.debian.org/702416 [5814803] Encode: Fixed a memory leak that occurred in the UTF-8 encoding.
DEBPKG:fixes/threads_shared_elements_crash - [perl #119089] http://bugs.debian.org/718438 threads::shared should not crash if shared elements outlive their aggregate.
DEBPKG:fixes/perlbug-patchlist - [3541c11] http://bugs.debian.org/710842 [perl #118433] Make perlbug look up the list of local patches at run time
DEBPKG:fixes/digest_sha_double_free - [ee8c6f4] [rt.cpan.org #86295] http://bugs.debian.org/711206 maint-5.18: Digest-SHA crash fix in 5.85
DEBPKG:fixes/pl_eval_start_use_after_free - [eae139f] [perl #115992] PL_eval_start use-after-free
DEBPKG:fixes/regcomp_fix_segv - [ebb390a] [perl #115994] fix segv in regcomp.c:S_join_exact()
DEBPKG:fixes/list_util_off_by_two - [623a911] fix off-by-two error in List::Util
DEBPKG:fixes/sdbm_off_by_one - [7f5f08b] [perl #111586] sdbm.c: fix off-by-one access to global ".dir"
DEBPKG:fixes/socket_unpack_sockaddr_un_heap_buffer_overflow - [e508642] [perl #111594] Socket::unpack_sockaddr_un heap-buffer-overflow
DEBPKG:fixes/data_dump_infinite_recurse - [19be3be] don't recurse infinitely in Data::Dumper
DEBPKG:debian/kfreebsd-softupdates - https://bugs.debian.org/796798 =?UTF-8?q?kFreeBSD=2010=20(possibly=20only=20with=20softupdates?= =?UTF-8?q?=20enabled)=20may=20defer=0Acalculating=20the=20mtime=20for=20m?=
DEBPKG:fixes/CVE-2016-2381_duplicate_env - remove duplicate environment variables from environ
DEBPKG:fixes/CVE-2016-1238/remove-dot-when-loading - [perl #127834] (perl #127834) remove . from the end of @INC if complex modules are loaded
DEBPKG:fixes/CVE-2016-1238/remove-dot-in-padwalker - [perl #127834] perl5db.pl: ensure PadWalker is loaded from standard paths
DEBPKG:fixes/CVE-2016-1238/remove-dot-in-dist - [perl #127834] dist/: remove . from @INC when loading optional modules
DEBPKG:fixes/CVE-2016-1238/remove-dot-in-cpan - [perl #127834] cpan/: remove . from @INC when loading optional modules
DEBPKG:debian/CVE-2016-1238/test-suite-without-dot - [perl #127810] Patch unit tests to explicitly insert "." into @INC when needed.
DEBPKG:debian/CVE-2016-1238/eumm-without-dot - [perl #127810] Add PERL_USE_UNSAFE_INC support to EU::MM for fortify_inc support.
DEBPKG:debian/CVE-2016-1238/cpan-without-dot - [perl #127810] Set PERL_USE_UNSAFE_INC for cpan usage
DEBPKG:debian/CVE-2016-1238/sitecustomize-in-etc - Look for sitecustomize.pl in /etc/perl rather than sitelib on Debian systems
DEBPKG:debian/CVE-2016-1238/mb-without-dot - Make Module::Build set PERL_USE_UNSAFE_INC
DEBPKG:debian/CVE-2016-1238/remove-inc-test - Remove test for '.' in @INC as it might not be
DEBPKG:fixes/xsloader-eval - [rt.cpan.org #115808] https://bugs.debian.org/829578 =?UTF-8?q?Don=E2=80=99t=20let=20XSLoader=20load=20relative=20path?= =?UTF-8?q?s?=
DEBPKG:fixes/file_path_chmod_race - https://bugs.debian.org/863870 [rt.cpan.org #121951] Prevent directory chmod race attack.
DEBPKG:fixes/extutils_file_path_compat - Correct the order of tests of chmod(). (#294)
Built under linux
Compiled at Jun 5 2017 18:24:09
%ENV:
PERL5LIB="/home/mtw/Perl/MyModules/Bio-ViennaNGS/lib/:/home/mtw/perl5/lib/perl5:/home/mtw/.local/lib/perl5/site_perl/5.12.4"
PERL_MB_OPT="--install_base /home/mtw/perl5"
PERL_MM_OPT="INSTALL_BASE=/home/mtw/perl5"
@INC:
/home/mtw/Perl/MyModules/Bio-ViennaNGS/lib/
/home/mtw/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
/home/mtw/perl5/lib/perl5
/home/mtw/.local/lib/perl5/site_perl/5.12.4
/etc/perl
/usr/local/lib/perl/5.14.2
/usr/local/share/perl/5.14.2
/usr/lib/perl5
/usr/share/perl5
/usr/lib/perl/5.14
/usr/share/perl/5.14
/usr/local/lib/site_perl
.