108 lines
4.9 KiB
Text
108 lines
4.9 KiB
Text
perl-blead
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==========
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cpanm (App::cpanminus) 1.7043 on perl 5.026000 built for x86_64-linux
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Work directory is /home/ryan/.cpanm/work/1493401403.1499
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You have make /usr/bin/make
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You have LWP 6.26
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You have /bin/tar: tar (GNU tar) 1.29
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Copyright (C) 2015 Free Software Foundation, Inc.
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License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
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This is free software: you are free to change and redistribute it.
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There is NO WARRANTY, to the extent permitted by law.
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Written by John Gilmore and Jay Fenlason.
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You have /usr/bin/unzip
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Searching Bio::DB::bbiFile () on cpanmetadb ...
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Unpacking Bio-BigFile-1.07.tar.gz
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--> Working on Bio::DB::bbiFile
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Fetching http://www.cpan.org/authors/id/L/LD/LDS/Bio-BigFile-1.07.tar.gz ... OK
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Bio-BigFile-1.07
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Bio-BigFile-1.07/Changes
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Bio-BigFile-1.07/MANIFEST
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Bio-BigFile-1.07/META.json
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Bio-BigFile-1.07/README
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Bio-BigFile-1.07/typemap
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Bio-BigFile-1.07/META.yml
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Bio-BigFile-1.07/DISCLAIMER
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Bio-BigFile-1.07/Build.PL
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Bio-BigFile-1.07/LICENSE
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Bio-BigFile-1.07/bin
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Bio-BigFile-1.07/bin/index_bigwigset.pl
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Bio-BigFile-1.07/bin/wigToBigWig.pl
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Bio-BigFile-1.07/bin/bigWigToWig.pl
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Bio-BigFile-1.07/ExampleData
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Bio-BigFile-1.07/ExampleData/dpy-27-variable.bw
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Bio-BigFile-1.07/ExampleData/refSeqTest.flat.bb
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Bio-BigFile-1.07/ExampleData/refSeqTest.flat.bed
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Bio-BigFile-1.07/ExampleData/hg18.chrom.sizes
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Bio-BigFile-1.07/ExampleData/refSeqTest.as
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Bio-BigFile-1.07/ExampleData/WS180.chrom.sizes
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Bio-BigFile-1.07/ExampleData/dpy-27-variable-trunk.wig.gz
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Bio-BigFile-1.07/lib
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Bio-BigFile-1.07/lib/Bio
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Bio-BigFile-1.07/lib/Bio/DB
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Bio-BigFile-1.07/lib/Bio/DB/BigWigSet.pm
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Bio-BigFile-1.07/lib/Bio/DB/BigWig.pm
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Bio-BigFile-1.07/lib/Bio/DB/BigBed.pm
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Bio-BigFile-1.07/lib/Bio/DB/BigFile.xs
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Bio-BigFile-1.07/lib/Bio/DB/BigFile.pm
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Bio-BigFile-1.07/lib/Bio/DB/BigFile
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Bio-BigFile-1.07/lib/Bio/DB/BigFile/Constants.pm
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Bio-BigFile-1.07/lib/Bio/DB/BigFile/Iterators.pm
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Bio-BigFile-1.07/t
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Bio-BigFile-1.07/t/01.bigwig.t
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Bio-BigFile-1.07/t/02.bigbed.t
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Bio-BigFile-1.07/t/04.bigbed_high.t
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Bio-BigFile-1.07/t/03.bigwig_high.t
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Bio-BigFile-1.07/t/05.bigwig_set.t
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Bio-BigFile-1.07/patches
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Bio-BigFile-1.07/patches/kent_src_patch_macosx.diff
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Entering Bio-BigFile-1.07
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Checking configure dependencies from META.json
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Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
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Checking if you have Module::Build 0.38 ... Yes (0.4222)
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Running Build.PL
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Configuring Bio-BigFile-1.07 ...
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This module requires the compiled jkweb.a library from Jim Kent's source tree.
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If you haven't already done so, please download the source from
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http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
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contents of the "kent/src/lib" subdirectory as directed in the README. Then
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enter the location of the "kent/src" subdirectory at the prompt below. To prevent
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this message from appearing in the future, set the environment variable KENT_SRC
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to point to the "kent/src" subdirectory.
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Created MYMETA.yml and MYMETA.json
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Creating new 'Build' script for 'Bio-BigFile' version '1.07'
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Checking dependencies from MYMETA.json ...
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Checking if you have Bio::Root::Version 1.005009001 ... Yes (1.007001)
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Checking if you have ExtUtils::CBuilder 0 ... Yes (0.280224)
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Checking if you have IO::String 0 ... Yes (1.08)
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OK
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Building and testing Bio-BigFile-1.07 ... Building Bio-BigFile
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Use of uninitialized value $_ in concatenation (.) or string at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/ExtUtils/CBuilder/Base.pm line 110.
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cc -I -I/home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/x86_64-linux/CORE -DVERSION="1.07" -DXS_VERSION="1.07" -fPIC -Wno-format -Wformat=0 -DMACHTYPE_ -c -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -o lib/Bio/DB/BigFile.o lib/Bio/DB/BigFile.c
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lib/Bio/DB/BigFile.xs:13:20: fatal error: common.h: No such file or directory
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#include "common.h"
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^
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compilation terminated.
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error building lib/Bio/DB/BigFile.o from 'lib/Bio/DB/BigFile.c' at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/ExtUtils/CBuilder/Base.pm line 174.
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! Installing Bio::DB::bbiFile failed. See /home/ryan/.cpanm/work/1493401403.1499/build.log for details. Retry with --force to force install it.
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FAIL
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Command [cpanm --reinstall --verbose Bio::DB::bbiFile] terminated with exit code 1 ($? = 256) under the following perl environment:
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Command terminated with non-zero status.
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Current perl:
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Name: perl-blead
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Path: /home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl
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Config: -de -Dprefix=/home/ryan/perl5/perlbrew/perls/perl-blead -Dusedevel -Aeval:scriptdir=/home/ryan/perl5/perlbrew/perls/perl-blead/bin
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Compiled at: Mar 30 2017 03:10:09
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perlbrew:
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version: 0.78
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ENV:
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PERLBREW_ROOT: /home/ryan/perl5/perlbrew
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PERLBREW_HOME: /home/ryan/.perlbrew
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PERLBREW_PATH: /home/ryan/perl5/perlbrew/bin:/home/ryan/perl5/perlbrew/perls/perl-blead/bin
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PERLBREW_MANPATH: /home/ryan/perl5/perlbrew/perls/perl-blead/man
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