Summary: | [science-overlay] dev-perl/Bio-BigFile-1.06 fails to emerge because of relocation problem | ||
---|---|---|---|
Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
Status: | UNCONFIRMED --- | ||
Severity: | normal | CC: | mmokrejs |
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Attachments: |
/var/tmp/portage/dev-perl/Bio-BigFile-1.06/temp/build.log
build.log |
Description
Juergen Rose
2011-12-26 15:13:16 UTC
I tried again to install Bio-BigFile-1.06. Now at first ucsc-genome-browser is updated to ucsc-genome-browser-260. Then 'emerge Bio-BigFile' fails with: ... * perl Build.PL --installdirs=vendor --libdoc= --destdir=/var/tmp/portage/dev-perl/Bio-BigFile-1.06/image/ --create_packlist=0 This module requires the compiled jkweb.a library from Jim Kent's source tree. If you haven't already done so, please download the source from http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the contents of the "kent/src/lib" subdirectory as directed in the README. Then enter the location of the "kent/src" subdirectory at the prompt below. To prevent this message from appearing in the future, set the environment variable KENT_SRC to point to the "kent/src" subdirectory. Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-BigFile' version '1.06' >>> Source configured. >>> Compiling source in /var/tmp/portage/dev-perl/Bio-BigFile-1.06/work/Bio-BigFile-1.06 ... Building Bio-BigFile x86_64-pc-linux-gnu-gcc -I/usr/include/ucsc-genome-browser -I/usr/lib64/perl5/5.12.4/x86_64-linux-thread-multi/CORE -DXS_VERSION="1.06" -DVERSION="1.06" -fPIC -Wno-format -Wformat=0 -DMACHTYPE_ -c -march=amdfam10 -O2 -pipe -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -march=amdfam10 -O2 -pipe -o lib/Bio/DB/BigFile.o lib/Bio/DB/BigFile.c ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs') x86_64-pc-linux-gnu-gcc -shared -march=amdfam10 -O2 -pipe -Wl,-O1 -Wl,--as-needed -o blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o /jkweb.a -lz -lssl x86_64-pc-linux-gnu-gcc: /jkweb.a: No such file or directory error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from lib/Bio/DB/BigFile.o at /usr/lib64/perl5/vendor_perl/5.12.4/ExtUtils/CBuilder/Base.pm line 310. * ERROR: dev-perl/Bio-BigFile-1.06 failed (compile phase): Because this is an other error I will file a seperate bug for it. I ran myself into this as well now. Created attachment 358590 [details]
build.log
+ 18 Sep 2013; Justin Lecher <jlec@gentoo.org> -Bio-BigFile-1.06.ebuild, + +Bio-BigFile-1.07.ebuild, metadata.xml: + Version BUmp, fix deps + Guys, please come up with a patch for ucsc-genome-browser to fix this issue. Please be aware, that one should only build libs with -fPIC but not apps. So globally adding it to the package won't work. |