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easybuilders / easybuild-easyconfigs

A collection of easyconfig files that describe which software to build using which build options with EasyBuild.
https://easybuild.io
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Perl problem with VCFtools #1878

Closed verdurin closed 7 months ago

verdurin commented 9 years ago

I've tried building VCFtools and it fails during the compilation of Perl:

== 2015-08-18 08:41:38,921 main.filetools DEBUG Possible new dir /home/operations/.local/easybuild/build/Perl/5.16.3/goolf-1.4.10/DB_File/DB_File-1.827 found == 2015-08-18 08:41:38,921 main.run DEBUG run_cmd: running cmd perl Makefile.PL PREFIX=/srv/data/sw/eb/software/Perl/5.16.3-goolf-1.4.10 (in /home/operations/.local/easybuild/build/Perl/5.16.3/goolf-1.4.10/DB_File/DB_File-1.827) == 2015-08-18 08:41:39,196 main.run DEBUG cmd " perl Makefile.PL PREFIX=/srv/data/sw/eb/software/Perl/5.16.3-goolf-1.4.10 " exited with exitcode 0 and output: Parsing config.in... Looks Good. Checking if your kit is complete... Looks good Note (probably harmless): No library found for -ldb Writing Makefile for DB_File Writing MYMETA.yml and MYMETA.json

== 2015-08-18 08:41:39,196 main.run DEBUG Using default regular expression: (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|.?\w) == 2015-08-18 08:41:39,197 main.run DEBUG run_cmd: running cmd make -j 8 (in /home/operations/.local/easybuild/build/Perl/5.16.3/goolf-1.4.10/DB_File/DB_File-1.827) == 2015-08-18 08:41:39,346 main.run DEBUG cmd " make -j 8 " exited with exitcode 2 and output: gcc -c -I/usr/local/BerkeleyDB/include -D_REENTRANT -D_GNU_SOURCE -fPIC -O2 -march=native -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -DVERSION=\"1.827\" -DXS_VERSION=\"1.827\" -fPIC "-I/srv/data/sw/eb/software/Perl/5.16.3-goolf-1.4.10/lib/perl5/5.16.3/x86_64-linux-thread-multi/CORE" -D_NOT_CORE -DmDB_Prefix_t=size_t -DmDB_Hash_t=u_int32_t version.c /srv/data/sw/eb/software/Perl/5.16.3-goolf-1.4.10/bin/perl /srv/data/sw/eb/software/Perl/5.16.3-goolf-1.4.10/lib/perl5/5.16.3/ExtUtils/xsubpp -noprototypes -typemap /srv/data/sw/eb/software/Perl/5.16.3-goolf-1.4.10/lib/perl5/5.16.3/ExtUtils/typemap -typemap typemap DB_File.xs > DB_File.xsc && mv DB_File.xsc DB_File.c Running Mkbootstrap for DB_File () chmod 644 DB_File.bs cp DB_File.bs blib/arch/auto/DB_File/DB_File.bs chmod 644 blib/arch/auto/DB_File/DB_File.bs cp DB_File.pm blib/lib/DB_File.pm AutoSplitting blib/lib/DB_File.pm (blib/lib/auto/DB_File) version.c:30:16: fatal error: db.h: No such file or directory compilation terminated. make: * [version.o] Error 1 make: * Waiting for unfinished jobs....

== 2015-08-18 08:41:39,383 main ERROR cmd " make -j 8 " exited with exitcode 2 and output: gcc -c -I/usr/local/BerkeleyDB/include -D_REENTRANT -D_GNU_SOURCE -fPIC -O2 -march=native -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -DVERSION=\"1.827\" -DXS_VERSION=\"1.827\" -fPIC "-I/srv/data/sw/eb/software/Perl/5.16.3-goolf-1.4.10/lib/perl5/5.16.3/x86_64-linux-thread-multi/CORE" -D_NOT_CORE -DmDB_Prefix_t=size_t -DmDB_Hash_t=u_int32_t version.c /srv/data/sw/eb/software/Perl/5.16.3-goolf-1.4.10/bin/perl /srv/data/sw/eb/software/Perl/5.16.3-goolf-1.4.10/lib/perl5/5.16.3/ExtUtils/xsubpp -noprototypes -typemap /srv/data/sw/eb/software/Perl/5.16.3-goolf-1.4.10/lib/perl5/5.16.3/ExtUtils/typemap -typemap typemap DB_File.xs > DB_File.xsc && mv DB_File.xsc DB_File.c Running Mkbootstrap for DB_File () chmod 644 DB_File.bs cp DB_File.bs blib/arch/auto/DB_File/DB_File.bs chmod 644 blib/arch/auto/DB_File/DB_File.bs cp DB_File.pm blib/lib/DB_File.pm AutoSplitting blib/lib/DB_File.pm (blib/lib/auto/DB_File) version.c:30:16: fatal error: db.h: No such file or directory compilation terminated. make: * [version.o] Error 1 make: * Waiting for unfinished jobs.... (at easybuild/tools/run.py:360 in parse_cmd_output) == 2015-08-18 08:41:39,384 main.easyblock WARNING build failed (first 300 chars): cmd " make -j 8 " exited with exitcode 2 and output: gcc -c -I/usr/local/BerkeleyDB/include -D_REENTRANT -D_GNU_SOURCE -fPIC -O2 -march=native -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -DVERSION=\"1.827\" -DXS_VERSION=\"1.827\ == 2015-08-18 08:41:39,384 main.EB_Perl INFO Closing log for application name Perl version 5.16.3

Again this is on a CentOS 7.1. VM, using 2.2.0.

boegel commented 9 years ago

@verdurin: known (yet unresolved) issue, see https://github.com/hpcugent/easybuild-easyconfigs/issues/342

boegel commented 9 years ago

913 may help in fixing this (i.e., either add DB as a dep to Perl, or flesh out DB_File form the Perl easyconfig)

verdurin commented 9 years ago

Thanks for the pointers. In the short term, I'm trying out the newer versions at:

http://www.molgenis.org/wiki/ComputeVM

I'll start work on a newer VCFtools .eb for the first GitHub release, too.

Micket commented 7 months ago

DB_File issues should be a thing of the past since we've had this for so long now. Closing.