Summary: | sci-biology/clover new ebuild | ||
---|---|---|---|
Product: | Gentoo Linux | Reporter: | dawe <daweonline> |
Component: | New packages | Assignee: | Default Assignee for New Packages <maintainer-wanted> |
Status: | CONFIRMED --- | ||
Severity: | enhancement | CC: | mmokrejs, sci-biology, weaver |
Priority: | High | Keywords: | EBUILD, InOverlay |
Version: | unspecified | ||
Hardware: | All | ||
OS: | Other | ||
Whiteboard: | [sci overlay] | ||
Package list: | Runtime testing required: | --- | |
Attachments: |
the ebuild for clover
this is the patch to have motif file in env variable clover-2006.07.17.ebuild clover-2006.07.17.ebuild clover-2010.02.19.ebuild |
Description
dawe
2006-07-31 05:08:18 UTC
Created attachment 93118 [details]
the ebuild for clover
this is the *raw* ebuild, without patching instructions.
Created attachment 93119 [details, diff]
this is the patch to have motif file in env variable
In a multiuser environment this patch can be useful, so that you don't have to tell each time where the motif file is to every user, biologist like me tend to forget quite soon this kind of things ;-)
Actually clover author doesn't think it is that useful, and he haven't released a patched version.
Since there is no license except a public-domain one, I don't really know if the patch can be distributed, you should know this better than me ;-)
Created attachment 113365 [details]
clover-2006.07.17.ebuild
Edit to simplify and conform to Gentoo standards
The latest version will be available at http://www.gentoo-sunrise.org/sunrise/browser/sunrise/sci-biology/clover NB: Because sci-biology/transfac is now available, and this package can use TRANSFAC data, it should be integrated and a use flag predicated dependency put in. However, I'm not clear on how the transfac files can be translated into clover readable PSSMs, or even whether sci-biology/transfac contains the needed data. /usr/share/transfac-3/matrix.dat is the data file needed, and conversion seems to be trivial. I'll provide an update later. >>> Emerging (2 of 4) sci-biology/clover-2006.07.17 * jaspar2005core RMD160 SHA1 SHA256 size ;-) ... [ ok ] * clover-2006-07-17.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] * checking ebuild checksums ;-) ... [ ok ] * checking auxfile checksums ;-) ... [ ok ] * checking miscfile checksums ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking clover-2006-07-17.tar.gz to /var/tmp/portage/sci-biology/clover-2006.07.17/work sed: can't read Makefile: No such file or directory * * ERROR: sci-biology/clover-2006.07.17 failed. * Call stack: * ebuild.sh, line 49: Called src_unpack * environment, line 988: Called die * The specific snippet of code: * sed -i "s:g++:$(tc-getCXX):; s:-Wall -O3:${CFLAGS}:" Makefile || die "sed failed" * The die message: * sed failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/sci-biology/clover-2006.07.17/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/clover-2006.07.17/temp/environment'. * This ebuild is from an overlay: '/usr/local/portage/layman/sunrise/' * >>> Failed to emerge sci-biology/clover-2006.07.17, Log file: after adding one line to the ebuild into the src_unpack function I got a bit further: >>> Emerging (1 of 3) sci-biology/clover-2006.07.17 * jaspar2005core RMD160 SHA1 SHA256 size ;-) ... [ ok ] * clover-2006-07-17.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] * checking ebuild checksums ;-) ... [ ok ] * checking auxfile checksums ;-) ... [ ok ] * checking miscfile checksums ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking clover-2006-07-17.tar.gz to /var/tmp/portage/sci-biology/clover-2006.07.17/work >>> Source unpacked. >>> Compiling source in /var/tmp/portage/sci-biology/clover-2006.07.17/work/clover-2006-07-17 ... make i686-pc-linux-gnu-g++ -O2 -march=pentium4 -mmmx -msse -msse2 -fomit-frame-pointer -pipe -DNDEBUG -o clover *.cpp In file included from args.cpp:8: MCFgen.hpp: In function ‘void mcf::die(const std::string&)’: MCFgen.hpp:57: error: ‘EXIT_FAILURE’ was not declared in this scope MCFgen.hpp:57: error: ‘exit’ was not declared in this scope In file included from count_oligos.cpp:7: MCFgen.hpp: In function ‘void mcf::die(const std::string&)’: MCFgen.hpp:57: error: ‘EXIT_FAILURE’ was not declared in this scope MCFgen.hpp:57: error: ‘exit’ was not declared in this scope In file included from normalize_pssm.cpp:8: MCFgen.hpp: In function ‘void mcf::die(const std::string&)’: MCFgen.hpp:57: error: ‘EXIT_FAILURE’ was not declared in this scope MCFgen.hpp:57: error: ‘exit’ was not declared in this scope make: *** [clover] Error 1 * * ERROR: sci-biology/clover-2006.07.17 failed. Created attachment 174464 [details]
clover-2006.07.17.ebuild
added just the "cd ${S}" line to the ebuild which is currently in sunrise
Created attachment 241027 [details]
clover-2010.02.19.ebuild
Version bump.
The ebuild is both in Sunrise and Science overlays. How shall we resolve this? For sunrise it doesn't matter, it can remain in the sunrise overlay as long as it does not enter portage. (In reply to comment #11) > For sunrise it doesn't matter, it can remain in the sunrise overlay as long as > it does not enter portage. > Too late, it's already gone. :) Bumped in sci overlay. You really aren't supposed to remove packages from Sunrise without prior masking unless they are moved to gx86. Otherwise, there is a risk that some users will end up with missing packages without a tip where to find a new one. |