Package Details: cufflinks 2.2.1-5

Git Clone URL: https://aur.archlinux.org/cufflinks.git (read-only, click to copy)
Package Base: cufflinks
Description: Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples..
Upstream URL: http://cole-trapnell-lab.github.io/projects/cufflinks/
Licenses: Artistic
Submitter: stratust
Maintainer: greyltc
Last Packager: greyltc
Votes: 2
Popularity: 0.000000
First Submitted: 2012-01-20 01:13 (UTC)
Last Updated: 2019-05-25 20:13 (UTC)

Latest Comments

greyltc commented on 2018-11-12 16:41 (UTC)

the build is broken and i've reported it: https://github.com/cole-trapnell-lab/cufflinks/issues/105

Rhinoceros commented on 2016-09-06 05:13 (UTC)

Won't build for me. ==> Starting build()... /tmp/cufflinks/PKGBUILD: line 21: ./configure: No such file or directory ==> ERROR: A failure occurred in build(). Aborting...

greyltc commented on 2015-06-07 14:37 (UTC)

What's partial about this solution?

khughitt commented on 2015-06-07 11:11 (UTC)

Partial solution: 1. fix url 2. modify LDFLAGS: export LDFLAGS="-L/usr/lib -lboost_system -lboost_filesystem -lboost_thread"

khughitt commented on 2015-06-05 16:07 (UTC)

After fixing URL, compilation still fails: /usr/include/boost/smart_ptr/shared_ptr.hpp:467:14: error: no type named ‘type’ in ‘struct boost::detail::sp_enable_if_auto_ptr<boost::shared_ptr<const ReadGroupProperties>, int>’ common.h:387:5: error: ‘LocusCount::LocusCount()’ is private LocusCount() {} //needs an empty constructor for serialization ^ In file included from common.h:34:0, from hits.h:23, from abundances.h:23, from abundances.cpp:16: /usr/include/boost/serialization/vector.hpp:90:9: error: within this context t.resize(count); Makefile:1418: recipe for target 'abundances.o' failed make[2]: *** [abundances.o] Error 1 make[2]: Leaving directory '/tmp/yaourt-tmp-keith/aur-cufflinks/src/cufflinks-2.2.1/src' Makefile:258: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/tmp/yaourt-tmp-keith/aur-cufflinks/src/cufflinks-2.2.1' Makefile:196: recipe for target 'all' failed make: *** [all] Error 2 Looks like many of the issues are related to BOOST.

greyltc commented on 2015-03-10 17:04 (UTC)

@stratust can you please update the PKGBUILD? I'm getting ==> ERROR: Failure while downloading cufflinks-2.2.1.tar.gz and I assume this is because the repo was moved (see below). Or feel free to orphan this package and I'll happily pick it up.

alexpe87 commented on 2014-12-16 10:35 (UTC)

They moved the repository to somewhere else, you should add this as the new URL: http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.tar.gz

wookietreiber commented on 2014-12-11 13:56 (UTC)

I narrowed it down to the relevant change being introduced in boost 1.56 (see github issue). Until the issue is fixed, I recommend to update the PKGBUILD to reflect depends boost<1.56.0

wookietreiber commented on 2014-12-11 13:02 (UTC)

currently does not compile, see https://github.com/cole-trapnell-lab/cufflinks/issues/3

vejnar commented on 2013-06-06 00:15 (UTC)

With 2.1.1, the gcc and foreach patches are no longer needed as far as I can tell. Could you please update the PKGBUILD?