Package Details: tophat 2.1.1-2

Git Clone URL: https://aur.archlinux.org/tophat.git (read-only)
Package Base: tophat
Description: fast splice junction mapper for RNA-Seq reads
Upstream URL: http://ccb.jhu.edu/software/tophat/index.shtml
Licenses: custom
Submitter: stratust
Maintainer: wookietreiber
Last Packager: wookietreiber
Votes: 9
Popularity: 0.030870
First Submitted: 2012-01-20 00:50
Last Updated: 2016-06-02 09:33

Latest Comments

wookietreiber commented on 2016-06-02 09:33

I can confirm this issue. I added a patch that should resolve the issue.

alexpe87 commented on 2016-06-02 08:05

Doesn't compile anymore unfortunately...

tophat_reports.cpp: In function ‘void driver(const string&, std::istream&, const std::vector<std::__cxx11::basic_str
ing<char> >&, const string&, const std::vector<std::__cxx11::basic_string<char> >&, const string&, FILE*, FILE*, FIL
E*, FILE*)’:
tophat_reports.cpp:2708:128: error: no matching function for call to ‘make_pair(Junction, JunctionStats&)’
ns.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
^
In file included from /usr/include/c++/6.1.1/bits/stl_algobase.h:64:0,
from /usr/include/c++/6.1.1/bits/char_traits.h:39,
from /usr/include/c++/6.1.1/string:40,
from /usr/include/boost/thread/exceptions.hpp:20,
from /usr/include/boost/thread/pthread/thread_data.hpp:10,
from /usr/include/boost/thread/thread_only.hpp:17,
from /usr/include/boost/thread/thread.hpp:12,
from /usr/include/boost/thread.hpp:13,
from tophat_reports.cpp:19:
/usr/include/c++/6.1.1/bits/stl_pair.h:425:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<ty
pename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&
&)
make_pair(_T1&& __x, _T2&& __y)
^~~~~~~~~
/usr/include/c++/6.1.1/bits/stl_pair.h:425:5: note: template argument deduction/substitution failed:
tophat_reports.cpp:2708:128: note: cannot convert ‘junction_stat’ (type ‘JunctionStats’) to type ‘JunctionStats&&’
ns.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
^
Makefile:1421: recipe for target 'tophat_reports.o' failed
make[2]: *** [tophat_reports.o] Error 1
make[2]: Leaving directory '/tmp/yaourt-tmp-peltzer/aur-tophat/src/tophat-2.1.1/src'
Makefile:313: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/tmp/yaourt-tmp-peltzer/aur-tophat/src/tophat-2.1.1'
Makefile:253: recipe for target 'all' failed
make: *** [all] Error 2
==> ERROR: A failure occurred in build().
Aborting...
==> ERROR: Makepkg was unable to build tophat.
==> Restart building tophat ? [y/N]
==> -------------------------------
==>

rod_d commented on 2015-10-02 19:02

Installed and working beautifully.

Even magically added #!/usr/bin/env python2 (which was something I had to manually edit before... so many programs freak out with Arch's default python being python3).

Super awesome packaging.

Thank you very much :)

wookietreiber commented on 2015-10-02 07:22

@rod_d I already updated to the new tarball.

rod_d commented on 2015-10-02 01:03

I installed a local version of tophat by downloading from their website. I'd prefer a proper package, of course, so I can easily get updates. When this gets resolved please let us know and I'll happily install from you instead. Thanks for your quick reply.

wookietreiber commented on 2015-10-01 14:04

Updated. @rod_d: Thanks for reporting.

wookietreiber commented on 2015-10-01 13:58

Yes, indeed, they changed the tarball without updating the actual version. Apparently, from looking at the diff between the two tarballs (I still have the older one), they initially forgot to add some files to the distribution and install them. Too bad, the tophat people aren't honest enough to publicly acknowledge this mistake and release a new version. This always makes me sad.

rod_d commented on 2015-09-30 17:14

==> Building and installing package
==> Making package: tophat 2.1.0-2 (Wed Sep 30 12:42:54 EDT 2015)
...
==> Validating source files with md5sums...
tophat-2.1.0.tar.gz ... FAILED
seqan-v1.4.2.tar.gz ... Passed
fix_build_w_seqan1.4.patch ... Passed
==> ERROR: One or more files did not pass the validity check!
==> ERROR: Makepkg was unable to build tophat.

Hi,
Is the correct md5 given in the PKGBUILD?
Thanks

wookietreiber commented on 2015-07-24 09:59

I finally got it to work without clang. I checked how debian was building tophat and found out they had a patch that got it to build with SeqAn 1.4. Unfortunately, make still has to use -j1 because of some race conditions.

greyltc commented on 2015-05-27 09:03

Beauty, thanks!

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