SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance. Fix: rename to .txt and unshar the shar ;) Patch attached with submission follows:
Responsible Changed From-To: freebsd-ports-bugs->amdmi3 I'll take it.
* Hannes (h2+fbsdports@fsfe.org) wrote: This will require some minor fixes. First, please fix issues reported by portlint (ports-mgmt/portlint), namely you should use tabs for identation and %%DATADIR%% instead if share/seqan in pkg-plist. Also: - CMAKE_BUILD_TYPE is not needed - ports system sets it to Release by default, and to Debug if WITH_DEBUG is set. Hardcoding release will disable this convenient feature. - pkg-message should be handled in a more tricky way: - use %%PREFIX%% instead of /usr/local in it - place it under files/pkg-message.in - add SUB_FILES=pkg-message in the port - display it in post-install with @${CAT} ${PKG_MESSAGE} (see 8.6 of http://www2.au.freebsd.org/doc/en/books/porters-handbook/book.html for details) - Specifying LICENSE_FILE twice overrides it, you should use LICENSE_FILE_BSD / LICENSE_FILE_GPLv3 Except for these nits it seems fine. -- Dmitry Marakasov . 55B5 0596 FF1E 8D84 5F56 9510 D35A 80DD F9D2 F77D amdmi3@amdmi3.ru ..: jabber: amdmi3@jabber.ru http://www.amdmi3.ru
State Changed From-To: open->feedback Ask for submitter fix.
Hi Dmitry, thanks for reviewing the port and your help! Quoting "Dmitry Marakasov" <amdmi3@amdmi3.ru>: > * Hannes (h2+fbsdports@fsfe.org) wrote: > > This will require some minor fixes. First, please fix issues reported by > portlint (ports-mgmt/portlint), namely you should use tabs for > identation and %%DATADIR%% instead if share/seqan in pkg-plist. Strangely, portlint does not report these issues here. Anway, I fixed them as proposed by you. > Also: > - CMAKE_BUILD_TYPE is not needed - ports system sets it to Release > by default, and to Debug if WITH_DEBUG is set. Hardcoding release > will disable this convenient feature. Makes sense. > - pkg-message should be handled in a more tricky way: > - use %%PREFIX%% instead of /usr/local in it > - place it under files/pkg-message.in > - add SUB_FILES=pkg-message in the port > - display it in post-install with @${CAT} ${PKG_MESSAGE} > (see 8.6 of > http://www2.au.freebsd.org/doc/en/books/porters-handbook/book.html > for details) Ah, ok. I was sure there had to be a better way, than what I did ;) I did however have to specify PKG_MESSAGE= ${WRKDIR}/pkg-message now aswell. Is that correct? Otherwise @${CAT} would just sit there waiting... > - Specifying LICENSE_FILE twice overrides it, you should use > LICENSE_FILE_BSD / LICENSE_FILE_GPLv3 I did that, but now portlint complains: # portlint WARN: Makefile: only one MASTER_SITE configured. Consider adding additional mirrors. FATAL: Makefile: extra item "LICENSE_FILE_BSD" placed in the LICENSE section. FATAL: Makefile: extra item "LICENSE_FILE_GPLv3" placed in the LICENSE section. 2 fatal errors and 1 warning found. Putting an extra blank line inbetween fixes this, but it is probably a bug in portlint, because really these things belong into the LICENSE section, or not? > Except for these nits it seems fine. I have attached a new shar. Can you check that? Thanks! Best, Hannes
Quoting Hannes <h2+fbsdports@fsfe.org>: > > Hi Dmitry, > > thanks for reviewing the port and your help! > > [...] > > I have attached a new shar. Can you check that? Thanks! > > Best, > Hannes > Did you have time to look at the port? The PR is still set to feedback, are there open issues or do you need further input from me? Thanks for your help. Best, Hannes
amdmi3 2012-06-06 17:51:33 UTC FreeBSD ports repository Modified files: biology Makefile Added files: biology/seqan Makefile distinfo pkg-descr pkg-plist biology/seqan/files patch-cmake-CMakeLists.txt patch-cmake-apps-CMakeLists.txt pkg-message.in Log: SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. The library is licensed under the 3-clause BSD license except the applications which are GPL. WWW: http://www.seqan.de/ PR: 167571 Submitted by: Hannes <h2+fbsdports@fsfe.org> Revision Changes Path 1.121 +1 -0 ports/biology/Makefile 1.1 +49 -0 ports/biology/seqan/Makefile (new) 1.1 +2 -0 ports/biology/seqan/distinfo (new) 1.1 +13 -0 ports/biology/seqan/files/patch-cmake-CMakeLists.txt (new) 1.1 +8 -0 ports/biology/seqan/files/patch-cmake-apps-CMakeLists.txt (new) 1.1 +6 -0 ports/biology/seqan/files/pkg-message.in (new) 1.1 +6 -0 ports/biology/seqan/pkg-descr (new) 1.1 +2145 -0 ports/biology/seqan/pkg-plist (new) _______________________________________________ cvs-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/cvs-all To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"
* Hannes (h2+fbsdports@fsfe.org) wrote: > Quoting Hannes <h2+fbsdports@fsfe.org>: > > > > Hi Dmitry, > > > > thanks for reviewing the port and your help! > > > > [...] > > > > I have attached a new shar. Can you check that? Thanks! > > > > Best, > > Hannes > > > > Did you have time to look at the port? The PR is still set to > feedback, are there open issues or do you need further input from me? Sorry, I've totally missed your followup. Committed with following minor changes: - s/YES/yes/ - Add USE_GCC for i386, as it triggers internal error in system gcc there -- Dmitry Marakasov . 55B5 0596 FF1E 8D84 5F56 9510 D35A 80DD F9D2 F77D amdmi3@amdmi3.ru ..: jabber: amdmi3@jabber.ru http://www.amdmi3.ru
State Changed From-To: feedback->closed New port added, with minor changes. Thanks!