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* Most commonly used build systems support silent builds, when theyDmitry Marakasov2016-09-091-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | hide actual commands executed and only show short summary line (like "CC foo.c"). CMake and ninja enable this by default, some autotools using ports do as well. This is unacceptable because we need complete build logs at any time, so we now switch to verbose build logs unconditionally. Note that this change deliberately affects ALL builds and not only package builds on cluster, because we need to be sure that user experiencing failure can always provide informative build log regardless of settings and without rerunning the build. Change summary: - Always do verbose builds for cmake, ninja and GNU configure (the latter includes check if --disable-silent-rules is actually supported by the configure script; there are isolated cases when it's not true) - Remove CMAKE_VERBOSE, NINJA_VERBOSE and CONFIGURE_ARGS=--disable-silent-rules from all ports which set them for this is no longer needed - Revert hacks for --disable-silent-rules support priorly committed to biology/ncbi-blast+ and net-p2p/mldonkey - no longer needed as well Submitted by: amdmi3 Reviewed by: mat Exp-run by: antoine Approved by: portmgr (mat, antoine) Differential Revision: D7534 Notes: svn path=/head/; revision=421635
* - Make configure script handle --disable-silent-rules gracefullyDmitry Marakasov2016-09-061-1/+1
| | | | | | | | PR: 212075 Approved by: portmgr blanket Notes: svn path=/head/; revision=421424
* - Update to 0.8.20Wen Heping2016-09-062-4/+4
| | | | | | | | PR: 212399 Submitted by: jrm@ftfl.ca(maintainer) Notes: svn path=/head/; revision=421406
* - Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk withTijl Coosemans2016-09-052-4/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Mk/Uses/linux.mk. - Replace USE_LINUX=yes with USES+=linux and USE_LINUX=(.*) with USES+=linux:\1 in all ports. - Replace USE_LINUX_APPS with USE_LINUX in all ports. - Use INSTALL_SCRIPT instead of INSTALL_PROGRAM to install scripts in some ports. - When USE_LINUX_RPM is defined, simplify the way DISTFILES and EXTRACT_ONLY are defined. - Remove BRANDELF_DIRS and BRANDELF_FILES handling. In the very rare cases that it is still necessary ports can run ${BRANDELF} from post-patch. - Remove AUTOMATIC_PLIST handling. Only one port used it. - Fix Linux MASTER_SITES. - Replace OVERRIDE_LINUX_BASE_PORT and OVERRIDE_LINUX_NONBASE_PORTS with default versions framework. - bsd.port.mk: - Move Linux related bits to Uses/linux.mk, except USE_LINUX_PREFIX. - Put USE_LINUX_PREFIX handling after USES processing. - Define DOCSDIR, DATADIR, etc. after handling USE_LINUX_PREFIX so it can give these variables a different default value. - When a package needs to run Linux ldconfig check before installation if Linux support is enabled. - emulators/linux_base-*: - Use USES=linux and remove duplication. - Remove files/lp. FreeBSD or CUPS lp(1) should work. - Remove files/yp.conf. No longer seems to be used. - Remove pkg-deinstall and move pkg-install into pkg-plist. - Update pkg-descr and pkg-message. - Fix handling of ldconfig cache in pkg-plist. - devel/fb-adb: Use a Linux shell to run a Linux script but patch the script to use FreeBSD mkdir so mkdir -p $path creates $path and not /compat/linux/$path. PR: 211645 Exp-run by: antoine Approved by: portmgr (antoine) Notes: svn path=/head/; revision=421387
* biology/molden: 5.4 -> 5.7Kurt Jaeger2016-08-262-6/+4
| | | | | | | | | | | | | - Adds editable text fields that are longer than the visible string and introduces a new way of selecting a range of amino acids. - introduces interfaces to the open source packages openbabel and pharmer. Openbabel is used to create 2D images of the molecules in a .sdf file. It is also used to do 2D fingerprint searching. Pharmer is used to pharmacophore (3D) searching against indexed databases of .sdf files. Notes: svn path=/head/; revision=420890
* Update to version 0.8.19Pawel Pekala2016-08-252-4/+4
| | | | | | | | PR: 212145 Submitted by: Joseph Mingrone (maintainer) Notes: svn path=/head/; revision=420873
* - Mark BROKEN: does not fetch (distfile was removed from ftp)Dmitry Marakasov2016-08-221-0/+2
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=420601
* biology/bedtools is not jobs safeJohn Marino2016-08-221-0/+2
| | | | | | | | The version.o target tries to use version_git.h before that header is created. Notes: svn path=/head/; revision=420587
* - Switch to options helpersDmitry Marakasov2016-08-183-16/+11
| | | | | | | | - Regenerate patches with `make makepatch` - Mark WXGTK option broken: does not build: src/convErr/gc_errhandling.cpp:75:12: error: cannot initialize return object of type 'const char *' with an rvalue of type 'const wxChar *' (aka 'const wchar_t *') Notes: svn path=/head/; revision=420392
* Update biology/diamond to 0.8.18.Brad Davis2016-08-142-4/+4
| | | | | | | | | PR: 211845 Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer) Approved by: bdrewery (implicit) Notes: svn path=/head/; revision=420200
* - Update to 1.9 [1]Wen Heping2016-08-082-10/+8
| | | | | | | | | | | | | | - Moved to github [1] - Depend on newer sqlalchemy10 [1] - Update pkg-descr and WWW [1] - Limit python to -2.7 [2] - Reset maintainer to python@ for better maintain PR: 211621 Submitted by: pi@ [1], koobs@ [2] Notes: svn path=/head/; revision=419818
* Update to version 0.8.17Pawel Pekala2016-08-052-5/+5
| | | | | | | | PR: 211582 Submitted by: Joseph Mingrone (maintainer) Notes: svn path=/head/; revision=419710
* biology/seqtools: 4.42.1 -> 4.43.0Kurt Jaeger2016-07-313-17/+227
| | | | | | | | | ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/release_notes.html - Mark broken on 9.x: Fails to build due to C++ std issues Notes: svn path=/head/; revision=419380
* Update to upstream release 0.8.16Thomas Zander2016-07-242-4/+4
| | | | | | | | PR: 211335 Submitted by: jrm@ftfl.ca (maintainer) Notes: svn path=/head/; revision=419014
* Cleanup $() variables in ports Makefiles.Mathieu Arnold2016-07-201-1/+1
| | | | | | | | | | Mostly replace with ${}, but sometime, replace with $$() because it is what was intended in the first place. (I think.) Sponsored by: Absolight Notes: svn path=/head/; revision=418840
* - update libgd to 2.2.2Dirk Meyer2016-07-201-1/+1
| | | | | | | | | | | | | | - new MASTER_SITES - add security patch PR: 210913 Submitted by: Piotr Kubaj MFH: 2016Q3 Security: CVE-2015-8874 Security: CVE-2016-3074 Security: http://www.openwall.com/lists/oss-security/2016/07/12/4 Notes: svn path=/head/; revision=418829
* When there is a do-install target, do not use a post-install target, doMathieu Arnold2016-07-193-4/+5
| | | | | | | | | | | | | | | everything at once. Sometime, rename post-install into a options helper target. I did not fix ports that were such a mess that I could not figure out what they really wanted to do. I also did not change ports that had some version of an auto-plist code in post-install, for the same reason. With hat: portmgr Sponsored by: Absolight Notes: svn path=/head/; revision=418767
* Trim excess tabs, no-op changePawel Pekala2016-07-141-13/+13
| | | | Notes: svn path=/head/; revision=418546
* Update to version 0.8.14Pawel Pekala2016-07-142-4/+4
| | | | | | | | PR: 211078 Submitted by: Joseph Mingrone (maintainer) Notes: svn path=/head/; revision=418544
* - Update to 0.8.11Dmitry Marakasov2016-07-072-5/+5
| | | | | | | | PR: 210877 Submitted by: jrm@ftfl.ca (maintainer) Notes: svn path=/head/; revision=418187
* Remove expired ports without open PRs:Rene Ladan2016-07-047-161/+0
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* - LICENSEDmitry Marakasov2016-07-022-10/+22
| | | | | | | | - Optionalize NLS - Switch to options helpers Notes: svn path=/head/; revision=417916
* biology/diamond: update 0.8.6 -> 0.8.9Jason Unovitch2016-06-302-4/+4
| | | | | | | | PR: 210710 Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer) Notes: svn path=/head/; revision=417803
* - Add missing dependency, fixing buildDmitry Marakasov2016-06-241-1/+5
| | | | | | | - Switch to options helpers Notes: svn path=/head/; revision=417414
* - Switch to options helpersDmitry Marakasov2016-06-212-7/+11
| | | | | | | - Regenerate patches with `make makepatch` Notes: svn path=/head/; revision=417195
* biology/diamond: update to 0.8.6Ruslan Makhmatkhanov2016-06-172-4/+4
| | | | | | | | PR: 210345 Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer) Notes: svn path=/head/; revision=417033
* - Fix run-time dependency issuesOlivier Duchateau2016-06-111-2/+13
| | | | | | | | | | - Bump PORTREVISION PR: 209767 Submitted by: Joseph Mingrone (maintainer) Notes: svn path=/head/; revision=416710
* biology/seaview: Update version 4.5.4.8=>4.6Muhammad Moinur Rahman2016-06-102-7/+4
| | | | | | | - UNBREAK Notes: svn path=/head/; revision=416671
* Update to 0.8.5Matthew Seaman2016-06-093-34/+18
| | | | | | | | PR: 209611 Submitted by: jrm@ftfl.ca (maintainer) Notes: svn path=/head/; revision=416575
* - Update to 1.35Wen Heping2016-06-082-3/+4
| | | | Notes: svn path=/head/; revision=416534
* Remove unneeded usage of:Mathieu Arnold2016-06-061-2/+1
| | | | | | | | | | | - MASTER_SITE_SUBDIR - ${MASTER_SITES_FOO} - :DEFAULT (and use a default when appropriate) Sponsored by: Absolight Notes: svn path=/head/; revision=416469
* Deprecate ports broken for more than 6 monthsAntoine Brodin2016-06-032-0/+4
| | | | Notes: svn path=/head/; revision=416324
* - Do install cmake and pkgconfig modulesDmitry Marakasov2016-05-272-3/+8
| | | | | | | | | | - While here, switch to options helpers PR: 209710 Submitted by: h2+fbsdports@fsfe.org (maintainer) Notes: svn path=/head/; revision=415945
* biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1Kurt Jaeger2016-05-268-20/+23
| | | | | | | | | | | Changes: https://sourceforge.net/p/samtools/mailman/message/35033807/ PR: 209653 Submitted by: cartwright@asu.edu (maintainer) Notes: svn path=/head/; revision=415914
* Remove useless WRKSRC definitions.Mathieu Arnold2016-05-251-2/+0
| | | | | | | | | While there, correct DEV_WARNINGS when they occur. Sponsored by: Absolight Notes: svn path=/head/; revision=415839
* - Fix trailing whitespace in pkg-messagesDmitry Marakasov2016-05-196-12/+12
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=415503
* - Fix trailing whitespace in pkg-descrs, categories [a-f]*Dmitry Marakasov2016-05-1921-36/+36
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=415498
* Fix DEPENDSAntoine Brodin2016-05-181-2/+2
| | | | Notes: svn path=/head/; revision=415454
* - Convert to USES=mysqlDmitry Marakasov2016-05-161-8/+4
| | | | | | | - Cosmetic fixes Notes: svn path=/head/; revision=415352
* - Update to 4.9aDmitry Marakasov2016-05-162-4/+7
| | | | | | | | | | - While here, simplify WRKSRC and use options helpers PR: 209535 Submitted by: jrm@ftfl.ca (maintainer) Notes: svn path=/head/; revision=415338
* biology/bowtie2: 2.2.7 -> 2.2.8Kurt Jaeger2016-05-132-3/+3
| | | | | | | | | | | | - Various website updates - Fixed the bowtie2-build issue that made TBB compilation fail PR: 208943 Submitted by: Joseph Mingrone <jrm@ftfl.ca> Approved by: Jason Bacon <bacon4000@gmail.com> (maintainer) Notes: svn path=/head/; revision=415148
* Prevent collision with getline(3)Baptiste Daroussin2016-05-131-0/+300
| | | | Notes: svn path=/head/; revision=415129
* Prevent collision with getline(3)Baptiste Daroussin2016-05-131-0/+291
| | | | Notes: svn path=/head/; revision=415128
* Prevent collision with getline(3)Baptiste Daroussin2016-05-114-6/+27
| | | | | | | While here regen patches Notes: svn path=/head/; revision=415036
* biology/seqan: update 1.3.1 -> 2.1.1Jason Unovitch2016-05-1012-1915/+3706
| | | | | | | | | | | biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage UPDATING: document SeqAn updates and seqan1 port for legacy usage PR: 204127 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org> Notes: svn path=/head/; revision=414898
* New port: biology/seqan-appsJason Unovitch2016-05-105-0/+220
| | | | | | | | | | | | | | | | | | | | SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. This port contains applications built on SeqAn and developed within the SeqAn project. Among them are famous read mappers like RazerS and Yara, as well as many other tools. Some applications are packaged seperately and the library can be found at biology/seqan. WWW: http://www.seqan.de/ PR: 204127 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org> Notes: svn path=/head/; revision=414897
* Add final slash in WWW entryOlivier Duchateau2016-05-091-1/+1
| | | | Notes: svn path=/head/; revision=414866
* The BIOM file format (canonically pronounced biome) is designed to be aOlivier Duchateau2016-05-094-0/+48
| | | | | | | | | | | | | | | | | | | | | | | | | | | general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project. The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome. WWW: http://biom-format.org/ PR: 209193 Submitted by: Joseph Mingrone Notes: svn path=/head/; revision=414865
* During the exp-run in bug 208158, it was found that biology/ugene givesDimitry Andric2016-05-074-0/+36
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | errors with libc++ 3.8.0: In file included from src/QScoreAdapter.cpp:1: In file included from src/QScoreAdapter.h:4: In file included from ../../include/U2Core/MAlignment.h:1: In file included from ../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignment.h:25: In file included from ../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignmentInfo.h:25: In file included from /usr/local/include/qt5/QtCore/QString:1: In file included from /usr/local/include/qt5/QtCore/qstring.h:41: In file included from /usr/local/include/qt5/QtCore/qchar.h:37: In file included from /usr/local/include/qt5/QtCore/qglobal.h:39: /usr/include/c++/v1/cstddef:43:15: fatal error: 'stddef.h' file not found #include_next <stddef.h> ^ This is because the port tries to add /usr/include as a system include directory, using -isystem, and this screws up the order of include directories. Fix it by patching up a number of .pri files to avoid using the -isystem flag. Approved by: h2+fbsdports@fsfe.org (maintainer) PR: 209366 MFH: 2016Q2 Notes: svn path=/head/; revision=414784
* DNA query sequences against a protein reference database (BLASTP and BLASTXWen Heping2016-05-065-0/+71
| | | | | | | | | | | | | | alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings. WWW: http://ab.inf.uni-tuebingen.de/software/diamond/ PR: 208998 Submitted by: jrm@ftfl.ca Notes: svn path=/head/; revision=414686
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