| Commit message (Collapse) | Author | Age | Files | Lines |
|
|
|
|
|
|
| |
Upstream changelog: https://github.com/bbuchfink/diamond/releases
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D9288
|
| |
|
|
|
|
|
|
|
| |
Upstream changes: https://github.com/bbuchfink/diamond/releases
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D9197
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Upstream changelog:
- Added compositional score adjustments (option --comp-based-stats
(0,1)). This is a useful feature for filtering false positive hits and
is enabled by default.
- Removed --single-domain option and replaced by --max-hsps, to set the
maximum number of Hsps per query/subject pair, to be consistent with
BLAST. This option is set to 1 by default as getting more than 1 Hsp
per subject seems to be confusing users.
- Added option --no-self-hits to filter identical self-hits.
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D9134
|
|
|
|
| |
Approved by: portmgr blanket
|
|
|
|
|
|
|
|
| |
Changes: http://www.boost.org/users/history/version_1_63_0.html
PR: 215598
Exp-run by: antoine
Approved by: office (bapt)
MFH: 2017Q1
|
|
|
|
|
|
|
|
|
|
| |
If you want to set WRKSRC, set GH_PROJECT instead.
- The GitHub URLs are case insensitive, but the distribution files you
get out of them are not.
- If the repository was renamed, the old URL will still work, but the
distribution name will be ith the new name.
Sponsored by: Absolight
|
|
|
|
|
|
|
| |
Many ports passed ZLIB_CFLAGS="-I/usr/include" ZLIB_LIBS="-L/usr/lib -lz"
which is unsafe at least with lang/gcc* that override some system headers
and have newer libgcc_s.so that our old version in base may not be
forward-compatible with.
|
|
|
|
| |
Approved by: portmgr (blanket)
|
|
|
|
|
|
|
|
|
|
|
| |
Upstream changes:
- slightly improved sensitivity
- added option to report unaligned queries: --unal (0=no, 1=yes)
- pairwise, XML and SAM format will report unaligned queries by default
- added option to filter alignments by subject cover (--subject-cover)
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D9000
|
|
|
|
|
|
| |
PR: 214997
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8882
|
|
|
|
| |
Changes: http://search.cpan.org/dist/BioPerl-Run/Changes
|
|
|
|
|
|
|
|
|
| |
- Update license information.
- Add python to USES (bowtie2-build bowtie2-inspect need python)
- Add DOCS and EXAMPLES options
Approved by: AMDmi3 (mentor) swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8182
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Changes in version 4.6.6:
Bug fix for cd-hit-dup in variable length input when write out R1 reads
Changes in version 4.6.5:
Add filter for -aL option so that short sequences will be skipped if not
satisfy representative sequences' -aL requirement. This will make compute
faster in clustering settings where sequences in the same cluster are
required to have similar length using -aL -AL option (e.g. -aL 0.9).
Approved by: AMDmi3 (mentor) swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8186
|
|
|
|
|
|
|
|
|
|
|
| |
Upstream changes since version 2.2.4:
- Fix compilation warnings/errors with newer version of gcc (5.3 & 6.1).
- Fix bug in parsing function that made it stop on sequences that consist
of only empty lines.
- New methods in bindings to enumerate the mers of a string.
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D8204
|
|
|
|
|
|
| |
biology/p5-BioPerl into biology/p5-Bio-Coordinate
- Bump PORTREVISION for dependency change
|
|
|
|
|
|
|
| |
Bio::Coordinate classes are used for working with various biological coordinate
systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.
WWW: http://search.cpan.org/dist/Bio-Coordinate/
|
|
|
|
|
|
|
|
|
|
|
|
| |
- Change MASTER_SITES back to CPAN
- Update LICENSE
- Add LICENSE_FILE
- Use PORTDOCS
- Convert to options target helper
- Use INSTALL_SCRIPT
- Pet portlint: fix diff header of patch file
Changes: http://search.cpan.org/dist/BioPerl-Run/Changes
|
|
|
|
|
|
|
|
| |
- Update *_DEPENDS
- Use TEST_DEPENDS: Test::Most and URI::Escape are test-only dependencies
- Use PORTDATA, PORTDOCS and PORTEXAMPLES
Changes: http://search.cpan.org/dist/BioPerl/Changes
|
|
|
|
|
|
| |
PR: 214997
Submitted by: mzaki@e-mail.ne.jp
Approved by: maintainer(timeout, > 14 days)
|
|
|
|
|
|
|
|
| |
- Update *_DEPENDS for biology/p5-bioperl renaming
- Add NO_ARCH
- Sort PLIST
Changes: http://search.cpan.org/dist/Bio-Graphics/Changes
|
|
|
|
|
|
| |
- Sort *_DEPENDS
- Add NO_ARCH
- Bump PORTREVISION for biology/p5-bioperl renaming
|
|
|
|
|
| |
- Add NO_ARCH
- Bump PORTREVISION for biology/p5-bioperl renaming
|
|
|
|
|
|
| |
- Add NO_ARCH
- Sort *_DEPENDS
- Bump PORTREVISION for biology/p5-bioperl renaming
|
|
|
|
|
| |
- Add NO_ARCH
- Bump PORTREVISION for biology/p5-bioperl renaming
|
|
|
|
|
| |
- Sort *_DEPENDS
- Bump PORTREVISION for dependent ports
|
|
|
|
|
|
|
|
| |
Upstream change: fixed an issue that could cause a crash when using view on
incomplete DAA files
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8832
|
| |
|
| |
|
| |
|
| |
|
|
|
|
|
| |
prevent massive PORTREVISION bumps. Bump dependent ports that have not
been bumped since.
|
|
|
|
|
| |
prevent massive PORTREVISION bumps. Bump dependent ports that have not
been bumped since.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms), part II.
The first part covered ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.
This adds ports with USES=fortran and ports using Mk/bsd.octave.mk
which in turn has USES=fortran.
PR: 214965
Reported by: thierry
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
| |
The only reason to use post-stage is because the port needs to do
"things" at a later time, like some plist manipulation.
While there, fold post-install in do-install targets when they are
defined.
PR: 214780
Submitted by: mat
Exp-run by: antoine
Sponsored by: Absolight
|
|
|
|
|
|
|
| |
timing out during fetch.
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D8651
|
|
|
|
|
|
|
|
|
|
|
|
| |
Correct LICENSE and set LICENSE_FILE
Upstream changelog:
- support for gzip compressed files containing multiple gzip streams
- support for the BLAST pairwise format (option -f 0)
- slightly improved sensitivity
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D8652
|
|
|
|
|
|
|
| |
It already sets DISTNAME to a very nice unique name, do not set it
yourself.
Sponsored by: Absolight
|
|
|
|
| |
version for GCC in the Ports Collection have moved to GCC 4.9.
|
|
|
|
|
|
|
|
|
|
|
|
| |
- Enable `long double` C99 math usage
- Switch 9.x back to building with GCC
Changes: http://www.boost.org/users/history/
PR: 199601
Submitted by: Chen Xu, bapt, amdmi3, truckman (based on)
Reviewed by: rakuco (kde) (earlier version)
Exp-run by: antoine (3 tries), truckman (consumers only, earlier versions)
Approved by: bapt (office)
|
|
|
|
| |
- Convert to new options target helper
|
|
|
|
|
|
|
|
|
| |
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms).
In particular that is ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.
|
| |
|
|
|
|
|
| |
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D8518
|
|
|
|
|
|
| |
tier-2 archs.
Approved by: portmgr (tier-2 blanket)
|
|
|
|
| |
Approved by: portmgr (tier-2 blanket)
|
|
|
|
|
|
| |
- Blixem: Features can now be added to multiple different groups/filters.
- Belvu: Fix a problem where column highlighting can get out of sync
with the text.
|
|
|
|
| |
Reported by: pkg-fallout
|
|
|
|
|
|
| |
Submitted by: marino
Reported by: Eduardo Lemos de Sa <eduardo.lemosdesa@gmail.com>
MFH: 2016Q4
|
| |
|
|
|
|
| |
Approved by: portmgr (tier-2 blanket)
|
|
|
|
| |
Approved by: portmgr (tier-2 blanket)
|
| |
|
|
|
|
|
|
|
| |
Release notes: https://github.com/bbuchfink/diamond/releases/tag/v0.8.26
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8447
|
|
|
|
|
|
|
| |
PR: 213743
Submitted by: mat
Exp-run by: antoine
Sponsored by: Absolight
|
|
|
|
| |
- Reset maintainer to ports@
|
|
|
|
|
|
|
|
| |
PR: 213195
Submitted by: mat
Exp-run by: antoine
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D8093
|
|
|
|
|
|
|
| |
PR: 213570
Submitted by: mat
Exp-run by: antoine
Sponsored by: Absolight
|
|
|
|
|
| |
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8268
|
|
|
|
|
|
|
|
|
|
|
| |
Upstream release notes:
Added option to change the genetic code used for translation of query in
blastx mode (option --query-gencode, see here for a list of possible values:
https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D8202
|
|
|
|
| |
Reported by: pkg-fallout
|
| |
|
|
|
|
|
|
| |
Reviewed by: swills (mentor)
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8083
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
- Update to version 4.9c
- Set LICENSE=GPLv3
- Use the variable PORTDOCS to automate the generation of the DOCS plist (as
suggested by mat@).
- Install dat/ examples/ and Technical/ directories as well as files in the root
directory of the distribution tarball.
- Fix broken permissions.
- Delete Windows executables.
- Build and install useful binaries not built by upstream's Makefile.
- Update pkg-descr.
Reviewed by: swills (mentor)
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8040
|
|
|
|
|
|
| |
Reviewed by: mat, swills (mentor)
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D7995
|
|
|
|
|
|
| |
PR: 212874
Submitted by: wen@(myself)
Approved by: maintainer
|
|
|
|
|
|
|
| |
- Fix spelling in pkg-descr
PR: 212682 [1]
Submitted by: Hannes Hauswedell (maintainer) [1]
|
|
|
|
|
|
|
|
|
|
| |
- If a port has another upstream, remove GOOGLE_CODE
- If a port only has GOOGLE_CODE mark it BROKEN
Some ports have a local mirror configured but for security reasons, it
is not considered upstream.
Sponsored by: Absolight
|
|
|
|
|
| |
PR: 212603
Submitted by: jrm@ftfl.ca (maintainer)
|
|
|
|
|
|
|
| |
All support platforms have libbz2.so in base, so this port will never
pull in archivers/bzip2.
Approved by: just-fix-it
|
|
|
|
| |
Changes: http://search.cpan.org/~cjfields/Bio-ASN1-EntrezGene-1.72/
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
| |
PR: 212075
Approved by: portmgr blanket
|
|
|
|
|
| |
PR: 212399
Submitted by: jrm@ftfl.ca(maintainer)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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)
|
|
|
|
|
|
|
|
|
|
| |
- 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.
|
|
|
|
|
| |
PR: 212145
Submitted by: Joseph Mingrone (maintainer)
|
|
|
|
| |
Approved by: portmgr blanket
|
|
|
|
|
| |
The version.o target tries to use version_git.h before that header is
created.
|
|
|
|
|
| |
- 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 *')
|
|
|
|
|
|
| |
PR: 211845
Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
Approved by: bdrewery (implicit)
|
|
|
|
|
|
|
|
|
|
|
| |
- 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]
|
|
|
|
|
| |
PR: 211582
Submitted by: Joseph Mingrone (maintainer)
|
|
|
|
|
|
| |
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
|
|
|
|
|
| |
PR: 211335
Submitted by: jrm@ftfl.ca (maintainer)
|
|
|
|
|
|
|
| |
Mostly replace with ${}, but sometime, replace with $$() because it is
what was intended in the first place. (I think.)
Sponsored by: Absolight
|
|
|
|
|
|
|
|
|
|
|
| |
- 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
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
| |
|
|
|
|
|
| |
PR: 211078
Submitted by: Joseph Mingrone (maintainer)
|
|
|
|
|
| |
PR: 210877
Submitted by: jrm@ftfl.ca (maintainer)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
2016-07-04 security/openpgpsdk: Broken for more than 6 months
2016-07-04 security/radiusniff: Broken for more than 6 months
2016-07-04 security/pear-Auth_OpenID: Broken for more than 6 months
2016-07-04 security/sshit: Broken for more than 6 months
2016-07-04 security/ifd-slb_rf60: Broken for more than 6 months
2016-07-04 security/rainbowcrack: Broken for more than 6 months
2016-07-04 security/vlog: Broken for more than 6 months
2016-07-04 security/cryptstring: Broken for more than 6 months
2016-07-04 x11/libdnd: Broken for more than 6 months
2016-07-04 x11/xlupe: Broken for more than 6 months
2016-07-04 x11/xco: Broken for more than 6 months
2016-07-04 x11/xclick: Broken for more than 6 months
2016-07-04 devel/ocfpcsc: Broken for more than 6 months
2016-07-04 devel/dits: Broken for more than 6 months
2016-07-04 devel/ruby-cache: Broken for more than 6 months
2016-07-04 devel/rapidsvn: Broken for more than 6 months
2016-07-04 devel/svnkit: Broken for more than 6 months
2016-07-04 devel/py-EnthoughtBase: Broken for more than 6 months
2016-07-04 devel/cl-uffi: Broken for more than 6 months
2016-07-04 devel/ruby-event-loop: Broken for more than 6 months
2016-07-04 devel/libqxt: Broken for more than 6 months
2016-07-04 devel/dasm: Broken for more than 6 months
2016-07-04 devel/libopendaap: Broken for more than 6 months
2016-07-04 devel/cl-uffi-sbcl: Depends on expiring devel/cl-uffi
2016-07-04 devel/cvs2p4: Broken for more than 6 months
2016-07-04 devel/bufferpool: Broken for more than 6 months
2016-07-04 devel/ifd-test: Broken for more than 6 months
2016-07-04 devel/eric4: Broken for more than 6 months
2016-07-04 devel/uclmmbase: Broken for more than 6 months
2016-07-04 devel/obfuscatejs: Broken for more than 6 months
2016-07-04 devel/oniguruma: Broken for more than 6 months
2016-07-04 devel/libbnr: Broken for more than 6 months
2016-07-04 devel/c4: Broken for more than 6 months
2016-07-04 devel/memcheck: Broken for more than 6 months
2016-07-04 devel/liblcfg: Broken for more than 6 months
2016-07-04 devel/omake: Broken for more than 6 months
2016-07-04 devel/svndelta: Broken for more than 6 months
2016-07-04 devel/papp: Broken for more than 6 months
2016-07-04 devel/mk: Broken for more than 6 months
2016-07-04 devel/avltree: Broken for more than 6 months
2016-07-04 devel/cbind: Broken for more than 6 months
2016-07-04 devel/tclgetopts: Broken for more than 6 months
2016-07-04 devel/antlrworks: Broken for more than 6 months
2016-07-04 devel/acme: Broken for more than 6 months
2016-07-04 devel/libopensync022: Broken for more than 6 months
2016-07-04 archivers/epkg: Broken for more than 6 months
2016-07-04 print/enscriptfonts: Broken for more than 6 months
2016-07-04 print/mup: Broken for more than 6 months
2016-07-04 lang/lua-mode.el: Broken for more than 6 months
2016-07-04 lang/s9fes: Broken for more than 6 months
2016-07-04 lang/alisp: Broken for more than 6 months
2016-07-04 lang/intel2gas: Broken for more than 6 months
2016-07-04 lang/stalin: Broken for more than 6 months
2016-07-04 french/eric4: Depends on expiring devel/eric4
2016-07-04 textproc/exslt: Broken for more than 6 months
2016-07-04 textproc/xt: Broken for more than 6 months
2016-07-04 textproc/ssddiff: Broken for more than 6 months
2016-07-04 textproc/xslint: Broken for more than 6 months
2016-07-04 textproc/cbedic: Broken for more than 6 months
2016-07-04 textproc/tralics: Broken for more than 6 months
2016-07-04 textproc/docbookide.el: Broken for more than 6 months
2016-07-04 textproc/glpi-plugins-AdditionalReports: Broken for more than 6 months
2016-07-04 textproc/tdhkit: Broken for more than 6 months
2016-07-04 textproc/p5-Groonga-API: Broken for more than 6 months
2016-07-04 textproc/glpi-plugins-DataInjection: Broken for more than 6 months
2016-07-04 dns/ldnsm: Broken for more than 6 months
2016-07-04 japanese/guesswork-classic: Broken for more than 6 months
2016-07-04 japanese/texinfo: Broken for more than 6 months
2016-07-04 japanese/jyuroku: Broken for more than 6 months
2016-07-04 japanese/mtools: Broken for more than 6 months
2016-07-04 palm/pdbar: Broken for more than 6 months
2016-07-04 graphics/gplot: Broken for more than 6 months
2016-07-04 graphics/white_dune: Broken for more than 6 months
2016-07-04 graphics/whirlgif: Broken for more than 6 months
2016-07-04 graphics/libaux: Broken for more than 6 months
2016-07-04 graphics/import-pictures: Broken for more than 6 months
2016-07-04 math/xgobi: Broken for more than 6 months
2016-07-04 math/fricas: Broken for more than 6 months
2016-07-04 math/dcdflib: Broken for more than 6 months
2016-07-04 math/libneural: Broken for more than 6 months
2016-07-04 math/open-axiom: Broken for more than 6 months
2016-07-04 irc/nefarious: Broken for more than 6 months
2016-07-04 irc/slirc: Broken for more than 6 months
2016-07-04 irc/ratbox-respond: Broken for more than 6 months
2016-07-04 irc/qwebirc: Broken for more than 6 months
2016-07-04 biology/platon: Broken for more than 6 months
2016-07-04 news/slnr: Broken for more than 6 months
2016-07-04 science/jmol: Broken for more than 6 months
2016-07-04 net/nstxd: Broken for more than 6 months
2016-07-04 net/sprinkle: Broken for more than 6 months
2016-07-04 editors/ssam: Broken for more than 6 months
2016-07-04 editors/fb: Broken for more than 6 months
2016-07-04 misc/quotes: Broken for more than 6 months
2016-07-04 misc/boxquote.el: Broken for more than 6 months
2016-07-04 misc/pypanda: Broken for more than 6 months
2016-07-04 misc/cuecat: Broken for more than 6 months
2016-07-04 deskutils/displaycalibrator: Broken for more than 6 months
2016-07-04 german/eric4: Depends on expiring devel/eric4
2016-07-04 multimedia/vic: Depends on expiring devel/uclmmbase
2016-07-04 multimedia/ggrab: Broken for more than 6 months
2016-07-04 emulators/dynamips: Broken for more than 6 months
2016-07-04 emulators/dynamips-devel: Broken for more than 6 months
2016-07-04 emulators/sim6811: Broken for more than 6 months
2016-07-04 emulators/minivmac: Broken for more than 6 months
2016-07-04 cad/qcad-partslib: Broken for more than 6 months
2016-07-04 comms/dump1090_mr: Broken for more than 6 months
2016-07-04 x11-fm/asfiles: Depends on expiring x11/libdnd
2016-07-04 x11-fonts/fonts-te: Broken for more than 6 months
2016-07-04 sysutils/rsyncmanager: Broken for more than 6 months
2016-07-04 sysutils/jfbterm: Broken for more than 6 months
2016-07-04 sysutils/daedalus: Broken for more than 6 months
2016-07-04 sysutils/pcfclock: Broken for more than 6 months
2016-07-04 sysutils/vlogger: Broken for more than 6 months
2016-07-04 sysutils/bontmia: Broken for more than 6 months
2016-07-04 mail/pop3gwd: Broken for more than 6 months
2016-07-04 mail/mailtray: Broken for more than 6 months
2016-07-04 mail/pflogstats: Broken for more than 6 months
2016-07-04 mail/exact: Broken for more than 6 months
2016-07-04 mail/wmpop3: Broken for more than 6 months
2016-07-04 mail/qmail-conf: Broken for more than 6 months
2016-07-04 mail/gld: Broken for more than 6 months
2016-07-04 mail/dsbl-testers: Broken for more than 6 months
2016-07-04 mail/vqregister: Broken for more than 6 months
2016-07-04 mail/atmail: Broken for more than 6 months
2016-07-04 mail/ml: Broken for more than 6 months
2016-07-04 net-im/icb: Broken for more than 6 months
2016-07-04 net-im/cicquin: Broken for more than 6 months
2016-07-04 net-im/pidgin-manualsize: Broken for more than 6 months
2016-07-04 net-im/pidgin-rhythmbox: Broken for more than 6 months
2016-07-04 russian/eric4: Depends on expiring devel/eric4
2016-07-04 russian/fortune-bashorgru: Broken for more than 6 months
2016-07-04 www/xpi-clearfields: Broken for more than 6 months
2016-07-04 www/pecl-varnish: Broken for more than 6 months
2016-07-04 www/py-requests-oauth-hook: Broken for more than 6 months
2016-07-04 www/hudson: Broken for more than 6 months
2016-07-04 www/xpi-mldonkey: Broken for more than 6 months
2016-07-04 www/xpi-cookiesafe: Broken for more than 6 months
2016-07-04 www/trac-mastertickets: Broken for more than 6 months
2016-07-04 www/dotclear: Broken for more than 6 months
2016-07-04 www/ruby-wgettsv: Broken for more than 6 months
2016-07-04 www/wwwstat: Broken for more than 6 months
2016-07-04 www/xpi-prism: Broken for more than 6 months
2016-07-04 www/xpi-fasterfox: Broken for more than 6 months
2016-07-04 www/siteframe: Broken for more than 6 months
2016-07-04 www/py-urljr: Broken for more than 6 months
2016-07-04 www/reviewboard: Broken for more than 6 months
2016-07-04 www/xpi-tabletools: Broken for more than 6 months
2016-07-04 www/wikindx: Broken for more than 6 months
2016-07-04 www/typolight: Broken for more than 6 months
2016-07-04 www/varnish-libvmod-header: Broken for more than 6 months
2016-07-04 www/xpi-gbrain: Broken for more than 6 months
2016-07-04 www/trac-robotstxt: Broken for more than 6 months
2016-07-04 www/simplog: Broken for more than 6 months
2016-07-04 www/chtml: Broken for more than 6 months
2016-07-04 databases/postgresql_autodoc: Broken for more than 6 months
2016-07-04 databases/oracle_odbc_driver: Broken for more than 6 months
2016-07-04 databases/mysql-xql: Broken for more than 6 months
2016-07-04 databases/mysql-udf-sys: Broken for more than 6 months
2016-07-04 games/lucidlife: Broken for more than 6 months
2016-07-04 games/gma: Broken for more than 6 months
2016-07-04 games/smiley: Broken for more than 6 months
2016-07-04 games/noegnud-littlehack: Broken for more than 6 months
2016-07-04 games/sdlquake2: Broken for more than 6 months
2016-07-04 games/daimonin: Depends on expiring games/daimonin-music
2016-07-04 games/noegnud-nethack: Broken for more than 6 months
2016-07-04 games/xbomber: Broken for more than 6 months
2016-07-04 games/xwelltris: Broken for more than 6 months
2016-07-04 games/ftjava: Broken for more than 6 months
2016-07-04 games/daimonin-music: Broken for more than 6 months
2016-07-04 games/gno3dtet: Broken for more than 6 months
2016-07-04 games/qtv: Broken for more than 6 months
2016-07-04 games/xwordpy: Broken for more than 6 months
2016-07-04 games/netris: Broken for more than 6 months
2016-07-04 games/rt2-demo: Broken for more than 6 months
2016-07-04 games/noegnud-addons: Broken for more than 6 months
2016-07-04 games/noegnud-nethack-deet: Broken for more than 6 months
2016-07-04 games/live-f1: Broken for more than 6 months
2016-07-04 games/xonix: Broken for more than 6 months
2016-07-04 games/fgkicker: Broken for more than 6 months
2016-07-04 games/tank: Depends on expiring graphics/libaux
2016-07-04 games/linux-nwserver: Broken for more than 6 months
2016-07-04 games/quake2-zaero: Broken for more than 6 months
2016-07-04 games/pyching: Broken for more than 6 months
2016-07-04 games/thevalley: Broken for more than 6 months
2016-07-04 games/xroads: Broken for more than 6 months
2016-07-04 games/fxsudoku: Broken for more than 6 months
2016-07-04 games/sudoku: Broken for more than 6 months
2016-07-04 games/kmancala: Broken for more than 6 months
2016-07-04 games/plonx: Broken for more than 6 months
2016-07-04 games/wmminichess: Broken for more than 6 months
2016-07-04 games/noegnud-slashem: Broken for more than 6 months
2016-07-04 games/latrine: Broken for more than 6 months
2016-07-04 games/pysycache-themes: Broken for more than 6 months
2016-07-04 games/nibbles: Broken for more than 6 months
2016-07-04 games/hlstatsx: Broken for more than 6 months
2016-07-04 audio/streamtuner: Broken for more than 6 months
2016-07-04 audio/mangler: Broken for more than 6 months
2016-07-04 audio/hawkvoice: Broken for more than 6 months
2016-07-04 audio/alac: Broken for more than 6 months
2016-07-04 x11-wm/e-module-mpdule: Broken for more than 6 months
2016-07-04 x11-wm/e-module-tclock: Broken for more than 6 months
2016-07-04 x11-wm/musca: Broken for more than 6 months
2016-07-04 x11-wm/e-module-places: Broken for more than 6 months
2016-07-04 x11-wm/e-module-forecasts: Broken for more than 6 months
2016-07-04 x11-wm/e-module-net: Broken for more than 6 months
2016-07-04 x11-wm/e-module-penguins: Broken for more than 6 months
2016-07-04 ftp/fget: Broken for more than 6 months
2016-07-04 net-mgmt/netmond: Broken for more than 6 months
2016-07-04 net-mgmt/ipfm: Broken for more than 6 months
|
|
|
|
|
| |
- Optionalize NLS
- Switch to options helpers
|
|
|
|
|
| |
PR: 210710
Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
|
|
|
|
| |
- Switch to options helpers
|
|
|
|
| |
- Regenerate patches with `make makepatch`
|
|
|
|
|
| |
PR: 210345
Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
|
|
|
|
|
|
|
| |
- Bump PORTREVISION
PR: 209767
Submitted by: Joseph Mingrone (maintainer)
|
|
|
|
| |
- UNBREAK
|
|
|
|
|
| |
PR: 209611
Submitted by: jrm@ftfl.ca (maintainer)
|
| |
|
|
|
|
|
|
|
|
| |
- MASTER_SITE_SUBDIR
- ${MASTER_SITES_FOO}
- :DEFAULT (and use a default when appropriate)
Sponsored by: Absolight
|
| |
|
|
|
|
|
|
|
| |
- While here, switch to options helpers
PR: 209710
Submitted by: h2+fbsdports@fsfe.org (maintainer)
|
|
|
|
|
|
|
|
| |
Changes:
https://sourceforge.net/p/samtools/mailman/message/35033807/
PR: 209653
Submitted by: cartwright@asu.edu (maintainer)
|
|
|
|
|
|
| |
While there, correct DEV_WARNINGS when they occur.
Sponsored by: Absolight
|
|
|
|
| |
Approved by: portmgr blanket
|
|
|
|
| |
Approved by: portmgr blanket
|
| |
|
|
|
|
| |
- Cosmetic fixes
|
|
|
|
|
|
|
| |
- While here, simplify WRKSRC and use options helpers
PR: 209535
Submitted by: jrm@ftfl.ca (maintainer)
|
|
|
|
|
|
|
|
|
| |
- 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)
|
| |
|
| |
|
|
|
|
| |
While here regen patches
|
|
|
|
|
|
|
|
| |
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>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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>
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
| |
|
|
|
|
|
|
|
| |
- fixes build on 9.x
- Added a feedback box to show the read depth at the selected coord.
Hover over this box to see the specific base support (i.e. the
number of A/C/G/Ts).
|
| |
|
|
|
|
|
| |
- Regenerate patches with `make makepatch`
- Simplify plist
|
|
|
|
|
|
| |
PR: 208825
Submitted by: wen@
Approved by: maintainer
|
| |
|
|
|
|
|
|
| |
https://groups.google.com/forum/#!topic/sbml-discuss/OEq_49c_X78
Notified by: portscout
|
|
|
|
|
|
|
| |
since around v1.18.0, UGENE is using Google's Breakpad library for crash
reporting, which is very system-specific and does not support FreeBSD at
the moment. Due to lack of resources and interest in porting it, simply
disable crash reporting code for the time being.
|
|
|
|
| |
- Switch to options helpers
|
|
|
|
|
| |
With hat: portmgr
Sponsored by: Absolight
|
|
|
|
|
|
| |
PR: 208351
Submitted by: wen@FreeBSD.org
Approved by: mauricio@arareko.net (maintainer)
|
|
|
|
|
|
| |
PR: 208367
Submitted by: bacon4000@gmail.com (maintainer)
Suggested by: rakuco
|
| |
|
|
|
|
|
|
|
|
| |
- Add LICENSE_FILE
- Remove USES=tar:bzip2 (incorrect and no-op with USE_GITHUB)
- Drop unneeded (and incorrect anyway) PKG_CONFIG_PATH
Approved by: portmgr blanket
|
|
|
|
|
|
|
|
|
|
|
|
| |
A k-mer is a substring of length k, and counting the occurrences of all such
substrings is a central step in many analyses of DNA sequence. JELLYFISH can
count k-mers quickly by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase parallelism.
WWW: http://www.genome.umd.edu/jellyfish.html
PR: 207929
Submitted by: bacon4000@gmail.com
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.
This is Bowtie version 2, which will need to coexists with Bowtie 1 for the
foreseeable future. Both are required by certain genomics pipelines, in some
cases (e.g. Trinity) by the same pipeline.
WWW: https://github.com/BenLangmead/bowtie2
PR: 207908
Submitted by: Jason Bacon <bacon4000@gmail.com>
|
|
|
|
|
|
|
|
|
|
|
| |
Slclust is a utility that performs single-linkage clustering with the option of
applying a Jaccard similarity coefficient to break weakly bound clusters into
distinct clusters.
WWW: http://sourceforge.net/projects/slclust/
PR: 207997
Submitted by: Jason Bacon <bacon4000@gmail.com>
|
|
|
|
|
|
|
|
|
| |
NGS paired-end and single ended data.
WWW: http://www.usadellab.org/cms/?page=trimmomatic
PR: 208044
Submitted by: bacon4000@gmail.com
|
|
|
|
|
|
|
|
|
|
|
|
| |
TransDecoder identifies candidate coding regions within transcript
sequences, such as those generated by de novo RNA-Seq transcript
assembly using Trinity, or constructed based on RNA-Seq alignments
to the genome using Tophat and Cufflinks.
WWW: http://transdecoder.github.io/
PR: 207993
Submitted by: Jason Bacon <bacon4000@gmail.com>
|
|
|
|
| |
- mostly internal changes, some build fixes
|
|
|
|
|
|
|
|
|
|
|
|
| |
Fix distinfo for the offending ports.
lang/yorick's tag was moved, and the added patch was no longer needed.
PR: 207644
Submitted by: mat
Exp-run by by: antoine
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D4268
|
|
|
|
|
|
|
|
|
|
|
| |
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.
WWW: http://bowtie-bio.sourceforge.net/index.shtml
PR: 206939
Submitted by: Jason Bacon <bacon4000@gmail.com>
|
|
|
|
|
|
|
|
|
|
| |
A set of tools written in Perl and C++ for working with VCF files, such as
those generated by the 1000 Genomes Project.
WWW: https://github.com/vcftools/vcftools
PR: 206926
Submitted by: Jason Bacon <bacon4000@gmail.com>
|
|
|
|
|
|
|
| |
- Update pkg-descr
PR: 205890
Submitted by: tkato432@yahoo.com
|
| |
|
| |
|
|
|
|
|
|
|
| |
- Blixem can now accept a 'command' tag in a gff line for a region
feature. The given command should return gff and will be run by
blixem on the given region.
- Blixem now supports fetching sequence data over https.
|
|
|
|
|
|
| |
Also link with libncurses, not libtermcap
approved by: infrastructure blanket
|
|
|
|
| |
approved by: infrastructure blanket
|
|
|
|
|
|
| |
- upstream distfile is moving target with same version number
Submitted by: antoine
|
|
|
|
| |
Reported by: pkg-fallout
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
genomics analysis tasks. The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome. For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.
Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.
WWW: http://bedtools.readthedocs.org/
PR: 204536
Submitted by: scottcheloha@gmail.com
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Changes:
- Missing hydrogens atoms of HETATM molecules (pdb files) are stored locally.
- Pdb files can now be clipped.
- Fixes missing residues. Introduces an alternative way of generating rotamers,
without using z-matrices. This potentially a faster algorithm.
- Supports Movie making through avconv/ffmpeg.
- calculates the Electron Localization Function (ELF).
- Updated code of ambfor/ambmd to speed up optimisations/MD of proteins
solvated in water (Jan, 2014).
PR: 204341
|
|
|
|
| |
PR: 205774
|
|
|
|
| |
Approved by: portmgr blanket
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
LICENSE= PD
Note that although Public Domain is not technically a license, it's
handled in the same way as licenses here, which is a common practice
(Arch, Gentoo, Fedora, Debian, even FOSSology do the same).
Convert all ports which redefine Public Domain LICENSE to LICENSE=PD.
Approved by: portmgr (bapt)
Differential Revision: D4149
|
| |
|
|
|
|
|
| |
This cython-based port has failed on me a couple of times in a bulk build.
I'm not sure what the actual problem is but the issue is itermittent.
|
|
|
|
|
|
|
| |
This port will not build if ENOTRECOVERABLE is not defined, period.
It's not necessary to check OPSYS and version, just apply the fallback
definition if it's not defined. This unbreaks DragonFly after last
commit.
|
|
|
|
| |
Sponsored by: Absolight
|
|
|
|
| |
Add a note to ports/LEGAL
|
|
|
|
|
| |
PR: 205558
Submitted by: cartwright@asu.edu(maintainer)
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's
PR: 205524
PR: 205525
PR: 205526
Submitted by: cartwright@asu.edu (maintainer)
|
| |
|
|
|
|
|
|
|
|
|
| |
- Update/Remove MASTER_SITE
PR: 204755
Submitted by: jwbacon@tds.net (maintainer)
Approved by: mat (mentor)
Differential Revision: D4493
|
|
|
|
|
| |
- Add LICENSE
- Pet portlint
|
|
|
|
|
|
|
| |
- Blixem
Further improve the display of features in the detail view
when they have transparent fill, making sure that they have a
visible border.
|
|
|
|
|
|
| |
- Blixem:
Improve the display of features in the detail view when they
have transparent fill.
|
|
|
|
| |
fetch: http://www.platonsoft.nl/spek/xraysoft/unix/platon.tar.gz: size mismatch: expected 12080181, actual 12080357
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
2015-11-26 audio/pecl-id3: Broken for more than 6 months
2015-11-26 dns/geta: Broken for more than 6 months
2015-11-26 finance/openerp-web: Broken for more than 6 months
2015-11-26 devel/py-async: Further using of this module is not encouraged by upstream
2015-11-26 chinese/kon2: Depends on expiring chinese/cce
2015-11-26 games/linux-skulltag: Depends on expiring audio/linux-fmodapi
2015-11-26 archivers/wzip: Broken for more than 6 months
2015-11-26 databases/sybtcl: Broken for more than 6 months
2015-11-26 biology/povchem: Broken for more than 6 months
2015-11-26 audio/btc: Broken for more than 6 months
2015-11-26 astro/wmglobe: Broken for more than 6 months
2015-11-26 graphics/pyro: Broken for more than 6 months
2015-11-26 graphics/jpeg2ps: Broken for more than 6 months
2015-11-26 chinese/gugod-clean: Broken for more than 6 months
2015-11-26 comms/bforce: Broken for more than 6 months
2015-11-26 cad/geda-docs: Broken for more than 6 months
2015-11-26 chinese/cwtexttf: Broken for more than 6 months
2015-11-26 comms/zmtx-zmrx: Broken for more than 6 months
2015-11-26 astro/sky2000: Broken for more than 6 months
2015-11-26 deskutils/libopensync-plugin-file: Broken for more than 6 months
2015-11-26 databases/sqlite-ext-mobigroup: Broken for more than 6 months
2015-11-26 chinese/bg5ps: Broken for more than 6 months
2015-11-26 deskutils/x-tile: Broken for more than 6 months
2015-11-26 graphics/pure-gl: Broken for more than 6 months
2015-11-26 audio/dvda-author: Broken for more than 6 months
2015-11-26 chinese/oxim: Broken for more than 6 months
2015-11-26 editors/spe: Broken for more than 6 months
2015-11-26 audio/mpdscribble: Broken for more than 6 months
2015-11-26 cad/geda-symcheck: Broken for more than 6 months
2015-11-26 audio/linux-fmodapi: Broken for more than 6 months
2015-11-26 audio/pure-audio: Broken for more than 6 months
2015-11-26 editors/bpatch: Broken for more than 6 months
2015-11-26 benchmarks/geekbench: Broken for more than 6 months
2015-11-26 graphics/icoconvert: Broken for more than 6 months
2015-11-26 cad/geda-utils: Broken for more than 6 months
2015-11-26 deskutils/tomboy-plugin-wordcount: Broken for more than 6 months
2015-11-26 graphics/sketch: Broken for more than 6 months
2015-11-26 ftp/spegla: Broken for more than 6 months
2015-11-26 graphics/clutter-box2d: Broken for more than 6 months
2015-11-26 audio/scmpc: Broken for more than 6 months
2015-11-26 ftp/gnusget: Broken for more than 6 months
2015-11-26 comms/gpsk31: Broken for more than 6 months
2015-11-26 cad/geda-gschem: Broken for more than 6 months
2015-11-26 audio/ampache: Broken for more than 6 months
2015-11-26 cad/slffea: Broken for more than 6 months
2015-11-26 audio/cripple: Broken for more than 6 months
2015-11-26 cad/geda-gattrib: Broken for more than 6 months
2015-11-26 cad/findhier: Broken for more than 6 months
2015-11-26 biology/njplot: Broken for more than 6 months
2015-11-26 audio/wmmp: Broken for more than 6 months
2015-11-26 x11/avant-window-navigator: Broken for more than 6 months
2015-11-26 cad/geda-netlist: Broken for more than 6 months
2015-11-26 deskutils/libopensync-plugin-sunbird: Broken for more than 6 months
2015-11-26 biology/ortep3: Broken for more than 6 months
2015-11-26 astro/aa: Broken for more than 6 months
2015-11-26 french/belote: Broken for more than 6 months
2015-11-26 converters/p5-String-SetUTF8: Broken for more than 6 months
2015-11-26 cad/geda-examples: Broken for more than 6 months
2015-11-26 editors/yasnippet: Broken for more than 6 months
2015-11-26 audio/musica: Broken for more than 6 months
2015-11-26 graphics/rubyphoto: Broken for more than 6 months
2015-11-26 german/bsdpaste: Broken for more than 6 months
2015-11-26 audio/amrcoder: Broken for more than 6 months
2015-11-26 sysutils/bashburn: Broken for more than 6 months
2015-11-26 editors/e93: Broken for more than 6 months
2015-11-26 audio/tepsonic: Broken for more than 6 months
2015-11-26 astro/ephem: Broken for more than 6 months
2015-11-26 chinese/cce: Broken for more than 6 months
2015-11-26 graphics/qcread: Broken for more than 6 months
2015-11-26 databases/py-sqlkit: Broken for more than 6 months
2015-11-26 databases/usogres: Broken for more than 6 months
2015-11-26 cad/libgeda: Broken for more than 6 months
2015-11-26 chinese/p5-Lingua-ZH-BPMFConvert: Broken for more than 6 months
2015-11-26 french/alphabet_sounds_fr: Broken for more than 6 months
2015-11-26 deskutils/mrundlg: Broken for more than 6 months
2015-11-26 databases/erlang-mysql: Broken for more than 6 months
2015-11-26 graphics/linux-XnViewMP: Broken for more than 6 months
2015-11-26 deskutils/akamaru: Broken for more than 6 months
2015-11-26 dns/p5-Net-DNS-ZoneCheck: Broken for more than 6 months
2015-11-26 astro/dgpsip: Broken for more than 6 months
2015-11-26 databases/pecl-handlersocket: Broken for more than 6 months
2015-11-26 audio/cymbaline: Broken for more than 6 months
2015-11-26 french/dico: Broken for more than 6 months
2015-11-26 comms/qpage: Broken for more than 6 months
2015-11-26 audio/sonice: Broken for more than 6 months
2015-11-26 cad/geda-symbols: Broken for more than 6 months
2015-11-26 databases/java-mybatis: Broken for more than 6 months
2015-11-26 databases/openbase-jdbc: Broken for more than 6 months
2015-11-27 www/mediawiki119: Please upgrade to mediawiki-1.25
2015-11-28 www/R-cran-Rpad: Unmaintained upstream
|
|
|
|
|
|
|
|
|
|
| |
Add working mirror.
Also update file size in distinfo - checksum is not changed
and I dunno why. But with old file size it warns that expected
size was different.
PR: 204491
Submitted by: Walter Schwarzenfeld <w.litter@aon.at>
|
| |
|
|
|
|
|
|
| |
- Side effect of the seqtools automated build system
Submitted by: pkg-fallout
|
|
|
|
|
| |
- Fix a bug in Belvu where the display was being initialised in
command-line-only modes.
|
| |
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
- Blixem
o There is now an optional setting to highlight "maybe-canonical"
splice sites in Blixem. This can be used to help identify
problems where the strand is incorrect in the input data - it
highlights splice sites in a different colour if they would be
canonical were they on the other strand.
o Fixed a bug with colinearity lines when an alignment's cigar
string contains introns.
o There are now separate feedback boxes for the selected sequence
name coordinates. Hover over each box to see a tooltip describing
its contents.
|
| |
|
|
|
|
|
|
|
|
| |
PR: 204056
Submitted by: mat
Reviewed by: bapt
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D2735
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
| |
- Add License
- Add SIMD option disabled by default to avoid creating official
packags with CPU specific optimizations
- Add pkg-message explaining how to get an optimized binary
- Assign maintainership to submitter
PR: 203334
Submitted by: jwbacon at tds.net
Approved by: Maintainer timeout
|
| |
|
| |
|
|
|
|
|
|
|
| |
- Pass maintainership to submitter
PR: 203817
Submitted by: Wendell Borges <wendell@bsd.com.br>
|
|
|
|
| |
- Switch to options helpers
|
|
|
|
|
| |
- Add LICENSE
- Drop unneeded WX_UNICODE
|
|
|
|
| |
Approved by: portmgr (blanket)
|
| |
|
| |
|
| |
|
|
|
|
|
|
|
|
| |
As per the web site, the license for GRAPPA is GPLv2
https://www.cs.unm.edu/~moret/GRAPPA/
PR: 202426
Submitted by: George <george@nycbug.org>
|
|
|
|
|
|
|
|
|
|
| |
genome (e.g. human genome). It has two major components, one for read shorter
than 150bp and the other for longer reads.
WWW: http://sourceforge.net/projects/bio-bwa/
PR: 203158
Submitted by: Jason Bacon <jwbacon@tds.net>
|
|
|
|
|
|
|
| |
WWW: http://sourceforge.net/projects/cdbfasta/
PR: 203233
Submitted by: Jason Bacon <jwbacon@tds.net>
|
|
|
|
|
|
|
| |
WWW: https://github.com/fstrozzi/Fastool
PR: 203293
Submitted by: Jason Bacon <jwbacon@tds.net>
|
|
|
|
|
|
|
|
|
|
| |
alignments of nucleotide or protein sequences. FastTree can handle alignments
with up to a million of sequences in a reasonable amount of time and memory.
WWW: http://www.microbesonline.org/fasttree/
PR: 203295
Submitted by: Jason Bacon <jwbacon@tds.net>
|
|
|
|
|
|
|
|
|
| |
FASTA/FASTQ files preprocessing.
WWW: http://hannonlab.cshl.edu/fastx_toolkit/
PR: 203318
Submitted by: Jason Bacon <jwbacon@tds.net>
|
|
|
|
|
|
|
| |
WWW: https://github.com/agordon/libgtextutils
PR: 203309
Submitted by: Jason Bacon <jwbacon@tds.net>
|
| |
|
|
|
|
|
|
| |
- Minor cleanup
Reported by: danfe@
|
|
|
|
|
|
|
|
|
| |
nucleotide sequences.
WWW: http://weizhong-lab.ucsd.edu/cd-hit/
PR: 203183
Submitted by: jwbacon@tds.net
|
|
|
|
|
|
|
|
|
|
|
| |
domain is available for stuff built from source.
Some ports were already installing in the System domain, for these just remove the Makefile lines explicitly specifying the install domain.
The rest are installed in the Local domain, remove any overrides, update their pkg-plists and any explicit paths in the Makefiles and then bump port revision.
Approved by: bapt (mentor)
Differential Revision: https://reviews.freebsd.org/D2977
|
| |
|
|
|
|
|
|
|
|
| |
All applications in the ports tree works correctly with unicode version of wxGTK
Newer version of wxGTK are unicode only (3.0+)
Note that now WX_UNICODE macro is noop
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
- Move Perl's man1 files along with its man3 files.
- Move where Perl installs its modules man1 pages.
- Convert the ports installing man1 pages.
- Make different Perl versions installable at the same time.
Though you should note that only the default version can be used to
install Perl modules, and the non default Perl versions cannot use the
modules installed via ports if they contain .so as they are installed
in a version specific directory.
Reviewed by: bapt (the Mk bits)
Exp-run by: antoine
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D3542
|
| |
|
| |
|
|
|
|
|
|
|
|
|
| |
- Add NO_ARCH
- Use BROKEN_RUBY22
- While I'm here, use single space after WWW:
Approved by: portmgr (blanket)
With hat: ruby
|
|
|
|
|
|
|
| |
__sync_* functions family
- Remove BROKEN_ia64: it never had been first-class architecture, killed
officially in -CURRENT for a while now
- Sanitize installation commands and sort the knobs while I am here
|
|
|
|
| |
- Remove redundant PKGMESSAGE assignment and sanitize symlinks while here
|
|
|
|
| |
copying variable argument lists, not just on AMD64.
|
|
|
|
|
|
|
|
| |
configure script was passing `-faltivec' to the compiler, while this flag is
non-standard and only supported on Mac OS X/Darwin systems.
Also replace Apple-specific Altivec detection with querying the "hw.altivec"
sysctl instead.
|
| |
|
|
|
|
|
| |
The port does not use iconv on its own, the only dependency comes via
libxml2, which has one header that includes iconv.h.
|
|
|
|
|
| |
Pointy hat to: mat
Sponsored by: Absolight
|
|
|
|
|
| |
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D3412?
|
|
|
|
|
|
|
|
| |
- add USES=desktop-file-utils
PR: 202138
Submitted by: s3erios@gmail.com
Approved by: h2+fbsdports@fsfe.org
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
UNIQUENAME was never unique, it was only used by USE_LDCONFIG and now,
we won't have conflicts there.
Use PKGBASE instead of LATEST_LINK in PKGLATESTFILE, the *only* consumer
is pkg-devel, and it works just fine without LATEST_LINK as pkg-devel
has the correct PKGNAME anyway.
Now that UNIQUENAME is gone, OPTIONSFILE is too. (it's been called
OPTIONS_FILE now.)
Reviewed by: antoine, bapt
Exp-run by: antoine
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D3336
|
|
|
|
| |
Minor under-the-hood changes
|
| |
|
|
|
|
|
|
|
| |
PR: 201888
Submitted by: brueffer
Approved by: maintainer
Sponsored by: Absolight
|
|
|
|
| |
Reported by: pkg-fallout
|
|
|
|
|
|
| |
- While here: move knobs to their expected location, remove useless check
for ${PORT_OPTIONS:MDOCS} when installing documentation, standardize
Makefile headers
|
|
|
|
| |
- Remove no longer required local source code tweaks (picked up upstream)
|
|
|
|
| |
- Use install-strip
|
|
|
|
|
|
|
| |
- Blixem bug fix in sorting features, RT 473624
- Compilation of the seqtools in parallel, RT 467905
- Fix bug with sorting by similarity/identity to first sequence (RT:473624)
- Fix an error compiling with multiple threads (RT:467905)
|
|
|
|
|
|
| |
and in fact now leads to incorrect permissions.
Remove all instances of it from perl@ ports.
|
| |
|
|
|
|
| |
- Convert to optionsNG
|
| |
|
| |
|
|
|
|
|
|
| |
- Fix shebangs
Approved by: porgmgr (bapt)
|
|
|
|
|
|
| |
downside to having this set is that portscout cannot find new releases
when the username changes (which happens often in large projects with
multiple maintainers).
|
|
|
|
| |
Use options helpers
|
| |
|
|
|
|
| |
MFH: 2015Q2
|
|
|
|
|
|
|
|
|
|
|
|
| |
BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All
commands work transparently with both VCFs and BCFs, both
uncompressed and BGZF-compressed.
WWW: http://www.htslib.org/
PR: 199747
Submitted by: cartwright@asu.edu
|
| |
|
|
|
|
|
| |
PR: 200603
Submitted by: Reed A. Cartwright <cartwright@asu.edu> (maintainer)
|
|
|
|
| |
Approved by: portmgr blanket
|
|
|
|
|
|
|
|
| |
- Add NO_ARCH
- Add missing EXAMPLES option
Approved by: portmgr blanket
MFH: 2015Q2
|
| |
|
|
|
|
|
| |
With hat: portmgr
Sponsored by: Absolight
|
| |
|
| |
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
- Replace ${MASTER_SITE_FOO} with FOO.
- Merge MASTER_SITE_SUBDIR into MASTER_SITES when possible. (This means 99.9%
of the time.)
- Remove occurrences of MASTER_SITE_LOCAL when no subdirectory was present and
no hint of what it should be was present.
- Fix some logic.
- And generally, make things more simple and easy to understand.
While there, add magic values to the FESTIVAL, GENTOO, GIMP, GNUPG, QT and
SAMBA macros.
Also, replace some EXTRACT_SUFX occurences with USES=tar:*.
Checked by: make fetch-urlall-list
With hat: portmgr
Sponsored by: Absolight
|
| |
|