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>
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>
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>
- 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.
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
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 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.
- 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)
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>
- 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.
- 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
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>
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>
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
__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
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.
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
- While here: move knobs to their expected location, remove useless check
for ${PORT_OPTIONS:MDOCS} when installing documentation, standardize
Makefile headers
- 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)
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).
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
- 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
When appropriate:
- Try to use DISTVERSION{SUF,PRE}FIX
- Replace PORTNAME-PORTVERSION by DISTNAME
- Convert MASTER_SITES to use macros
- Other light cleanup
With hat: portmgr
Sponsored by: Absolight
While here:
Regenerate p5-AcePerl's patches using makepatch.
Make p5-Bio-ASN1-EntrezGene depend on p5-bioperl, instead of the
other way around. Bump PORTREVISION on those two ports.
Blixem
- Added functionality to shift-select a range of coordinates,
and copy the reference/match sequence for that range.
- DNA search now highlights the resultant range of coordinates.
- Added a splitter bar to allow the variations track to be resized.
- Dotter
Fix a crash pressing Esc on an undocked alignment or greyramp tool.
- All
Code reorganisation: the codebase is now in C++ rather than C,
and a new module 'gbtools' has been created for generic
utility functions.
The distfile was rerolled but nobody knows why (not a good sign). The
maintainer has added a new MASTER_SITE with the original distfile in
order to unbreak fetch.
PR: 199474
Submitted by: maintainer (Jason Bacon)
The second MASTER_SITES entry worked fine, so this must have been a
transient fetch problem. I removed the first entry which is still
failing though.
Approved by: blanket
As noted by previous commit, upstream rerolls the same distfile
frequently. When FreeBSD cache was removed, the port broke. I'm fixing
it again with a new digest, but I'm also defining DIST_SUBDIR, which is
the correct thing to do with rerolls-by-policy.
Also I removed the bad backup MASTER_SITES and tested in poudriere.
While here, reset the port. The last time the maintainer was seen was
in 2005, when the port was created. Also, rewrap the package description
such that it keeps within 75 characters; also move the url so it won't
wrap across lines.
Simplify gnustep ports
Hook into the regular ports framework:
- LIB_DEPENDS for library dependencies
- Use regular USE_LDCONFIG
Reuse USES=objc (automatic)
USE_GNUSTEP is now a macro to set the dependencies and build feature needed.
Accepted arguments: back base build gui
Merge deskutils/preferencepanes into deskutils/systempreferences
- Explicitly list all required Qt components in USE_QT4 instead of relying
on them being silently picked up through `www/webkit-qt4' dependency
- Group *_build components together while here
- Remove one REINPLACE_CMD call that is no longer needed
Due to questionable c++, GCC 4.9 and newer cannot build seqan. An update
has been in the works that will enable clang compilers and all versions
of GCC to build seqan, but it is not quite ready yet. While waiting for
it, limit the version of GCC used to 4.8.
PR: 196851
include GH_PROJECT/GH_ACCOUNT/GH_TAGNAME. This prevents the distfile
having the same name despite changing one of these values and causing
a bad checksum.
Differential Revision: https://reviews.freebsd.org/D2103
Reviewed by: mat
With hat: bdrewery
- Update version 4.5.2=>4.5.3.4
- Add LICENSE (GPLv3)
- Remove PDFLIBS as OPTIONS as it is no loner an optional requirement
PR: 198602
Submitted by: pi
Approved by: bapt marino (implicit)
- Remove dependencies in core
- Put testing depends in TEST_DEPENDS
- Remove unnecessary bsd.port.options.mk inclusions
- Remove checks for Perl versions that no longer exist in the ports tree
- Sort plists, some of which were so jumbled that I have to assume
the plist was randomized before committing
A lot of the plist changes in this commit are moving PERL5_MAN3 after
SITE_PERL. It's repo churn now, but it makes updating the ports later
far easier.
Reduce restrictions from RESTRICTED to NO_CDROM -- the licensing
allows use by academic community as long as it is not redistributed.
Upstream still do not version their "releases", so next time they
reroll the tarball, the download will start breaking again. But
this time, it will be possible to fetch it from FreeBSD mirrors.
Hide most of the optional data files under the DOCS-option and
streamline various build-related scriptlets.
stop rerolling releases (and breaking downstream checksums) now.
While here, allow parallel builds (seems to work again now) and stop
extraction of unused subdirectories.
- Blixem
o Previously-unsupported GFF feature types can now be displayed
as a new 'basic feature' type.
o Styles are now applied to the detail view as well as the big
picture, so feature display is more consistent across the two
views.
o Fix a bug where styles were not being applied to
dynamically-loaded features.
- Dotter
o Added a 'maximise' button for the greyramp tool.
o Small fixes to inconsistencies in context-sensitive menus and
keyboard shortcuts.
The otter port tries to build libotter.a before an object is completely
built (share.o in my case) and ariadne tries to start building in a
directory before it is created (under multiple jobs).
All had similar errors that it couldn't find something during the build,
yet built on a subsequent pass with no adjustments. Most I've seen before
on previous bulk runs.
2015-01-01 biology/boinc-simap: Project shutting down, see http://boincsimap.org/boincsimap/forum_thread.php?id=88
2015-01-01 security/openssh-portable-base: Overwrite-base option/port/pkg will be removed. There is no real need for foot-shooting.
2015-01-01 devel/cedet: Fails to build, use Emacs' builtin cedet package instead
2015-01-01 devel/ecb: does not work with newer Emacs versions, use the elpa package instead
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.
WWW: http://www.htslib.org/
PR: 195592
Submitted by: Reed A. Cartwright <cartwright@asu.edu>
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.
WWW: http://www.htslib.org/
PR: 195591
Submitted by: Reed A. Cartwright <cartwright@asu.edu>
Before, we had:
site_perl : lib/perl5/site_perl/5.18
site_perl/perl_arch : lib/perl5/site_perl/5.18/mach
perl_man3 : lib/perl5/5.18/man/man3
Now we have:
site_perl : lib/perl5/site_perl
site_arch : lib/perl5/site_perl/mach/5.18
perl_man3 : lib/perl5/site_perl/man/man3
Modules without any .so will be installed at the same place regardless of the
Perl version, minimizing the upgrade when the major Perl version is changed.
It uses a version dependent directory for modules with compiled bits.
As PERL_ARCH is no longer needed in plists, it has been removed from
PLIST_SUB.
The USE_PERL5=fixpacklist keyword is removed, the .packlist file is now
always removed, as is perllocal.pod.
The old site_perl and site_perl/arch directories have been kept in the
default Perl @INC for all Perl ports, and will be phased out as these old
Perl versions expire.
PR: 194969
Differential Revision: https://reviews.freebsd.org/D1019
Exp-run by: antoine
Reviewed by: perl@
Approved by: portmgr
- Add LICENSE, no EXAMPLES included in distfile now
- Rework pkg-descr, remove author info - it's available on homepage
PR: 194163
Submitted by: tkato432@yahoo.com
- Blixem
o Added the facility to run Dotter on an ad-hoc sequence (RT:408836).
o Added the facility to run Dotter against a transcript.
- Dotter
Minimise the greyramp tool to a simple contrast slider. Use
Ctrl-G to toggle between this and the full greyramp tool.
- Belvu
Fix a bug with tree bootstrapping in Belvu.
PR: 190854
Submitted by: Jason Bacon
The Basic Local Alignment Search Tool (BLAST) finds regions of local
similarity between sequences. The program compares nucleotide or protein
sequences to sequence databases and calculates the statistical
significance of matches. BLAST can be used to infer functional and
evolutionary relationships between sequences as well as help identify
members of gene families.
- Update MASTER_SITES
- Add my LOCAL to MASTER_SITES
- Use USE_CSTD
- Use MAKE_CMD
- Reformat pkg-descr
- Update WWW
- Take maintainership
- Bump PORTREVISION for devel/protobuf shlib change
Changes: https://code.google.com/p/protobuf/source/browse/trunk/CHANGES.txt
- Convert to USES=libtool and bump dependent ports
- Add INSTALL_TARGET=install-strip
- Remove patches that renamed include directories and libraries so they
didn't conflict with early development versions of glib/gtk 2.0
- Remove patches integrated upstream (it's nice to have direct contact)
- Sort USES and pkg-plist, cleanup Makefile a bit while here
Approved by: maintainer (implicit)
biology/phrab
biology/phred
biology/consed
Although these programs are licensed freely for academic and nonprofit
purposes, users have to contact the authors to obtain the tarballs.
PR: 191336
Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer)
Please use USES=python instead of USE_PYTHON.
USE_PYTHON=yes becomes USES=python
USE_PYTHON=2.7+ becomes USES=python:2.7+
USE_PYTHON_BUILD=3.3 becomes USES=python:3.3,build
...
A new PYTHON_FEATURES variable was added, which enables certain features for a
port and replaces some knobs at the same time;
PYTHON_FEATURES=distutils replaces USE_PYDISTUTILS
PYTHON_FEATURES=autoplist replaces PYDISTUTILS_AUTOPLIST
PYTHON_FEATURES=py3kplist replaces PYTHON_PY3K_PLIST_HACK
PYTHON_FEATURES=noegginfo replaces PYDISTUTILS_NOEGGINFO
PYTHON_FEATURES=concurrent replaces PYTHON_CONCURRENT_INSTALL
PYTHON_FEATURES=pythonprefix replaces USE_PYTHON_PREFIX
Some knobs have been deprecated and are to be removed in the near future:
PYTHON_MASTER_SITES - use MASTER_SITE_PYTHON instead
PYTHON_PKGNAMESUFFIX - use PYTHON_PKGNAMEPREFIX instead
PYDISTUTILS_INSTALLNOSINGLE - deprecated without replacement
Some knobs have been removed completely:
PYTHON_MASTER_SITE_SUBDIR
PYTHON_DISTNAME
PYTHON_WRKSRC
Several variables specific to the Python framework are no longer passed to the
build environment to avoid polluting dependency builds.
PYTHON_VERSION is not passed to .MAKEFLAGS anymore
PYTHON_DEFAULT_VERSION,
PYTHON_DEFAULT_PORTVERSION and
PYTHONBASE are not passed to the make environment anymore
The conversion required a couple of ports to be updated to fit the changes and
new requirements. Those included "bsd.python.mk" directly or contained checks
in places, for which the USES framework would fail to provide correct values.
Python modules directly using the upstream Python package (such as py-tkinter
or py-sqlite3) were updated to avoid using the now unnecessary and remmoved
knobs from "bsd.python.mk".
Phabric: D399
exp-run: 167368 192357
PR: 167368 192357
Reviewed by: antoine, wg
Exp-run award: antoine
With hat: python@
Approved by: portmgr
I don't think selecting clang as a function of OSVERSION is generally
desired, but if it's going to happen, make sure FreeBSD-specific
conditions are limited to FreeBSD by comparing OPSYS first.
The main problem was the WRKDIR is not within STAGEDIR. Fix this while
moving all the directory creation steps into one. While here
set TAR to use switches as outlined in its man page.
Also, the permission setting in stagedir is not necessary, so it's simply
been removed.
Where possible, correct a few instances where PORTDOCS was being used
to flag stuff in EXAMPLESDIR. For some ports, mostly those owned by
ruby@, PORTDOCS is applied to pretty much everything whether it's
documentation or example.
The distfiles are regenerated often, too frequently to be suitable for
ports. Fonz has decided to host the tarball of a known version to
restore this unmaintained port.
PR: 191685
Submitted by: Fonz
