- 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
===> Configuring for p5-bioperl-run-1.6.1_4
Invalid prerequisite condition '0/processing XML data/Bio::Tools::Run::EMBOSSacd' for XML::Twig at /usr/local/lib/perl5/site_perl/5.16/Module/Build/Base.pm line 1702.
*** [do-configure] Error code 25
Reported by: pkg-fallout
With hat: portmgr
Sylvio's last commit was 17 months ago, a full 5 months after all of his
ports could have been reset per policy. Given the push to complete
staging (48 ports are still unstaged, something like 70+ have already
been staged by other committers) and given that PRs are automatically
assigned but never addressed, it's better just to reset all the ports and
PRs so that it's clear to others that these ports are free to maintain.
Approved by: portmgr (implicit)
Starting with perl 5.20, they're not installed any more if empty,
and on FreeBSD, they're (always ?) empty.
PR: 190681
Submitted by: mat
Exp-Run by: antoine
Sponsored by: Absolight
For the story when moved to google code the project released a version 0.5 which was newer than the 0.5.1 from earlier hosting
To be consistent named it 0.5.1s20100824 (following what debian did)
Switch treeviewx to use unicode version of wx
Add a patch from Ubuntu to fix loading trees.
It's possible that EXTRACT_CMD won't be predefined in the near future
in order to support distfiles in multiple formats. We know the post-
extraction tool needs to be tar, so let's specify it directly.
This port needs staging. It doesn't like like a quick job so I'm leaving
that to the listed maintainer.
Approved by: infrastructure improvements blanket
Approved by: portmgr (implicit) (to skip stage check)
Maintainers for these ports have been notified on 5 separate occasions
over the course of several months about pending actions required.
We really appreciate the time and effort you put in to maintain
these ports.
If you are still interested in helping to maintain these ports just
reply to me or file a PR and I will happily assign the port to you
again.
Approved by: portmgr (implicit)
Since FreeBSD 8.4 and FreeBSD 9.1 make(1) do support :tu and :tl as a
replacement for :U and :L (which has been marked as deprecated)
bmake which is the default on FreeBSD 10+ only support by default
:tu/:tl a hack has been added at the time to support :U and :L to ease
migration. This hack is now not necessary anymore
Note that this makes the ports tree incompatible with make(1) from
FreeBSD 8.3 or earlier
With hat: portmgr
2014-04-16 ports-mgmt/pkgsearch: Upstream disappeared
2014-04-17 science/flounder: Unmaintained since 2002
2014-04-17 security/nbaudit: Unmaintained since 2002
2014-04-17 security/saint: Unmaintained since 2002
2014-04-17 graphics/gozer: Unmaintained since 2002
2014-04-17 misc/pdfmap: Unmaintained since 2002
2014-04-17 devel/showgrammar: Unmaintained since 2002
2014-04-17 biology/libgenome: Unmaintained since 2002
2014-04-17 deskutils/narval: Unmaintained since 2002
2014-04-17 devel/fampp: Unmaintained since 2002
2014-04-17 net-p2p/py-fngrab: Unmaintained since 2002
2014-04-17 misc/wmfirew: Unmaintained since 2002
2014-04-17 x11-wm/e16utils: Unmaintained since 2002
2014-04-17 misc/salias: Unmaintained since 2002
2014-04-17 print/latex2slides: Unmaintained since 2002
2014-04-17 lang/sxm: Unmaintained since 2002
2014-04-17 textproc/pybook: Unmaintained since 2002
2014-04-17 mail/mailcrypt: Unmaintained since 2002
2014-04-17 japanese/elvis: Unmaintained since 2002
2014-04-17 devel/prototype: Unmaintained since 2002
2014-04-17 print/wprint: Unmaintained since 2002
2014-04-17 science/euler: Unmaintained since 2002
2014-04-17 multimedia/gopchop: Unmaintained since 2002
2014-04-17 science/gdis: Unmaintained since 2002
2014-04-17 net/googolplex: Unmaintained since 2002
2014-04-17 lang/logo: Unmaintained since 2002
2014-04-17 textproc/roap: Unmaintained since 2002
2014-04-17 x11-wm/afterstep-i18n: Unmaintained since 2002
2014-04-17 games/yamsweeper: Unmaintained since 2002
2014-04-17 net-mgmt/echolot: Unmaintained since 2002
2014-04-17 security/pam_smb: Unmaintained since 2002
2014-04-18 devel/lua-redis-parser: Broken for more than 6 months
2014-04-18 biology/finchtv: Broken for more than 6 months
2014-04-18 net-im/ari-yahoo: Broken for more than 1 year (http://www.icculus.org/ari-yahoo/)
a zeising, kwm production, with help from dumbbell, bdrewery:
NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE
This update switches over to use the new xorg stack by default on FreeBSD 9
and 10 stable, on osversions where vt(9) is available.
It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in
/etc/make.conf .
FreeBSD 8-STABLE and released versions of FreeBSD still use
the old version.
A package repository with binary packages for new xorg will
be available soon.
This patch also contains updates of libxcb and related ports, pixman, as well
as some drivers and utilities.
Bump portrevisions for xf86-* ports, as well as virtualbox-ose-additions due
to xserver version change.
Apart from these updates, the way shared libraries are handled has been
changed for all xorg ports, as well as libxml2 and freetype, which means
ltverhack is gone and as a consequence shared libraries have been bumped.
The plan is that this change will make library bumps less likely in the
future.
All affected ports have had their portrevisions bumped as a consequence of
this.
Fix some issues where WITH_NEW_XORG weren't detected properly on CURRENT.
Update instructions, hardware support, and more notes can be found on
https://wiki.freebsd.org/Graphics
Thanks to: all testers, bdrewery and the FreeBSD x11@ team
exp-run by: bdrewery [1]
PR: ports/187602 [1]
Approved by: portmgr (bdrewery), core (jhb)
2014-04-12 net/pvm++: Unmaintained since 2001
2014-04-12 devel/ixlib: Unmaintained since 2001
2014-04-12 mail/althea: Unmaintained since 2001
2014-04-12 graphics/claraocr: Unmaintained since 2001
2014-04-12 graphics/qvplay: Unmaintained since 2001
2014-04-12 print/guitartex: Unmaintained since 2001
2014-04-12 print/pnm2ppa: Unmaintained since 2001
2014-04-12 graphics/opendis: Unmaintained since 2001
2014-04-12 net/gnome-mud: Unmaintained since 2001
2014-04-12 graphics/maverik: Unmaintained since 2001
2014-04-12 biology/rasmol: Unmaintained since 2001
2014-04-12 mail/mail2procmailrc: Unmaintained since 2001
2014-04-12 science/felt: Unmaintained since 2001
2014-04-12 textproc/pardiff: Unmaintained since 2001
2014-04-12 lang/klone: Unmaintained since 2001
2014-04-12 net/rmsg: Unmaintained since 2001
2014-04-12 net/sharity-light: Unmaintained since 2001
2014-04-12 biology/genpak: Unmaintained since 2001
2014-04-12 net/forg: Unmaintained since 2001
2014-04-12 misc/txt2regex: Unmaintained since 2001
2014-04-12 textproc/ipdf: Unmaintained since 2001
2014-04-12 graphics/plotmtv: Unmaintained since 2001
2014-04-12 devel/happydoc: Unmaintained since 2001
2014-04-12 print/cpp2latex: Unmaintained since 2001
2014-04-12 graphics/svg2swf: Unmaintained since 2001
2014-04-12 devel/flick: Unmaintained since 2001
2014-04-12 mail/smail: Unmaintained since 2001
2014-04-12 net/net-http: Unmaintained since 2001
2014-04-12 security/cfv: Unmaintained since 2001
2014-04-12 graphics/camediaplay: Unmaintained since 2001
2014-04-12 math/umatrix: Unmaintained since 2001
GCC 4.6.4 to GCC 4.7.3. This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.
Part II, Bump PORTREVISIONs.
PR: 182136
Supported by: Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by: bdrewery (two -exp runs)
Fasta3 distfile was significantly changed. This should have been released
as a new version (e.g. 36.3.6e), so it's not clear why the distfile was
rerolled. There are significant changes to makefiles, conf files and even
a few .c and .h files. They all look like legitimate updates to me
though.
Set DIST_SUBDIR since this port is now known for rerolling, then
regenerate distinfo. Also add Fasta license and bump revision.
to preserve version 1.x and to update to 3.0
print/py-reportlab:
- Update print/py-reportlab to 3.0 based on print/py-reportlab2
- Support STAGEDIR
- Use PYDISTUTILS_AUTOPLIST
* Remove pkg-plist, accordingly
- Set CONFLICTS
- Add PORTSCOUT
- Replace tab with a single space after WWW: in pkg-descr
print/py-reportlab1:
- Support STAGEDIR
- Add PKGNAMESUFFIX not to duplicate ports with the same name
- Set CONFLICTS
- Use PYDISTUTILS_AUTOPLIST
* Remove pkg-plist, accordingly
- Make use of PORTDOCS
- Set OPTIONS_DEFINE explicitly
- Fix include statement
- Make docs unconditional to stage
- Replace tab with a single space after WWW: in pkg-descr
print/py-reportlab2:
- Update CONFLICTS
- Set PORTSCOUT
dependent ports:
- Switch dependency from print/py-reportlab to print/py-reportlab1
* biology/py-biopython
* deskutils/gourmet
* deskutils/griffith
* games/pythonsudoku
* misc/pdfmap
* print/py-trml2pdf
* www/py-satchmo
PR: ports/186970
Submitted by: tota (myself)
Approved by: Muhammad Moinur Rahman (maintainer)
USE_GCC=yes has been omitted though.
Remove USE_FORTRAN handling from bsd.port.mk and bsd.gcc.mk.
Minor cleanups in some ports like USE_GMAKE, NOPORTDOCS,...
Exp-run: bdrewery
Approved by: portmgr (bdrewery)
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.
This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.
Approved by: portmgr (bapt)
