| Commit message (Collapse) | Author | Age | Files | Lines |
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re-rolled.
- Move post-patch target into files/patch-xwin.c to remove sed invocation.
- Respect NOPORTDATA and DATADIR.
- Bring files/patch-aa back (to preserve history) and retire patch-makefile.
- Fixup files/patch-xwin.c so it applies cleanly to this version.
Notes:
svn path=/head/; revision=222711
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Notes:
svn path=/head/; revision=222520
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While I'm here, make it respect NOPORTDOCS.
Notes:
svn path=/head/; revision=222479
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PR: ports/128476
Submitted by: fulvio ciriaco <oivulf@gmail.com>
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PR: 128057
Submitted by: Christian Sturm <athaba at inode dot at>
Notes:
svn path=/head/; revision=221933
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PR: ports/128193
Submitted by: Mauricio Herrera Cuadra <mauricio at arareko.net> (maintainer)
Notes:
svn path=/head/; revision=221872
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PR: 127776
Submitted by: Wen heping <wenheping@gmail.com>
Approved by: maintainer
Notes:
svn path=/head/; revision=221438
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- Pass maintainership to submitter
PR: 127683
Submitted by: Wen heping <wenheping@gmail.com>
Notes:
svn path=/head/; revision=221025
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Reported by: QA Tindie
Approved by: portmgr
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Hat: portmgr
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svn path=/head/; revision=219711
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Reported by: QA Tindie
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svn path=/head/; revision=219325
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Notes:
svn path=/head/; revision=219315
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Notes:
svn path=/head/; revision=219017
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Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.
To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.
To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.
Changes to Mk/*:
- Add runtime detection magic in bsd.port.mk
- Remove CONFIGURE_TARGET hack in various bsd.*.mk
- USE_GNOME=gnometarget is now an no-op
Changes to individual ports, other than removing the CONFIGURE_TARGET hack:
= pkg-plist changed (due to the ugly CONFIGURE_TARGET prefix in * executables)
- comms/gnuradio
- science/abinit
- science/elmer-fem
- science/elmer-matc
- science/elmer-meshgen2d
- science/elmerfront
- science/elmerpost
= use x86_64 as ARCH
- devel/g-wrap
= other changes
- print/magicfilter
GNU_CONFIGURE -> HAS_CONFIGURE since it's not generated by autoconf
Total # of ports modified: 1,027
Total # of ports affected: ~7,000 (set GNU_CONFIGURE to yes)
PR: 126524 (obsoletes 52917)
Submitted by: rafan
Tested on: two pointyhat 7-amd64 exp runs (by pav)
Approved by: portmgr (pav)
Notes:
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Submitted by: Steve Kargl <sgk at troutmask.apl.washington.edu> at ports@ ML
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svn path=/head/; revision=218644
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Notes:
svn path=/head/; revision=218469
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PR: 125912
Submitted by: Wen heping <wenheping@gmail.com>
Approved by: maintainer timeout
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svn path=/head/; revision=218425
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Approved by: gabor (mentor)
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svn path=/head/; revision=217884
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FreeBSD versions: 5.3 and up, 6.x, 7.x, 8-CURRENT
Notes:
svn path=/head/; revision=217485
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MAKE_ENV
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svn path=/head/; revision=217468
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PR: ports/125891
Submitted by: M. L. Dodson <mldodson@comcast.net> (maintainer)
Notes:
svn path=/head/; revision=217415
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Approved by: araujo (mentor)
Notes:
svn path=/head/; revision=217338
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- bump PORTREVISION
Prompted by: QA Tindy run
Notes:
svn path=/head/; revision=216729
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- Pass maintainership to submitter.
PR: ports/125497
Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com>
Notes:
svn path=/head/; revision=216706
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Notes:
svn path=/head/; revision=216541
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Notes:
svn path=/head/; revision=216502
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Notes:
svn path=/head/; revision=216430
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PR: ports/124648
Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
Reviewed by: lippe
Approved by: gabor (mentor, implicit)
Notes:
svn path=/head/; revision=216421
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PR: ports/125134
Submitted by: Wen heping <wenheping@gmail.com>
Approved by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
Notes:
svn path=/head/; revision=216283
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Notes:
svn path=/head/; revision=215701
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- Bump PORTREVISION.
Reported by: QA Tindy
Approved by: gabor (mentor, implicit)
Notes:
svn path=/head/; revision=215432
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sequences. It stands for Sequence Search and Alignment by Hashing
Algorithm. It achieves its fast search speed by converting sequence
information into a `hash table' data structure, which can then be
searched very rapidly for matches.
WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/
PR: ports/124525
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by: gabor (mentor, implicit)
Notes:
svn path=/head/; revision=215429
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Notes:
svn path=/head/; revision=215107
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- Bump port revision
Reported by: pointyhat via pav
Notes:
svn path=/head/; revision=214547
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The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).
PR: ports/124340
Submitted by: edwin@
Approved by: portmgr (pav)
Notes:
svn path=/head/; revision=214428
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- Sanitize Makefile a little bit
Notes:
svn path=/head/; revision=214280
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Notes:
svn path=/head/; revision=214138
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Notes:
svn path=/head/; revision=214021
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Notes:
svn path=/head/; revision=213667
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assembly
Consed is a tool for viewing, editing, and finishing sequence
assemblies.
The port is constituted of 4 parts:
biology/phred: base caller with quality evaluation
biology/phrap: sequence assembler for shotgun sequencing
biology/consed: workbench
biology/phd2fasta: small utility
All these can be used separately; however, most function
of consed depends on the others.
Although these programs are licensed freely for academic
and nonprofit purposes, users have to contact the authors
to get the softwares.
Phred (including phd2fasta) and phrap are emailed,
and consed can be downloaded to a restricted IP address.
For commercial users, the licensing fee is ca. $10,000 at
the time of writing.
PR: ports/118548
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Notes:
svn path=/head/; revision=213596
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assembly
Consed is a tool for viewing, editing, and finishing sequence
assemblies.
The port is constituted of 4 parts:
biology/phred: base caller with quality evaluation
biology/phrap: sequence assembler for shotgun sequencing
biology/consed: workbench
biology/phd2fasta: small utility
All these can be used separately; however, most function
of consed depends on the others.
Although these programs are licensed freely for academic
and nonprofit purposes, users have to contact the authors
to get the softwares.
Phred (including phd2fasta) and phrap are emailed,
and consed can be downloaded to a restricted IP address.
For commercial users, the licensing fee is ca. $10,000 at
the time of writing.
PR: ports/118548
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Notes:
svn path=/head/; revision=213594
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assembly
Consed is a tool for viewing, editing, and finishing sequence
assemblies.
The port is constituted of 4 parts:
biology/phred: base caller with quality evaluation
biology/phrap: sequence assembler for shotgun sequencing
biology/consed: workbench
biology/phd2fasta: small utility
All these can be used separately; however, most function
of consed depends on the others.
Although these programs are licensed freely for academic
and nonprofit purposes, users have to contact the authors
to get the softwares.
Phred (including phd2fasta) and phrap are emailed,
and consed can be downloaded to a restricted IP address.
For commercial users, the licensing fee is ca. $10,000 at
the time of writing.
PR: ports/118548
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Notes:
svn path=/head/; revision=213592
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assembly
Consed is a tool for viewing, editing, and finishing sequence assemblies.
The port is constituted of 4 parts:
biology/phred: base caller with quality evaluation
biology/phrap: sequence assembler for shotgun sequencing
biology/consed: workbench
biology/phd2fasta: small utility
All these can be used separately; however, most function
of consed depends on the others.
Although these programs are licensed freely for academic
and nonprofit purposes, users have to contact the authors
to get the softwares.
Phred (including phd2fasta) and phrap are emailed,
and consed can be downloaded to a restricted IP address.
For commercial users, the licensing fee is ca. $10,000 at
the time of writing.
PR: ports/118548
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Notes:
svn path=/head/; revision=213590
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Notes:
svn path=/head/; revision=213548
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- Support CC/CFLAGS properly
- Strip binary
PR: 123866
Submitted by: Ports Fury
Notes:
svn path=/head/; revision=213507
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PR: ports/123530
Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by: araujo (myself)
Approved by: flz (portmgr)
Notes:
svn path=/head/; revision=213332
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Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
Notes:
svn path=/head/; revision=213206
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Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
Notes:
svn path=/head/; revision=213205
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Notes:
svn path=/head/; revision=213074
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in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP
package). NJplot is especially convenient for rooting the unrooted trees
obtained from parsimony, distance or maximum likelihood tree-building methods.
The package contains the following programs:
njplot - draw phylogenetic trees and interactively modify them
newicktops - non-interactive version rendering into a PostScript file
newicktotxt - non-interactive version rendering into a text file
unrooted - draw unrooted circular trees
If you use NJplot in a published work, please cite the following reference:
Perriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for
biological sequence banks. Biochimie, 78, 364-369.
WWW: http://pbil.univ-lyon1.fr/software/njplot.html
PR: ports/118438
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Notes:
svn path=/head/; revision=213034
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