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non port: biology/kallisto/Makefile

Number of commits found: 25

Saturday, 4 Nov 2023
13:15 Jason W. Bacon (jwb) search for other commits by this committer
biology/kallisto: Update to 0.50.1,1

Update kallisto index version to 13
A few other new features
Changes: https://github.com/pachterlab/kallisto/releases

Reported by:    portscout
commit hash: 8a2deaeb09da2b11c7061bd7120c9078717157ee commit hash: 8a2deaeb09da2b11c7061bd7120c9078717157ee commit hash: 8a2deaeb09da2b11c7061bd7120c9078717157ee commit hash: 8a2deaeb09da2b11c7061bd7120c9078717157ee 8a2deae
Monday, 24 Jul 2023
15:44 Jason W. Bacon (jwb) search for other commits by this committer
biology/kallisto: Clean up build

Silence warnings due to detected compiler standards
Enable BAM support in cmake
Patch out remaining aggressive optimizations
commit hash: ddc812686212150df9dd26893ec936b26102aff2 commit hash: ddc812686212150df9dd26893ec936b26102aff2 commit hash: ddc812686212150df9dd26893ec936b26102aff2 commit hash: ddc812686212150df9dd26893ec936b26102aff2 ddc8126
Friday, 14 Jul 2023
16:12 Jason W. Bacon (jwb) search for other commits by this committer
biology/kallisto: Tag only for 64-bit architectures

Also patch out -march=native

Reported by:    pkg-fallout
commit hash: 2b96a02432aeacb3a5f477be3477b95f8bd9d2ca commit hash: 2b96a02432aeacb3a5f477be3477b95f8bd9d2ca commit hash: 2b96a02432aeacb3a5f477be3477b95f8bd9d2ca commit hash: 2b96a02432aeacb3a5f477be3477b95f8bd9d2ca 2b96a02
Friday, 7 Jul 2023
18:00 Jason W. Bacon (jwb) search for other commits by this committer
biology/kallisto: Update to 0.50.0

New, more memory-efficient index
Several other new features and enhancements
End of support for bulk RNASeq features

changes: https://github.com/pachterlab/kallisto/releases

Reported by:    portscout
commit hash: cab50560d1b5cdd1c99b23ba5fcbfdcd58fd8910 commit hash: cab50560d1b5cdd1c99b23ba5fcbfdcd58fd8910 commit hash: cab50560d1b5cdd1c99b23ba5fcbfdcd58fd8910 commit hash: cab50560d1b5cdd1c99b23ba5fcbfdcd58fd8910 cab5056
Sunday, 23 Apr 2023
09:09 Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b 8d3e020
Wednesday, 7 Sep 2022
21:10 Stefan E├čer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Wednesday, 20 Jul 2022
14:35 Tobias C. Berner (tcberner) search for other commits by this committer
science/hdf5: bump PORTREVISION of consumers

The SO-version increased in the update to 1.12.2 in
a43418b81530f7e897abfbe18dd59f44265a1a0f .

Reported by:	VVD <vvd@unislabs.com>
commit hash: 5564b3b420db29745d2d4981d1963200ddf53e35 commit hash: 5564b3b420db29745d2d4981d1963200ddf53e35 commit hash: 5564b3b420db29745d2d4981d1963200ddf53e35 commit hash: 5564b3b420db29745d2d4981d1963200ddf53e35 5564b3b
Thursday, 16 Jun 2022
15:13 Po-Chuan Hsieh (sunpoet) search for other commits by this committer
*/*: Replace science/szip with science/libaec

- Bump PORTREVISION of dependent ports for dependency change

szip does not allow redistribution in binary form without proper commercial
license. Its LICENSE_PERMS should be set to no-auto-accept which blocks building
this port, therefore building dependent ports are also blocked. Switch all
dependent ports to science/libaec to avoid conflicts and license issue.

PR:		228743, 246097, 250165
commit hash: 328ae4074233a5b85e0e38efece1af5dcc218160 commit hash: 328ae4074233a5b85e0e38efece1af5dcc218160 commit hash: 328ae4074233a5b85e0e38efece1af5dcc218160 commit hash: 328ae4074233a5b85e0e38efece1af5dcc218160 328ae40
Wednesday, 19 Jan 2022
13:57 Jason W. Bacon (jwb) search for other commits by this committer
biology/kallisto: Update to 0.48.0

Fixes segfault with --genomebam in 0.46.2
Unbundle htslib
A few new features and performance improvements

Changes:        https://github.com/pachterlab/kallisto/tags
commit hash: c9bd01bdf4c1dae17b53482e9dabe000d310cf50 commit hash: c9bd01bdf4c1dae17b53482e9dabe000d310cf50 commit hash: c9bd01bdf4c1dae17b53482e9dabe000d310cf50 commit hash: c9bd01bdf4c1dae17b53482e9dabe000d310cf50 c9bd01b
Wednesday, 7 Apr 2021
08:09 Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c cf118cc
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Tuesday, 26 Jan 2021
01:34 jwb search for other commits by this committer
biology/kallisto: Add -lz for pending hdf5 upgrade

PR:             252965
Submitted by:   thierry
Original commitRevision:562627 
Monday, 3 Aug 2020
15:45 jwb search for other commits by this committer
biology/kallisto: Revert to 0.46.1

0.46.2 has long-standing regressions that are not being addressed, including
a seg fault when using --genomebam.
Also revert to bundled htslib in preparation for biology/htslib upgrade
to 1.10.  Kallisto source contains modified bits of htslib 1.4.1 that are
incompatible with htslib > 1.9.
Original commitRevision:544077 
Wednesday, 1 Apr 2020
23:35 jwb search for other commits by this committer
kallisto: Patch for build with GCC

PR:             ports/245240
Submitted by:   pkubaj
Original commitRevision:530250 
Saturday, 15 Feb 2020
23:09 jwb search for other commits by this committer
biology/kallisto: Upgrade to 0.46.2

Kallisto no longer builds in hdf5 by default, but it is still required
for some downstream tools like Sleuth.  Forcing it ON for now, but will
disable it in a future upgrade.

Reported by:    portscout
Original commitRevision:526244 
Wednesday, 6 Nov 2019
00:18 jwb search for other commits by this committer
biology/kallisto: Upgrade to 0.46.1

Minor bug fixes and enhancements

Reported by:    portscout
Original commitRevision:516853 
Friday, 26 Jul 2019
20:46 gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
Original commitRevision:507372 
Wednesday, 12 Jun 2019
15:24 jwb search for other commits by this committer
biology/kallisto: Upgrade to 0.46.0

Reported by:    portscout
Original commitRevision:504011 
Sunday, 24 Feb 2019
20:32 jwb search for other commits by this committer
kallisto: Upgrade to 0.45.1, unbundle hstlib
Original commitRevision:493810 
Saturday, 5 Jan 2019
22:46 sunpoet search for other commits by this committer
Update science/hdf5 to 1.10.4

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://portal.hdfgroup.org/display/support/HDF5%201.10.4#releasenotes
PR:		233070
Submitted by:	wen
Original commitRevision:489412 
Wednesday, 12 Dec 2018
01:35 gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
Original commitRevision:487272 
Wednesday, 5 Sep 2018
22:05 sunpoet search for other commits by this committer
Update science/hdf5 to 1.10.2

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://portal.hdfgroup.org/display/support/HDF5%201.10.2#releasenotes
		https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.2/src/hdf5-1.10.2-RELEASE.txt
PR:		231009
Exp-run by:	antoine
Original commitRevision:479046 
Sunday, 29 Jul 2018
22:18 gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542
Original commitRevision:475857 
Saturday, 2 Jun 2018
19:40 linimon search for other commits by this committer
Adjust USES to fix building on gcc-based archs (in particular, powerpc64).

On the clang architectures, these changes have no effect: the baser
compiler already includes the needed features.

While here, remove now-redundant CXXFLAGS statements and pet portlint
(no other content change).

Tested on both powerpc64 and amd64.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:471400 
Saturday, 2 Dec 2017
20:44 jwb search for other commits by this committer
[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq
data

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13328
Original commitRevision:455382 

Number of commits found: 25