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non port: biology/peak-classifier/Makefile

Number of commits found: 15

Saturday, 2 Mar 2024
19:37 Nuno Teixeira (eduardo) search for other commits by this committer
biology/peak-classifier: Move man pages to share/man

Approved by:	portmgr (blanket)
commit hash: 3312d5f90102d628fcf1e50c6b84ae719f66c494 commit hash: 3312d5f90102d628fcf1e50c6b84ae719f66c494 commit hash: 3312d5f90102d628fcf1e50c6b84ae719f66c494 commit hash: 3312d5f90102d628fcf1e50c6b84ae719f66c494 3312d5f9
Saturday, 28 Oct 2023
11:38 Jason W. Bacon (jwb) search for other commits by this committer
biology/peak-classifier: Update to 0.1.4.13

Updates for new libxtend API
commit hash: d6b521a455883ea2b387fb9cf61637ea879b746c commit hash: d6b521a455883ea2b387fb9cf61637ea879b746c commit hash: d6b521a455883ea2b387fb9cf61637ea879b746c commit hash: d6b521a455883ea2b387fb9cf61637ea879b746c d6b521a
Wednesday, 6 Sep 2023
20:50 Po-Chuan Hsieh (sunpoet) search for other commits by this committer
biology/peak-classifier: Clean up USES=python

Approved by:	portmgr (blanket)
With hat:	python
commit hash: 1d86601d3200c531e7fcd174cdd1feaf6d616518 commit hash: 1d86601d3200c531e7fcd174cdd1feaf6d616518 commit hash: 1d86601d3200c531e7fcd174cdd1feaf6d616518 commit hash: 1d86601d3200c531e7fcd174cdd1feaf6d616518 1d86601
Friday, 11 Aug 2023
20:44 Jason W. Bacon (jwb) search for other commits by this committer
biology/peak-classifier: Update to 0.1.4.11

Updates for biolibc GFF3 API changes
commit hash: 9b09bd9028308deec3cc1610f673aba3a0450583 commit hash: 9b09bd9028308deec3cc1610f673aba3a0450583 commit hash: 9b09bd9028308deec3cc1610f673aba3a0450583 commit hash: 9b09bd9028308deec3cc1610f673aba3a0450583 9b09bd90
Tuesday, 27 Jun 2023
19:34 Rene Ladan (rene) search for other commits by this committer
all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>
commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb 3d9a815
Saturday, 10 Jun 2023
11:57 Jason W. Bacon (jwb) search for other commits by this committer
biology/peak-classifier: Update to 0.1.4.8

Updates for libxtend API
Minor fixes
commit hash: 55b91b159bfdb2c2201a68d7eebe857aad3a8b2c commit hash: 55b91b159bfdb2c2201a68d7eebe857aad3a8b2c commit hash: 55b91b159bfdb2c2201a68d7eebe857aad3a8b2c commit hash: 55b91b159bfdb2c2201a68d7eebe857aad3a8b2c 55b91b1
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
Sunday, 11 Dec 2022
20:09 Jason W. Bacon (jwb) search for other commits by this committer
biology/peak-classifier: Update to 0.1.4-5

Update for biolibc API changes
commit hash: 4b09e48aecc23e12eb75330493000fa114cfab5d commit hash: 4b09e48aecc23e12eb75330493000fa114cfab5d commit hash: 4b09e48aecc23e12eb75330493000fa114cfab5d commit hash: 4b09e48aecc23e12eb75330493000fa114cfab5d 4b09e48
Wednesday, 7 Sep 2022
21:10 Stefan Eßer (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
Saturday, 11 Jun 2022
14:26 Jason W. Bacon (jwb) search for other commits by this committer
biology/peak-classifier: Update to 0.1.4

Update for bl_gff_t API streamlining

Changes:        https://github.com/auerlab/peak-classifier/tags
commit hash: 620c716685c4419012e33c5093238ce8d7621821 commit hash: 620c716685c4419012e33c5093238ce8d7621821 commit hash: 620c716685c4419012e33c5093238ce8d7621821 commit hash: 620c716685c4419012e33c5093238ce8d7621821 620c716
Tuesday, 15 Mar 2022
21:41 Jason W. Bacon (jwb) search for other commits by this committer
biology/peak-classifier: Update to 0.1.3

Minor update for biolibc 0.2.2 API changes
commit hash: aa7ea85d2bf2cf468e22ddc3dcc74008d2759281 commit hash: aa7ea85d2bf2cf468e22ddc3dcc74008d2759281 commit hash: aa7ea85d2bf2cf468e22ddc3dcc74008d2759281 commit hash: aa7ea85d2bf2cf468e22ddc3dcc74008d2759281 aa7ea85
Tuesday, 14 Dec 2021
19:45 Jason W. Bacon (jwb) search for other commits by this committer
biology/peak-classifier: Update to 0.1.2

Mainly updates for evolving libxtend and biolibc APIs
A few minor fixes and enhancements
commit hash: 084fcf005687bbc5c855f58a873087f3d759b6d8 commit hash: 084fcf005687bbc5c855f58a873087f3d759b6d8 commit hash: 084fcf005687bbc5c855f58a873087f3d759b6d8 commit hash: 084fcf005687bbc5c855f58a873087f3d759b6d8 084fcf0
Thursday, 2 Sep 2021
23:15 Jason W. Bacon (jwb) search for other commits by this committer
biology/peak-classifier: Update to 0.1.1.21

Fix regression: Replace BL_BED_SET_STRAND() macro with
bl_bed_set_strand(), which performs sanity checks
commit hash: 7e94c6d1f86cebaa77367f9a86ca452efaf70bae commit hash: 7e94c6d1f86cebaa77367f9a86ca452efaf70bae commit hash: 7e94c6d1f86cebaa77367f9a86ca452efaf70bae commit hash: 7e94c6d1f86cebaa77367f9a86ca452efaf70bae 7e94c6d
Saturday, 28 Aug 2021
01:34 Jason W. Bacon (jwb) search for other commits by this committer
biology/peak-classifier: Update to 0.1.1.20

Updates for libxtend and biolibc API changes
commit hash: b16616b283a7564fbd6a001b47decd2d89fcc5c5 commit hash: b16616b283a7564fbd6a001b47decd2d89fcc5c5 commit hash: b16616b283a7564fbd6a001b47decd2d89fcc5c5 commit hash: b16616b283a7564fbd6a001b47decd2d89fcc5c5 b16616b
Monday, 14 Jun 2021
16:40 Jason W. Bacon (jwb) search for other commits by this committer
biology/peak-classifier: Classify peaks based on GFF features

Classify ChIP/ATAC-Seq peaks based on features provided in a GFF

Peaks are provided in a BED file sorted by chromosome and position.
The GFF must be sorted by chromosome and position, with gene-level
features separated by ### tags and each gene organized into
subfeatures such as transcripts and exons.  This is the default for
common data sources.
commit hash: 5a2a6eb32954aa49c79269b08fd7e26ca4436f3d commit hash: 5a2a6eb32954aa49c79269b08fd7e26ca4436f3d commit hash: 5a2a6eb32954aa49c79269b08fd7e26ca4436f3d commit hash: 5a2a6eb32954aa49c79269b08fd7e26ca4436f3d 5a2a6eb

Number of commits found: 15