non port: biology/viennarna/Makefile |
Number of commits found: 26 |
Saturday, 2 Mar 2024
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20:35 Nuno Teixeira (eduardo)
biology/viennarna: Move man pages to share/man
Approved by: portmgr (blanket)
5ebea8e |
Monday, 1 Jan 2024
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11:49 Thierry Thomas (thierry)
*/*: chase the upgrade of BLAS / LAPACK to 3.12.0
PR: 275860
f2489ab |
Friday, 3 Nov 2023
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22:02 Yuri Victorovich (yuri)
biology/viennarna: update 2.6.3 → 2.6.4
3a75bcf |
Friday, 18 Aug 2023
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06:57 Muhammad Moinur Rahman (bofh)
biology/viennarna: Mark BROKEN on 14
Fails to compile with:
error: no member named 'bind2nd' in namespace 'std'
Approved by: portmgr (blanket)
Sponsored by: The FreeBSD Foundation
4b87c88 |
Saturday, 22 Jul 2023
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08:55 Yuri Victorovich (yuri)
biology/viennarna: Update 2.6.2 → 2.6.3
c8adede |
Sunday, 16 Jul 2023
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21:38 Yuri Victorovich (yuri)
biology/viennarna: Remove unnecessary library from .pc file; Correct pkg-descr
3e4f91e |
20:50 Yuri Victorovich (yuri)
biology/viennarna: Update 2.5.1 → 2.6.2
bb900f7 |
Wednesday, 7 Sep 2022
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21:10 Stefan Eßer (se)
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)
b7f0544 |
Sunday, 31 Jul 2022
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08:12 Yuri Victorovich (yuri)
biology/viennarna: Update 2.5.0 -> 2.5.1
Also add test target.
c7b2968 |
Sunday, 6 Feb 2022
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18:36 Stefan Eßer (se)
Update CONFLICTS definitions in categories a* to c*
Update the CONFLICTS definitions of ports in the following categories:
- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters
An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.
There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.
Approved by: portmgr (implicit)
bdd2d4a |
Tuesday, 25 Jan 2022
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05:44 Yuri Victorovich (yuri)
biology/viennarna: Update 2.4.18 -> 2.5.0
8615039 |
Wednesday, 12 Jan 2022
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19:41 Tobias C. Berner (tcberner)
math/gsl: bump portrevision of consumers after update to 2.7.1
PR: 260201
654acd8 |
Wednesday, 16 Jun 2021
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19:31 Tobias C. Berner (tcberner)
math/gsl: update to 2.7
From [1]
* What is new in gsl-2.7:
* fixed doc bug for gsl_histogram_min_bin (lhcsky at 163.com)
* fixed bug #60335 (spmatrix test failure, J. Lamb)
* fixed bug #36577
* clarified documentation on interpolation accelerators (V. Krishnan)
* fixed bug #45521 (erroneous GSL_ERROR_NULL in ode-initval2, thanks to M.
Sitte)
* fixed doc bug #59758
* fixed bug #58202 (rstat median for n=5)
* added support for native C complex number types in gsl_complex
when using a C11 compiler
* upgraded to autoconf 2.71, automake 1.16.3, libtool 2.4.6
* updated exponential fitting example for nonlinear least squares
* added banded LU decomposition and solver (gsl_linalg_LU_band)
* New functions added to the library:
- gsl_matrix_norm1
- gsl_spmatrix_norm1
- gsl_matrix_complex_conjtrans_memcpy
- gsl_linalg_QL: decomp, unpack
- gsl_linalg_complex_QR_* (thanks to Christian Krueger)
- gsl_vector_sum
- gsl_matrix_scale_rows
- gsl_matrix_scale_columns
- gsl_multilarge_linear_matrix_ptr
- gsl_multilarge_linear_rhs_ptr
- gsl_spmatrix_dense_add (renamed from gsl_spmatrix_add_to_dense)
- gsl_spmatrix_dense_sub
- gsl_linalg_cholesky_band: solvem, svxm, scale, scale_apply
- gsl_linalg_QR_UD: decomp, lssolve
- gsl_linalg_QR_UU: decomp, lssolve, QTvec
- gsl_linalg_QR_UZ: decomp
- gsl_multifit_linear_lcurvature
- gsl_spline2d_eval_extrap
* bug fix in checking vector lengths in gsl_vector_memcpy (dieggsy@pm.me)
* made gsl_sf_legendre_array_index() inline and documented
- gsl_sf_legendre_nlm()
[1] http://git.savannah.gnu.org/cgit/gsl.git/tree/NEWS
PR: 256423
Exp-run by: antoine
63e653a |
Saturday, 24 Apr 2021
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01:57 Yuri Victorovich (yuri)
biology/viennarna: Update 2.4.17 -> 2.4.18
874e67e |
Wednesday, 7 Apr 2021
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08:09 Mathieu Arnold (mat)
One more small cleanup, forgotten yesterday.
Reported by: lwhsu
cf118cc |
Tuesday, 6 Apr 2021
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14:31 Mathieu Arnold (mat)
Remove # $FreeBSD$ from Makefiles.
305f148 |
Sunday, 6 Dec 2020
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20:14 yuri
biology/viennarna: Update 2.4.16 -> 2.4.17
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Wednesday, 11 Nov 2020
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23:27 yuri
biology/viennarna: Update 2.4.15 -> 2.4.16
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Monday, 7 Sep 2020
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21:49 yuri
biology/viennarna: Update 2.4.14 -> 2.4.15
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Monday, 4 May 2020
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21:31 dinoex
- update libgd to 2.3.0
- new option RAQM
- resurrect deprecated gdlib-config
- bump dependend ports
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Monday, 6 Jan 2020
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04:17 yuri
biology/viennarna: Update 2.4.13 -> 2.4.14
Reported by: repology
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Monday, 4 Nov 2019
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21:08 zeising
Add USES=xorg USES=gl, ports categories b
Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'.
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Friday, 25 Oct 2019
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23:41 tcberner
math/gsl: update to 2.6
- math/p5-Math-GSL does not seem to have any upstream activity to make it work
with this version -> mark it broken
- this also breaks the two consumers of this port
- biology/gemma: has a conflict with cblas, and is makred broken.
PR: 241363
Exp-run by: antoine
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Friday, 26 Jul 2019
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20:46 gerald
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
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Monday, 24 Jun 2019
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19:30 yuri
biology/viennarna: Make it less/not prone to failures due to hardcoded C++
library name
configure and Makefile.in provided in tarballs have -lstdc++ hard-coded in them.
The previous version of the port patches these to be -lc++, which still might
fail on gcc systems, depending on which C++ library is used.
This change adds USES=autoreconf which makes it to regenerate configure and
Makefile.in and hopefully have the proper C++ library in these files.
GNU libtool links with the C compiler, not with the C++ compiler, in this
project. This is what I think triggers link failures due to a wrong C++
library getting into the link lines. GNU libtool likely chooses C compiler
because this project has its 'main' functions in .c files,
but also includes C++ object modules. This likely causes GNU tools confusion and
it uses the C compiler to link and fails due to wrong C++ libraries added there.
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09:29 yuri
New port: biology/viennarna: Alignment tools for the structural analysis of RNA
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Number of commits found: 26 |