| Commit message (Collapse) | Author | Age | Files | Lines |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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
|
|
|
|
| |
Same issue as with powerpc.
|
|
|
|
|
|
|
|
|
|
| |
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.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
- Upgrade math/blas, math/cblas, math/lapack, math/lapacke and math/xlapack
to 3.9.1;
Latest release notes at <http://www.netlib.org/lapack/lapack-3.9.1.html>
- Chase this upgrade in biology/treekin;
- Add a test target;
- Remove a conflict with math/openblas (PR 244296);
- Fix the build with Gcc10 (PR 247485).
PR: 247542
Approved by: expr-run by antoine@
|
| |
|
| |
|
| |
|
|
|
|
|
|
| |
Updates for new biolibc API
Changes: https://github.com/auerlab/vcf-split/releases
|
|
|
|
|
|
| |
Updates for new biolibc API
Changes: https://github.com/auerlab/vcf2hap/releases
|
|
|
|
|
|
| |
Updates for new biolibc API
Changes: https://github.com/auerlab/ad2vcf/releases
|
|
|
|
| |
Changes: https://github.com/auerlab/biolibc/releases
|
|
|
|
|
| |
LLVM on powerpc doesn't have libomp.
Same issue happens on armv6 and armv7 but someone has to test whether doing the same for those architectures is enough.
|
|
|
|
|
| |
LLVM on powerpc doesn't have libomp:
cdhit-common.c++:36:9: fatal error: 'omp.h' file not found
|
|
|
|
| |
https://github.com/veg/hyphy/releases/tag/2.5.31
|
|
|
|
|
|
| |
Also fix number of lines in pkg-descr, and replace space with tab.
Reported by: fallout
|
|
|
|
| |
Reported by: portscout
|
|
|
|
|
|
| |
Add "extra" binaries to install
Changes: https://github.com/lh3/minimap2/releases/tag/v2.20
|
| |
|
|
|
|
| |
operations on k-mers
|
|
|
|
|
|
| |
Fix deadlock issue in multithreaded execution
Reported by: portscout
|
|
|
|
| |
Reported by: portscout
|
|
|
|
| |
Reported by: portscout
|
| |
|
|
|
|
| |
- CONFIG defaults to 64-bit mode now, adjust the check
|
|
|
|
|
|
|
|
| |
Drop tbb dependency (upstream switched to C++ threads)
Add support for powerpc64
Reported by: portscout
Tested by: pkubaj (powerpc64*)
|
|
|
|
|
| |
Update license message. Confirmed via conversation with UCSC that some
proprietary code is used in the "free" tools build. UCSC is working on it.
|
|
|
|
|
| |
PR: 248459
Exp-run by: antoine
|
|
|
|
| |
Approved by: portmgr blanket
|
|
|
|
| |
Approved by: portmgr blanket
|
| |
|
| |
|
|
|
|
| |
analysis
|
| |
|
|
|
|
|
|
|
|
|
| |
Since the previous update changed USES=python from 3.6+ to 3.7+, all
dependent ports must have USES=python:3.7+ as well, otherwise it breaks
the @py36 flavor.
PR: 255347
Reported by: sunpoet
|
|
|
|
| |
Reported by: portscout
|
|
|
|
|
|
|
|
|
| |
Move ports to the licenses framework.
RESTRICTED → auto-accept (unless expressly stated otherwise)
NO_CDROM → dist-mirror pkg-mirror auto-accept
Differential Revision: https://reviews.freebsd.org/D30010
|
|
|
|
|
|
|
|
| |
For ports that already use the licenses framwork, merge the content of
RESTRICTED/NO_CDROM/LEGAL* entries into LICENSEs.
Approved by: rene
Differential Revision: https://reviews.freebsd.org/D30010
|
|
|
|
| |
Reported by: portscout
|
| |
|
|
|
|
| |
Add py.typed and distribute .pyi files
|
|
|
|
|
|
|
|
|
|
| |
- Fix typos
- Remove duplicate variables
- Remove nop variables
- Clean up commented PORTREVISION
- Add missing USES
Reported by: portscan
|
|
|
|
| |
Reported by: portscout
|
|
|
|
| |
A few fixes to pass upstream test script
|
|
|
|
|
|
|
| |
Changes: https://github.com/jiixyj/epoll-shim/compare/v0.0.20210322...v0.0.20210418
Reported by: portscout
Approved by: manu
Differential Revision: https://reviews.freebsd.org/D29822
|
|
|
|
| |
Take maintainership.
|
| |
|
|
|
|
|
|
|
|
|
| |
These are the command-line bioinformatics utilities associated with the UCSC
genome browser. Care has been taken to install only the freely available
tools. However, the license information at https://genome.ucsc.edu/license/
is not entirely clear and we may add non-free utilities in the future.
Contact UCSC if you are using this port for commercial purposes.
|
|
|
|
|
|
| |
Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected
databases (publication, sequence, structure, gene, variation, expression, etc.)
from a UNIX terminal window.
|
| |
|
| |
|