Deprecate x11/libXp, since it is about to be deprecated upstream. Do *not*
yet set a removal date for x11/libXp, this will be decided later, once most
dependencies are fixed.
Deprecate all ports depending on x11/libXp.
* astro/xephem
* audio/xmcd
* audio/xmmix
* biology/ncbi-toolkit
* deskutils/xmdiary
* ftp/llnlxdir
* ftp/llnlxftp
* graphics/SciPlot
* misc/xtar
* multimedia/mpeg2play
* science/afni
* textproc/mgdiff
Sprinkle USES=xorg as needed.
Discussed with: bapt
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq
reads to mammalian-sized genomes using the ultra high-throughput short read
aligner Bowtie, and then analyzes the mapping results to identify splice
junctions between exons.
Note:
TopHat has been Superseded by HISAT2 and is no longer maintained upstream.
This port is provided mainly for revisiting old studies where TopHat was used.
MultiQC searches a given directory for analysis logs and compiles an HTML
report. It's a general use tool, perfect for summarising the output from
numerous bioinformatics tools.
Haplohseq identifies regions of allelic imbalance (AI) in sequencing data
obtained from impure samples where AI events exist in a potentially low
proportion of cells in the sample. Input to the software includes a VCF file
of genotypes and estimated phased genotypes.
lang/gcc5 will expire in ~1 month. If someone still uses lang/gcc48
they should backport C++11 fix instead. QA on GCC architecuters is
currently limited to powerpc64 which uses GCC_DEFAULT.
PR: 193528
- Remove PGTEST and SQLITETEST options: DBD::Pg and DBD::SQLite have been removed from BioPerl by upstream for the move of modules and programs into separate distributions
Changes: https://metacpan.org/changes/distribution/BioPerl
This port can't use Altivec. Instead, it's possible to use GCC's translation layer from SSE. Adjust build flags to do it.
PR: 239645
Approved by: yuri (maintainer), tcberner (mentor)
Differential Revision: https://reviews.freebsd.org/D21160
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
Now it builds with gradle-5.
Improvements im Makefile to simplify the port update process, in line with some other gradle-based ports.
Reported by: repology
GCC 8 and 9 are incompatible in handling const variables with OpenMP
default(none). All const variables default to shared even with default(none)
present. 8 errors out if a const variable is explicitly defined as shared and
9 requires an explicit definition.
Using an upstream trunk patch for now, which checks the compiler version.
Also discussing more portable approaches to avoid future issues.
Reported by: jrm
GCC 9 requires OpenMP variables to be explicitly defined as shared or private
where earlier versions fell back on default. New patch sent upstream.
PR: 238471
Reported by: gerald
