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
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
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.
* Add missing dependency devel/py-nose that is required to build. With
Python 3.6/3.7 there are no build issues because the sdist contains
Python Eggs of "nose" for these versions.
While I'm here:
* Set NO_ARCH because the port has no architecture specific files.
* Make it concurrent safe, package installs a script and bump
PORTREVISION due package change.
PR: 253815
Approved by: portmgr (build fix)
MFH: No (The port was added after the 2021Q1 branch)
* Apply the same fix as in 9cb5898561 by
stripping libraries by wildcard paths.
* Also use PYTHONPREFIX_SITELIBDIR instead PYTHON_SITELIBDIR to make
the port PREFIX safe while I'm here.
PR: 253815
Approved by: python (with hat)
Genetic variant annotation and functional effect prediction toolbox. It
annotates and predicts the effects of genetic variants on genes and proteins
(such as amino acid changes).
This package includes BBMap, a short read aligner, as well as various other
bioinformatic tools. It is written in pure Java, can run on any platform, and
has no dependencies other than Java being installed (compiled for Java 6 and
higher). All tools are efficient and multithreaded.
Sequence reading library developed by the Ribosomal Database Project. It can
handle genbank, embl, fasta, fastq, sff and sto files, can read from files or
streams, and can handle indexing files.
CrossMap is a program for genome coordinates conversion between different
assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used
file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF,
and gVCF.
A python extension, written in C, for quick access to bigBed files and access
to and creation of bigWig files. This extension uses libBigWig for local and
remote file access.
2021-04-01 ftp/wzdftpd: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 astro/roadmap: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/cosmo: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/bomberinstinct: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/drm: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/bygfoot: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/cre: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 irc/hybserv: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 irc/xaric: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 mail/elmo: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 misc/cave: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 security/bugs: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 security/dmitry: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 security/doorman: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 shells/esh: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 sysutils/cpu: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 textproc/libcrm114: No known users, dead upstream
2021-04-01 x11/wmmatrix: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/wmxss: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/tycoon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/xgrab: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/xbanner: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/bricons: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 x11/xmon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 games/cavezofphear: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 astro/saoimage: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/ksmp3play: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/jamin: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/musicbox-tag-editor: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/nspmod: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/cdplay: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/gimmix: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/ghostess: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/wmrecord: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/toolame: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 audio/shout: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 biology/grappa: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 biology/phylip: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 biology/lagan: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 cad/varkon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 cad/transcalc: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 comms/seyon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 comms/efax: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 converters/vda2fbd: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 converters/shftool: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 devel/openzz: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 devel/sourcenav: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 devel/gb: Unmaintained and dead upstream
2021-04-01 dns/checkdns: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 dns/inadyn-mt: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 editors/gate: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 editors/thoteditor: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 emulators/cinc: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 emulators/e-uae: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 emulators/dtcyber: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 ftp/jftpgw: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-01 ftp/pureadmin: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
2021-04-02 textproc/hs-pandoc-citeproc: Integrated into textproc/hs-pandoc
Use GCC for its SSE -> AltiVec translation:
In file included from src/ssw.cpp:38:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:33:5: error: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
__builtin_ia32_emms();
For ports optionally dependending on Python 2.7, just mark those options
as expired. Remove konquerer from the x11/kde-baseapps metaport and bump
its PORTREVISION.
Submitted by: rene
Reviewed by: portmgr, adridg, ehaupt, lme, madpilot, pizzamig, se, sunpoet, yuri
Approved by: portmgr
Differential Revision: https://reviews.freebsd.org/D28665
vcf2hap is a simple tool for generating a .hap file from a VCF. The .hap file
is required by haplohseq. vcf2hap is extremely fast and requires a trivial
amount of memory regardless of the size of the VCF file.
ad2vdf extracts allelic depth info from a SAM stream and adds it to a
corresponding single-sample VCF file. SAM input is read via stdin and the VCF
input file is taken as a command-line argument. This allows expensive BAM/CRAM
decoding to be performed in parallel by a separate samtools process.
Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands
of output files simultaneously. Parsing the TOPMed human chromosome 1 BCF
with bcftools takes two days, so extracting the 137,977 samples one at a time
or using thousands of parallel readers of the same file is impractical.
Vcf-split solves this by generating thousands of single-sample outputs during
a single sweep through the multi-sample input.
Biolibc is a library of fast, memory-efficient, low-level functions for
processing biological data. Like libc, it consists of numerous disparate,
general-purpose functions which could be used by a wide variety of
applications. These include functions for streaming common file formats such
as SAM and VCF, string functions specific to bioinformatics, etc.
biology/samtools: Update to 1.12
biology/bcftools: Update to 1.12
Numerous enhancements, performance improvements, and bug fixes since 1.11
Build-tested all other htslib dependents, no revbumps should be needed
Reported by: portscout
Generate random genomic data in FASTA/FASTQ, SAM, or VCF format, suitable for
small academic examples or test inputs of arbitrary size. Output can be piped
directly to programs or redirected to a file and edited to taste.
GCC is also necessary on powerpc64:
In file included from skbio/alignment/_ssw_wrapper.c:626:
In file included from skbio/alignment/_lib/ssw.h:17:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
Use GCC:
In file included from skbio/alignment/_ssw_wrapper.c:626:
In file included from skbio/alignment/_lib/ssw.h:17:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
* PyQt5: update to 5.15.3
This is a minor feature and bug-fix release. There are corresponding releases of the other PyQt5-related packages.
- Added the missing QImage.setAlphaChannel().
- Support for the QtNetworkAuth library has been moved to a separate PyQtNetworkAuth package.
- Wheels no longer bundle the corresponding Qt libraries and instead automatically install them from an external wheel.
* QScintilla2: update to 2.12.0
This adds support for Qt6 and removes support for Qt4.
- Change the new distname (again)i due to a conflict
- Use the new sip-build system
* devel/py-qtbuilder: update to 1.9.0
* devel/py-sip: fix flavor for sip-distinfo
PR: 253865
Exp-run by: antoine
Numerous small bug fixes and enhancements, code refactoring
py-xopen: Update to 1.1.0
Required by cutadapt 3.3
Drop python 3.5 support
Add isal support (not yet utilized in FreeBSD port)
In file included from /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/dispatcher.cpp:7:
/usr/local/include/cpuinfo_x86.h:228:2: error: "Including cpuinfo_x86.h from a non-x86 target."
#error "Including cpuinfo_x86.h from a non-x86 target."
Use GCC's SSE->Altivec translation:
In file included from ksw.c:29:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
Intel oneAPI tbb 2021.1 (onetbb) has been released[1][2] and has deprecated
several interfaces over tbb 2020, breaking most dependent ports.
Old tbb 2020 will be kept for a certain time to allow transition but will be
removed in a near future as it CONFLICTS with devel/onetbb. New ports should
now use devel/onetbb instead of devel/tbb.
We tried to move a maximum number of dependent ports to devel/onetbb (or
disable dependency when not possible), but some of them still remain stuck
to devel/tbb. Remaining ones have not been identified as major dependencies
themselves and will be fixed as soon as updates are available from upstream.
PR: 252648, 252688 [3], 252683 [4], 252651 [5], 252690 [3], 252693 [3],
252695 [3], 252696 [3], 252786 [3], 252649, 252868 [6], 252870 [5],
252684 [7], 252785 [7]
Approved by: yuri [3], jwb [4], thierry [5], FreeBSD@Shaneware.biz [6],
maintainer timeout [7]
[1] https://software.intel.com/content/www/us/en/develop/articles/intel-oneapi-threading-building-blocks-release-notes.html
[2] https://software.intel.com/content/www/us/en/develop/articles/tbb-revamp.html
* devel/gnustep-make: Update to 2.8.0
* lang/gnustep-base: Update to 1.27.0
* x11-toolkits/gnustep-back: update to 0.28.0
* x11-toolkits/gnustep-gui: update to 0.28.0
Also bump PORTREVISION on dependent ports.
CMake Error in CMakeLists.txt:
Target "runTests" requires the language dialect "CXX14" , but CMake does
not know the compile flags to use to enable it.
Approved by: portmgr (tier-2 blanket)
CMake Error in CMakeLists.txt:
Target "rampler" requires the language dialect "CXX11" , but CMake does not
know the compile flags to use to enable it.
Approved by: portmgr (tier-2 blanket)
- USES=compiler:openmp still forces building with GCC. This is no longer
necessary on tier 1 platforms, which have openmp in base.
- Mark broken on i386, because base clang doesn't have 64 bit atomic
functions for i386 (see bug 230888).
PR: 247753, 252379
Submitted by: cmt (based on)
USES=compiler:openmp still forces building with GCC. This is no longer
necessary on tier 1 platforms, which have openmp in the base system.
PR: 247753, 252379
Replace compiler:openmp with compiler:c++11-lang and localbase
Set USE_GCC for i386 to work around limitations in clang atomic (PR 230888)
PR: port/247753, ports/252379
Replace compiler:openmp with compiler:c++14-lang
Clang build also requires localbase:ldflags and a source patch to explicitly
set variables to shared
GCC-based platforms still require -latomic
PR: port/247753, ports/252379
Replace compiler:openmp with compiler:c++11-lang
Clang build also requires localbase:ldflags
Build tested on amd64, i386 and powerpc64 12.x-RELEASE
PR: port/247753, ports/252379
