Picard is a set of command line tools for manipulating high-throughput
sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file
formats are defined in the Hts-specs repository.
Bioawk is an extension to Brian Kernighan's awk, adding the support of several
common biological data formats, including optionally gzip'ed BED, GFF, SAM,
VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few
built-in functions and an command line option to use TAB as the input/output
delimiter. When the new functionality is not used, bioawk is intended to behave
exactly the same as the original BWK awk.
The Subread package comprises a suite of software programs for processing
next-gen sequencing read data including:
Subread: a general-purpose read aligner
Subjunc: a read aligner developed for aligning RNA-seq reads
featureCounts: a software program developed for counting reads to genomic
features such as genes, exons, promoters and genomic bins.
Sublong: a long-read aligner that is designed based on seed-and-vote.
exactSNP: discovers SNPs by testing signals against local background noise.
utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:81:5: error: 'get_deleter' declared as a 'virtual' field
This may have something to do with compiler:openmp in USES. However,
it has broken for more than 6 months at this point.
Approved by: portmgr (tier-2 blanket)
- Repocopy textproc/py-sphinx to textproc/py-sphinx18
Update it to 1.8.5 (latest version from 1.8.X).
This version supports Python 2 and 3.
Add test target.
- textproc/py-sphinx: Update to 3.0.2
Python 3 only (3.5+).
Add test target.
- Mk/Uses/python.mk: Add PY_SPHINX
Shared macro to use with flavors and not break
ports with USES=python (all versions).
Python >=3.5 --> textproc/py-sphinx (v3.0.2)
Python < 3.5 --> textproc/py-sphinx18 (v1.8.5)
All ports that uses sphinx were changed to use the new variable
${PY_SPHINX} in the dependency line, exceptions:
* Ports that fails to build with sphinx 3.0.2 because of code.
They are pointing to textproc/py-sphinx18 directly.
There aren't many ports.
* Ports that doesn't know Python flavors.
- Add several patches to fix Sphinx consumers
The most common issues are related with pkg-plist, the output
files from Sphinx changes between versions, keep this dynamically
is the better approach.
This will save time in future sphinx updates.
PR: 245629
Exp-run by: antoine
Use GCC instead of Clang:
/usr/lib/clang/10.0.0/include/mmintrin.h:216:19: error: use of undeclared identifier '__builtin_ia32_punpckhbw'
return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
Some changes have been made in this release that break backwards
compatibility. Let USES=gmake force users to upgrade to this version so
port maintainers don't have to support older versions.
PR: 245725
Exp-run by: antoine
Approved by: portmgr (antoine)
Adjusted for ports rescued since r534032
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2020-05-05 sysutils/wtail: Broken for more than 6 months
2020-05-05 textproc/csv2latex: Broken for more than 6 months
2020-05-05 textproc/da-hyphen: Broken for more than 6 months
2020-05-05 textproc/glark: Broken for more than 6 months
2020-05-05 textproc/html2tex: Broken for more than 6 months
2020-05-05 textproc/htmlsection: Broken for more than 6 months
2020-05-05 textproc/kenlm: Broken for more than 6 months
2020-05-05 textproc/libguess: Broken for more than 6 months
2020-05-05 textproc/libxml++26-reference: Broken for more than 6 months
2020-05-05 textproc/no-hunspell: Broken for more than 6 months
2020-05-05 textproc/p5-MARC: Broken for more than 6 months
2020-05-05 textproc/p5-texcount: Broken for more than 6 months
2020-05-05 textproc/pcrs: Broken for more than 6 months
2020-05-05 textproc/pear-Structures_DataGrid_DataSource_RSS: Broken for more than 6 months
2020-05-05 textproc/pear-Structures_DataGrid_DataSource_XML: Broken for more than 6 months
2020-05-05 textproc/permute: Broken for more than 6 months
2020-05-05 textproc/pocketreader: Broken for more than 6 months
2020-05-05 textproc/py-sgrep: Broken for more than 6 months
2020-05-05 textproc/rss2html: Broken for more than 6 months
2020-05-05 textproc/ruby-xmlparser: Broken for more than 6 months
2020-05-05 textproc/sv-hyphen: Broken for more than 6 months
2020-05-05 textproc/tclExpat: Broken for more than 6 months
2020-05-05 textproc/tex2im: Broken for more than 6 months
2020-05-05 textproc/topic: Broken for more than 6 months
2020-05-05 textproc/uz-hunspell: Broken for more than 6 months
2020-05-05 textproc/xmlprpr: Broken for more than 6 months
2020-05-05 www/ach: Broken for more than 6 months
2020-05-05 www/apache-forrest: Broken for more than 6 months
2020-05-05 www/apercu: Broken for more than 6 months
2020-05-05 www/cblog: Broken for more than 6 months
2020-05-05 www/drood: Broken for more than 6 months
2020-05-05 www/drraw: Broken for more than 6 months
2020-05-05 www/flood: Broken for more than 6 months
2020-05-05 www/grafana2: Broken for more than 6 months
2020-05-05 www/imgsizer: Broken for more than 6 months
2020-05-05 www/jdresolve: Broken for more than 6 months
2020-05-05 www/linkcheck: Broken for more than 6 months
2020-05-05 www/madsonic-standalone: Broken for more than 6 months
2020-05-05 www/mod_auth_external2: Broken for more than 6 months
2020-05-05 www/mod_chroot: Broken for more than 6 months
2020-05-05 www/mod_cvs2: Broken for more than 6 months
2020-05-05 www/mod_domaintree: Broken for more than 6 months
2020-05-05 www/mod_encoding: Broken for more than 6 months
2020-05-05 www/mod_flickr: Broken for more than 6 months
2020-05-05 www/mod_gzip2: Broken for more than 6 months
2020-05-05 www/mod_layout22: Broken for more than 6 months
2020-05-05 www/mod_proctitle: Broken for more than 6 months
2020-05-05 www/mod_tsa: Broken for more than 6 months
2020-05-05 www/mod_vhs: Broken for more than 6 months
2020-05-05 www/p5-AnyEvent-Mojo: Broken for more than 6 months
2020-05-05 www/p5-Apache-Gallery: Broken for more than 6 months
2020-05-05 www/p5-WWW-Google-Video: Broken for more than 6 months
2020-05-05 www/p5-WWW-Shorten-KUSO: Broken for more than 6 months
2020-05-05 www/p5-WWW-Shorten-isgd: Broken for more than 6 months
2020-05-05 www/photo_gallery: Broken for more than 6 months
2020-05-05 www/pwebstats: Broken for more than 6 months
2020-05-05 www/py-django-profiles: Broken for more than 6 months
2020-05-05 www/red5: Broken for more than 6 months
2020-05-05 www/redmine-sidebar_hide: Broken for more than 6 months
2020-05-05 www/rssowl: Broken for more than 6 months
2020-05-05 www/skytemplate: Broken for more than 6 months
2020-05-05 www/surfraw: Broken for more than 6 months
2020-05-05 www/sws: Broken for more than 6 months
2020-05-05 www/tickr: Broken for more than 6 months
2020-05-05 www/tinytinyhttpd: Broken for more than 6 months
2020-05-05 www/udmsearch: Broken for more than 6 months
2020-05-05 www/vee: Broken for more than 6 months
2020-05-05 www/webreport: Broken for more than 6 months
2020-05-05 www/webstats: Broken for more than 6 months
2020-05-05 www/www6to4: Broken for more than 6 months
2020-05-05 x11/deskpaint: Broken for more than 6 months
2020-05-05 x11/dmenu2: Broken for more than 6 months
2020-05-05 x11/gcb: Broken for more than 6 months
2020-05-05 x11/gpctool: Broken for more than 6 months
2020-05-05 x11/ipager: Broken for more than 6 months
2020-05-05 x11/keylaunch: Broken for more than 6 months
2020-05-05 x11/props: 64-bit unsupported
2020-05-05 x11/roxbg: Broken for more than 6 months
2020-05-05 x11/sisctrl: Broken for more than 6 months
2020-05-05 x11/wdm: Broken for more than 6 months
2020-05-05 x11/xaniroc: Broken for more than 6 months
2020-05-05 x11/xmove: Broken for more than 6 months
2020-05-05 x11/xnodecor: Broken for more than 6 months
2020-05-05 x11/xvattr: Broken for more than 6 months
2020-05-05 x11-clocks/tktz: Broken for more than 6 months
2020-05-05 x11-clocks/xtimer: Broken for more than 6 months
2020-05-05 x11-themes/gnome-icons-dropline-neu: Broken for more than 6 months
2020-05-05 x11-themes/gnome-icons-dropline-nou: Broken for more than 6 months
2020-05-05 x11-themes/gnome-icons-gion: Broken for more than 6 months
2020-05-05 x11-themes/gnome-icons-jini: Broken for more than 6 months
2020-05-05 x11-themes/gtk-aurora-engine: Broken for more than 6 months
2020-05-05 x11-themes/gtk-blueprint-engine: Broken for more than 6 months
2020-05-05 x11-themes/gtk-murrina-fancy-clearlooks: Broken for more than 6 months
2020-05-05 x11-themes/gtk-murrina-lightblue: Broken for more than 6 months
2020-05-05 x11-themes/gtk-murrine-themes: Broken for more than 6 months
2020-05-05 x11-themes/murrine-configurator: Broken for more than 6 months
2020-05-05 x11-themes/nimbus: Broken for more than 6 months
2020-05-05 x11-themes/openbox-themes: Broken for more than 6 months
2020-05-05 x11-themes/rezlooks: Broken for more than 6 months
2020-05-05 x11-themes/ubuntulooks: Broken for more than 6 months
2020-05-05 x11-toolkits/slingshot: 64-bit unsupported
2020-05-05 x11-toolkits/xview-clients: 64-bit unsupported
2020-05-05 x11-wm/fluxconf: Broken for more than 6 months
2020-05-05 x11-wm/ion: Broken for more than 6 months
2020-05-05 x11-wm/matwm2: Broken for more than 6 months
2020-05-05 x11-wm/nickleby: Broken for more than 6 months
2020-05-05 x11-wm/olvwm: 64-bit unsupported
2020-05-05 x11-wm/ratmenu: Broken for more than 6 months
