From ChangeLog: https://github.com/stephaneguindon/phyml/releases/tag/v3.3.20200621
This release fixes a few minor bugs (see recent commits). The manual also gives
extra XML configuration information in order to apply fancy substitution models
(e.g., CAT-like) on single- or multiple-gene data sets
Reported by: portscout
Chase the devel/libffi update
Bump portrevision of all dependent ports to chace shard library version bump
in libffi.
Update LIB_DEPENDS lines where needed to not require a specific version of
libffi.so.
PR: 247028 (for tracking)
In file included from ebwt.h:43,
from ebwt_build.cpp:11:
processor_support.h:52:22: error: extended character “ is not valid in an identifier
52 | std::cerr << “ERROR: please define __cpuid() for this build.\n”;
| ^
processor_support.h:52:72: error: extended character ” is not valid in an identifier
52 | std::cerr << “ERROR: please define __cpuid() for this build.\n”;
| ^
http://package18.nyi.freebsd.org/data/121amd64-default-PR244494/2020-06-10_18h04m44s/logs/errors/bowtie-1.1.2_9.log
PR: 246700
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
