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
*** File 'Makefile.config.FreeBSD.powerpc' is missing. Please run ./configure
The configuration script may have other problems as well. This needs
to be addressed by upstream (if there is interest).
Approved by: portmgr (tier-2 blanket)
configure and Makefile.in provided in tarballs have -lstdc++ hard-coded in them.
The previous version of the port patches these to be -lc++, which still might fail on gcc systems, depending on which C++ library is used.
This change adds USES=autoreconf which makes it to regenerate configure and Makefile.in and hopefully have the proper C++ library in these files.
GNU libtool links with the C compiler, not with the C++ compiler, in this project. This is what I think triggers link failures due to a wrong C++
library getting into the link lines. GNU libtool likely chooses C compiler because this project has its 'main' functions in .c files,
but also includes C++ object modules. This likely causes GNU tools confusion and it uses the C compiler to link and fails due to wrong C++ libraries added there.
Use new GCC from ports on GCC architectures.
Merge 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5, fixes build on GCC architectures.
Also include sys/endian.h and use bswap32 and bswap64 for byte-swapping (PR at https://github.com/bcgsc/abyss/pull/287 ).
PR: 238737
Approved by: yuri (maintainer), mat (mentor)
Differential Revision: https://reviews.freebsd.org/D20717
Autoconf reports that HAVE_ASM_BSR is true (1). However, it's a false
positive.
I do not have enough knowledge of autoconf to fix this problem correctly,
so fix src/config.h in post-configure. Patches welcome.
A proper fix will most likely also fix the build on other tier-2 archs,
but I have not taken the time to test that yet.
Approved by: portmgr (tier-2 blanket)
The BOLT-LMM software package currently consists of two main algorithms, the
BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML
algorithm for variance components analysis (i.e., partitioning of
SNP-heritability and estimation of genetic correlations).
GEMMA is a software toolkit for fast application of linear mixed models (LMMs)
and related models to genome-wide association studies (GWAS) and other
large-scale data sets.
VSEARCH supports de novo and reference based chimera detection, clustering,
full-length and prefix dereplication, rereplication, reverse complementation,
masking, all-vs-all pairwise global alignment, exact and global alignment
searching, shuffling, subsampling and sorting. It also supports FASTQ file
analysis, filtering, conversion and merging of paired-end reads.
The aim of this project is to create an alternative to the USEARCH tool
developed by Robert C. Edgar (2010).
- Expire after the last version without /usr/lib/libomp.so
- Drop SOVERSION for seamless transition (i.e., avoid conditionals)
PR: 236907
Approved by: bapt (maintainer)
Differential Revision: https://reviews.freebsd.org/D19767
fastp is a tool designed to provide fast all-in-one preprocessing for FastQ
files. This tool is developed in C++ with multithreading supported to afford
high performance.
