freebsd-ports/biology
Dmitry Marakasov 30a00f2227 Most commonly used build systems support silent builds, when they
hide actual commands executed and only show short summary line (like
"CC foo.c"). CMake and ninja enable this by default, some autotools
using ports do as well. This is unacceptable because we need complete
build logs at any time, so we now switch to verbose build logs
unconditionally. Note that this change deliberately affects ALL
builds and not only package builds on cluster, because we need to
be sure that user experiencing failure can always provide informative
build log regardless of settings and without rerunning the build.

Change summary:

- Always do verbose builds for cmake, ninja and GNU configure (the
  latter includes check if --disable-silent-rules is actually supported
  by the configure script; there are isolated cases when it's not true)
- Remove CMAKE_VERBOSE, NINJA_VERBOSE and
  CONFIGURE_ARGS=--disable-silent-rules from all ports which set them
  for this is no longer needed
- Revert hacks for --disable-silent-rules support priorly committed
  to biology/ncbi-blast+ and net-p2p/mldonkey - no longer needed as well

Submitted by:	amdmi3
Reviewed by:	mat
Exp-run by:	antoine
Approved by:	portmgr (mat, antoine)
Differential Revision:	D7534
2016-09-09 19:42:46 +00:00
..
ariadne Cleanup $() variables in ports Makefiles. 2016-07-20 15:33:20 +00:00
artemis
avida
babel
bcftools biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1 2016-05-26 20:28:55 +00:00
bedtools biology/bedtools is not jobs safe 2016-08-22 04:32:18 +00:00
biococoa
biojava When there is a do-install target, do not use a post-install target, do 2016-07-19 11:04:13 +00:00
blat - Fix trailing whitespace in pkg-messages 2016-05-19 11:09:14 +00:00
bowtie
bowtie2
bwa
cd-hit
cdbfasta
chemeq
clustalw Remove useless WRKSRC definitions. 2016-05-25 15:43:34 +00:00
consed - Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with 2016-09-05 19:23:42 +00:00
crux
diamond - Update to 0.8.20 2016-09-06 06:34:59 +00:00
emboss - update libgd to 2.2.2 2016-07-20 09:33:31 +00:00
fasta
fasta3 - Fix trailing whitespace in pkg-messages 2016-05-19 11:09:14 +00:00
fastdnaml
fastool
fasttree
fastx-toolkit
fluctuate
garlic
gff2ps
gmap
gperiodic - LICENSE 2016-07-02 09:05:22 +00:00
grappa - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
hmmer
htslib biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1 2016-05-26 20:28:55 +00:00
iolib
jalview - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
jellyfish
lagan - Fix trailing whitespace in pkg-messages 2016-05-19 11:09:14 +00:00
lamarc - Switch to options helpers 2016-08-18 09:31:58 +00:00
libgtextutils
libsbml
linux-foldingathome - Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk with 2016-09-05 19:23:42 +00:00
mafft - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
mapm3 - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
migrate
molden biology/molden: 5.4 -> 5.7 2016-08-26 06:00:47 +00:00
mopac
mrbayes
mummer
muscle
ncbi-blast+ Most commonly used build systems support silent builds, when they 2016-09-09 19:42:46 +00:00
ncbi-toolkit - Add missing dependency, fixing build 2016-06-24 09:04:45 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
p5-Bio-Phylo - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
p5-Bio-SCF
p5-bioperl - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
p5-bioperl-run
p5-transdecoder
paml - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
phrap
phred
phylip
phyml
plink
plinkseq
primer3
protomol
psi88 - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
py-biom-format - Fix run-time dependency issues 2016-06-11 09:25:04 +00:00
py-biopython
pycogent - Update to 1.9 [1] 2016-08-08 11:21:04 +00:00
pyfasta - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
python-nexus - Update to 1.35 2016-06-08 07:39:05 +00:00
recombine When there is a do-install target, do not use a post-install target, do 2016-07-19 11:04:13 +00:00
ruby-bio
samtools biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1 2016-05-26 20:28:55 +00:00
seaview biology/seaview: Update version 4.5.4.8=>4.6 2016-06-10 11:06:42 +00:00
seqan - Do install cmake and pkgconfig modules 2016-05-27 16:10:36 +00:00
seqan1 When there is a do-install target, do not use a post-install target, do 2016-07-19 11:04:13 +00:00
seqan-apps - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
seqio
seqtools biology/seqtools: 4.42.1 -> 4.43.0 2016-07-31 14:19:09 +00:00
sim4
slclust Remove unneeded usage of: 2016-06-06 15:25:42 +00:00
ssaha - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
t_coffee
tinker
treepuzzle
treeviewx
trimmomatic
tRNAscan-SE
ugene
vcftools
velvet
wise - Switch to options helpers 2016-06-21 09:05:06 +00:00
xmolwt - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
Makefile Remove expired ports without open PRs: 2016-07-04 20:48:23 +00:00