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freebsd-ports/biology
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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 - Add empty directory to plist 2015-03-11 14:41:53 +00:00
avida mark some of the ports that don't build on powerpc64 for me 2015-12-13 16:07:27 +00:00
babel Unbreak the build on PowerPC (at least) by always using va_copy() macro for 2015-09-02 10:10:06 +00:00
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 Make all GNUstep ports install into the System domain so that the Local domain is available for stuff built from source. 2015-09-19 10:33:34 +00:00
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 New port: biology/bowtie. 2016-03-05 13:21:26 +00:00
bowtie2 biology/bowtie2: 2.2.7 -> 2.2.8 2016-05-13 20:12:44 +00:00
bwa mark some of the ports that don't build on powerpc64 for me 2015-12-13 16:07:27 +00:00
cd-hit - Update maintainer mail address 2015-12-11 08:48:56 +00:00
cdbfasta - Update maintainer mail address 2015-12-11 08:48:56 +00:00
chemeq - Add LICENSE 2016-04-10 11:24:32 +00:00
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 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
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 - Do not falsely advertise that PowerPC build runs out of space and fails 2015-09-02 10:35:25 +00:00
fasta3 - Fix trailing whitespace in pkg-messages 2016-05-19 11:09:14 +00:00
fastdnaml Convert LICENSE= "GPLxx # or later" to "GPLxx+" 2016-01-12 16:20:31 +00:00
fastool - Update maintainer mail address 2015-12-11 08:48:56 +00:00
fasttree - Update maintainer mail address 2015-12-11 08:48:56 +00:00
fastx-toolkit Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
fluctuate - Switch to options helpers 2015-11-19 00:51:15 +00:00
garlic
gff2ps Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
gmap mark some of the ports that don't build on powerpc64 for me 2015-12-13 16:07:27 +00:00
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 - Update maintainer mail address 2015-12-11 08:48:56 +00:00
htslib biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1 2016-05-26 20:28:55 +00:00
iolib - Update to 1.14.8 2016-05-01 01:03:48 +00:00
jalview - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
jellyfish Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
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 Cleanup GH_* and variables order. 2015-12-29 14:30:46 +00:00
libsbml Upgrade from 5.12.0 to 5.13.0. Release-announcement available here: 2016-04-16 01:54:15 +00:00
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 - Switch to options helpers 2016-04-17 10:15:59 +00:00
molden biology/molden: 5.4 -> 5.7 2016-08-26 06:00:47 +00:00
mopac Convert LICENSE= "GPLxx # or later" to "GPLxx+" 2016-01-12 16:20:31 +00:00
mrbayes
mummer Fix build on mips by properly respecting compiler and flags 2015-08-05 12:18:41 +00:00
muscle mark some of the ports that don't build on powerpc64 for me 2015-12-13 16:07:27 +00:00
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 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-ASN1-EntrezGene - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
p5-Bio-Das Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-Das-Lite Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-GFF3 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-Glite Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-Graphics Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-Bio-MAGETAB Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
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 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-bioperl - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
p5-bioperl-run Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
p5-transdecoder Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
paml - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
phrap
phred
phylip Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
phyml Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
plink Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
plinkseq many ports: mark broken on powerpc64 2016-04-21 16:43:14 +00:00
primer3
protomol Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
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 - Update to 1.66 2016-04-17 03:55:01 +00:00
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 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
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
seqan-apps - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +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
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 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. 2016-04-01 13:29:15 +00:00
tinker Convert ports to use the options helpers in categories [abc]*, and minor fixes. 2015-08-19 13:29:59 +00:00
treepuzzle
treeviewx Convert LICENSE= "GPLxx # or later" to "GPLxx+" 2016-01-12 16:20:31 +00:00
trimmomatic Trimmomatic performs a variety of useful trimming tasks for illumina 2016-03-17 08:21:14 +00:00
tRNAscan-SE Prevent collision with getline(3) 2016-05-13 18:38:34 +00:00
ugene During the exp-run in bug 208158, it was found that biology/ugene gives 2016-05-07 19:38:53 +00:00
vcftools New port: biology/vcftools. 2016-02-26 17:07:59 +00:00
velvet Designatate 4 ports as unsafe for parallel building 2015-01-19 17:43:57 +00:00
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