freebsd-ports/biology
Gerald Pfeifer 3be3e90f93 Update to libmpc version 1.0.1 which brings the following fixes:
- Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
 - 0^0, which returned (NaN,NaN) previously, now returns (1,+0).
 - Removed compatibility with K&R compilers, which was untestable due
   to lack of such compilers.
 - New functions
   . mpc_log10
   . mpc_mul_2si, mpc_div_2si
 - Speed-ups
   . mpc_fma
 - Bug fixes
   . mpc_div and mpc_norm now return a value indicating the effective
     rounding direction, as the other functions.
   . mpc_mul, mpc_sqr and mpc_norm now return correct results even if
     there are over- or underflows during the computation.
   . mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has
     infinite part and equals output variable is corrected.
   . mpc_fr_sub: Wrong return value for imaginary part is corrected.

Convert to the new LIB_DEPENDS standard and remove hard-coded
.so versions from a couple of dependent ports.

Bump PORTREVISIONS of all dependent ports.

PR:		183141
Approved by:	portmgr (bdrewery)
2013-10-26 00:52:33 +00:00
..
ariadne
artemis
avida biology/avida: add <unistd.h>, <typoinfo> for modern compilers 2013-10-01 22:00:47 +00:00
babel
biococoa Update BioCocoa to the latest release. 2013-10-08 18:34:45 +00:00
biojava
blast
blat
boinc-simap Use value of BOINC_CLIENT_HOME in pkg-message 2013-09-24 12:00:40 +00:00
chemeq
clustalw
consed
crux Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
dotter Deprecated some ports broken for more than 6 month 2013-10-18 07:19:25 +00:00
embassy
emboss
fasta
fasta3
fastdnaml
finchtv
fluctuate
garlic
genpak
gff2ps
gmap
gperiodic - Remove manual creation and removal of share/applications, as it's now in the mtree (categories starting with [bce]) 2013-10-22 13:57:35 +00:00
grappa
hmmer
iolib
jalview
lagan
lamarc - Remove NO_STAGE as these have been tested to be safe 2013-09-25 00:54:08 +00:00
libgenome
libsbml - Switch to build with lang/ruby19 2013-10-10 18:08:34 +00:00
linux-foldingathome
mafft
mapm3
migrate
molden Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
mopac
mrbayes
mummer
muscle
ncbi-toolkit
njplot Fix NO_STAGE attribution 2013-09-22 18:05:04 +00:00
ortep3 Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-GFF3 - Update to 1.7 2013-10-03 16:19:59 +00:00
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-bioperl
p5-bioperl-run
paml
phd2fasta
phrap
phred
phylip
phyml
platon Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
plink Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
plinkseq
povchem
primer3
protomol
psi88 Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
py-biopython Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
pycogent Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
pyfasta Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
pymol
python-nexus
rasmol
recombine
ruby-bio
seaview
seqan Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
seqio
sim4
ssaha
t_coffee Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
tinker Update to libmpc version 1.0.1 which brings the following fixes: 2013-10-26 00:52:33 +00:00
treepuzzle - Remove NO_STAGE as these have been tested to be safe 2013-09-25 00:54:08 +00:00
treeviewx
tRNAscan-SE
ugene - Remove manual creation and removal of share/applications, as it's now in the mtree (categories starting with [bce]) 2013-10-22 13:57:35 +00:00
velvet
wise
xmolwt
Makefile