freebsd-ports/biology
Larry Rosenman 6840168813 2017-04-30 devel/stormlib-ghost++: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/py-coil: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/py-cmdln: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/privman: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/c-unit: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/py-px: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/nglogc: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/bncsutil-ghost++: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/liblouisxml: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/nxt-python: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/spdict: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/guiloader-c++: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/streamhtmlparser: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/winpdb: Unfetchable for more than six months (google code has gone away)
2017-04-30 net/opendpi: Unfetchable for more than six months (google code has gone away)
2017-04-30 net/py-pybeanstalk: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-im/qwit: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-im/linux-instantbird: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-im/jabber-pyicq: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-im/qwit-devel: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-im/naim: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-im/pwytter: Unfetchable for more than six months (google code has gone away)
2017-04-30 sysutils/sievelog: Unfetchable for more than six months (google code has gone away)
2017-04-30 sysutils/ldapenter: Unfetchable for more than six months (google code has gone away)
2017-04-30 sysutils/py-danzfs: Unfetchable for more than six months (google code has gone away)
2017-04-30 sysutils/plasma-applet-apcups: Unfetchable for more than six months (google code has gone away)
2017-04-30 sysutils/scanmem: Unfetchable for more than six months (google code has gone away)
2017-04-30 sysutils/pdsh: Unfetchable for more than six months (google code has gone away)
2017-04-30 deskutils/superswitcher: Unfetchable for more than six months (google code has gone away)
2017-04-30 deskutils/plasma-applet-playwolf: Unfetchable for more than six months (google code has gone away)
2017-04-30 deskutils/nagaina: Unfetchable for more than six months (google code has gone away)
2017-04-30 deskutils/vboxgtk: Unfetchable for more than six months (google code has gone away)
2017-04-30 deskutils/libgcal: Unfetchable for more than six months (google code has gone away)
2017-04-30 math/carve: Unfetchable for more than six months (google code has gone away)
2017-04-30 math/foma: Unfetchable for more than six months (google code has gone away)
2017-04-30 math/libjbigi: Unfetchable for more than six months (google code has gone away)
2017-04-30 multimedia/gcap: Unfetchable for more than six months (google code has gone away)
2017-04-30 multimedia/freetuxtv: Unfetchable for more than six months (google code has gone away)
2017-04-30 multimedia/bangarang: Unfetchable for more than six months (google code has gone away)
2017-04-30 multimedia/opencinematools: Unfetchable for more than six months (google code has gone away)
2017-04-30 multimedia/vstream-client: Unfetchable for more than six months (google code has gone away)
2017-04-30 biology/treeviewx: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/pylot: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/xpi-pencil: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/mod_myvhost: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/feedonfeeds: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/mod_jail: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/jspacker: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/cocoon: Overly complex port with no maintainer since 2008, requires openjdk 1.6
2017-04-30 www/mod_authz_unixgroup24: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/trac-down: Upstream is gone
www/tengine
2017-04-30 www/arora: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/py-postmarkup: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/py-dotcloud.cli: deprecated in upstream
2017-04-30 www/closure-linter: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/httpsqs: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/sventon: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/mod_authnz_external22: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/mod_authn_otp: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/php-plurk-api: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/py-django-app-plugins: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/mod_authz_unixgroup22: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/squidstats: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/mod_log_firstbyte: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/gaeo: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/xpi-pentadactyl: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-mgmt/py-flowtools: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/ydict: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/py-cconv: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/fqterm: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/libgooglepinyin: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/p5-cconv: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/fcitx-googlepinyin: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/php-cconv: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/ibus-table-chinese: Unfetchable for more than six months (google code has gone away)
2017-04-30 databases/jdbm2: Unfetchable for more than six months (google code has gone away)
2017-04-30 databases/akonadi-googledata: Unfetchable for more than six months (google code has gone away)
2017-04-30 lang/ofc: Unfetchable for more than six months (google code has gone away)
2017-04-30 comms/esmska: Unfetchable for more than six months (google code has gone away)
2017-04-30 x11/keynav: Unfetchable for more than six months (google code has gone away)
2017-04-30 x11/hotwire-shell: Unfetchable for more than six months (google code has gone away)
2017-04-30 security/fuzzdb: Unfetchable for more than six months (google code has gone away)
2017-04-30 security/truecrack: Unfetchable for more than six months (google code has gone away)
2017-04-30 security/skipfish: Unfetchable for more than six months (google code has gone away)
2017-04-30 security/py-yara-editor: Unfetchable for more than six months (google code has gone away)
2017-04-30 security/nmapsi4: Unfetchable for more than six months (google code has gone away)
2017-04-30 security/cmd5checkpw: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-p2p/unworkable: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-p2p/rtgui: Unfetchable for more than six months (google code has gone away)
2017-04-30 audio/xpi-musicpm: Unfetchable for more than six months (google code has gone away)
2017-04-30 audio/pidgin-musictracker: Unfetchable for more than six months (google code has gone away)
2017-04-30 audio/logitechmediaserver-superdatetime: Unfetchable for more than six months (google code has gone away)
2017-04-30 audio/last-cmus: Unfetchable for more than six months (google code has gone away)
2017-04-30 audio/mehdiaplayer: Unfetchable for more than six months (google code has gone away)
2017-04-30 japanese/nhocr: Unfetchable for more than six months (google code has gone away)
2017-04-30 misc/xsw: Unfetchable for more than six months (google code has gone away)
2017-04-30 dns/py-adns: Unfetchable for more than six months (google code has gone away)
2017-04-30 dns/py-bonjour: Unfetchable for more than six months (google code has gone away)
2017-04-30 games/robocalypto: Unfetchable for more than six months (google code has gone away)
2017-04-30 games/libfov: Unfetchable for more than six months (google code has gone away)
2017-04-30 games/dcross: Unfetchable for more than six months (google code has gone away)
2017-04-30 games/lostfeathers: Unfetchable for more than six months (google code has gone away)
2017-04-30 games/hexglass: Unfetchable for more than six months (google code has gone away)
2017-04-30 textproc/ibus-table: Unfetchable for more than six months (google code has gone away)
2017-04-30 textproc/chm2pdf: Unfetchable for more than six months (google code has gone away)
2017-04-30 textproc/dtdinst: Unfetchable for more than six months (google code has gone away)
2017-04-30 textproc/py-xmltv: Unfetchable for more than six months (google code has gone away)
2017-04-30 textproc/ibus-m17n: Unfetchable for more than six months (google code has gone away)
2017-04-30 textproc/libroxml: Unfetchable for more than six months (google code has gone away)
2017-04-30 mail/gnome-gmail-notifier: Unfetchable for more than six months (google code has gone away)
2017-04-30 irc/py-gozerbot: Unfetchable for more than six months (google code has gone away)
2017-04-30 irc/tircd: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/qiviewer: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/py-gchartwrapper: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/svgfig: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/iulib: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/seam-carving-gui: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/py-pyggel: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/rubygem-gemojione2: Use graphics/rubygem-gemojione instead
2017-04-30 15:47:51 +00:00
..
ariadne Cleanup $() variables in ports Makefiles. 2016-07-20 15:33:20 +00:00
artemis - Fix shebangs 2017-04-21 16:28:25 +00:00
avida Mark various ports as broken on armv6: invokes x86 asm. 2017-02-26 12:56:41 +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 - Mark it BROKEN 2016-10-28 01:49:40 +00:00
blat biology/blat: Fix build on DF (taken from dports) 2016-12-18 04:46:53 +00:00
bowtie - Fix shebangs 2017-04-22 09:25:44 +00:00
bowtie2 Update devel/tbb to 2017.5 2017-03-07 12:44:41 +00:00
bwa Mark various ports broken on aarch64 and armv6. 2017-01-31 03:40:46 +00:00
cd-hit Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
cdbfasta Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/ 2017-01-20 20:33:30 +00:00
chemeq biology/chemeq: fix build on GCC (taken from dports) 2016-12-18 04:22:26 +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 Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
diamond biology/diamond: Update to version 0.8.38 2017-04-21 14:46:07 +00:00
emboss - update libgd to 2.2.2 2016-07-20 09:33:31 +00:00
fasta ${RM} already has -f. 2016-10-21 12:51:40 +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 Never set WRKSRC when using USE_GITHUB. 2017-01-03 18:12:13 +00:00
fasttree Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +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 various ports as broken on armv6: invokes x86 asm. 2017-02-26 12:56:41 +00:00
gperiodic Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +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 Use USES=pathfix where applicable. 2016-10-21 15:21:13 +00:00
iolib Fix USE_GITHUB's GH_TAGNAME usage. 2017-02-28 08:33:44 +00:00
jalview - Fix trailing whitespace in pkg-descrs, categories [a-f]* 2016-05-19 10:21:23 +00:00
jellyfish Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
lagan - Fix trailing whitespace in pkg-messages 2016-05-19 11:09:14 +00:00
lamarc biology/lamarc: Fix build on DF (taken from dports) 2016-12-18 04:34:33 +00:00
libgtextutils Use USES=pathfix where applicable. 2016-10-21 15:21:13 +00:00
libsbml Cleanup no longer needed CHMOD usage after r424898. 2016-11-02 22:45:14 +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 Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
mopac Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
mrbayes
mummer Fix build on mips by properly respecting compiler and flags 2015-08-05 12:18:41 +00:00
muscle Mark various leaf ports broken on aarch64, and, where appropriate, other 2016-11-11 09:31:02 +00:00
ncbi-blast+ Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
ncbi-toolkit Remove libjpeg.so.11 compatibility link that was added in r374303 to 2016-12-08 16:39:11 +00:00
njplot biology/njplot: Add site in MASTER_SITES because package builders are 2016-11-28 15:19:42 +00:00
p5-AcePerl Move -fPIC to where Linux puts it so it is limited to a single library. 2017-02-13 22:43:58 +00:00
p5-Bio-ASN1-EntrezGene - Add LICENSE 2016-12-18 15:25:13 +00:00
p5-Bio-Coordinate - Add p5-Bio-Coordinate 1.007001 2016-12-19 15:54:39 +00:00
p5-Bio-Das - Add LICENSE 2016-12-18 15:25:18 +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 Bump PORTREVISION for ports affected by the fix the last commit. 2017-01-31 16:21:45 +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 - Add LICENSE_FILE 2016-12-18 15:25:22 +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 shebangs 2017-04-22 12:45:43 +00:00
p5-BioPerl-Run Bump PORTREVISION for ports affected by the fix the last commit. 2017-01-31 16:21:45 +00:00
p5-transdecoder Never set WRKSRC when using USE_GITHUB. 2017-01-03 18:12:13 +00:00
paml Cleanup no longer needed CHMOD usage after r424898. 2016-11-02 22:45:14 +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 Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
plinkseq biology/plinkseq: unbreak with clang 4.0 2017-02-27 14:09:25 +00:00
primer3
protomol biology/protomol: Support build with C++11 (taken from dports) 2016-12-18 05:34:42 +00:00
psi88 Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
py-biom-format biology/py-biom-format: Update to version 2.1.6 2017-04-29 13:59:15 +00:00
py-biopython - Update to 1.68 2016-09-23 01:54:45 +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 1.42 2017-03-01 07:00:37 +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
rubygem-bio Update to 1.5.1 2017-02-06 23:03:17 +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 4.6=>4.6.1 2017-04-11 18:58:18 +00:00
seqan - Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1] 2016-09-14 19:38:58 +00:00
seqan-apps Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +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 Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
sim4
slclust Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/ 2017-01-20 20:33:30 +00:00
ssaha Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
t_coffee Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
tinker Bump PORTREVISIONs for ports depending on the canonical version of GCC and 2017-04-01 15:23:30 +00:00
treepuzzle
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 - Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOL 2017-01-09 13:16:49 +00:00
vcftools Assume "pkg-config zlib" works after 9.x reached EOL 2017-01-03 17:06:49 +00:00
velvet
wise Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
xmolwt Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
Makefile 2017-04-30 devel/stormlib-ghost++: Unfetchable for more than six months (google code has gone away) 2017-04-30 15:47:51 +00:00