*/*: sync with upstream

Taken from: HardenedBSD
This commit is contained in:
Franco Fichtner 2018-10-07 08:41:37 +02:00
parent 2ff88bda95
commit 6b0fddc208
3319 changed files with 19848 additions and 14481 deletions

View File

@ -0,0 +1,69 @@
Upstream patch for https://gitlab.gnome.org/GNOME/pyatspi2/issues/1
diff --git pyatspi/registry.py pyatspi/registry.py
index cb28395..f73ee16 100644
--- pyatspi/registry.py
+++ pyatspi/registry.py
@@ -50,9 +50,9 @@ class Registry(object):
reference to the Accessibility.Registry singleton. Doing so is harmless and
has no point.
- @@ivar async: Should event dispatch to local listeners be decoupled from event
- receiving from the registry?
- @@type async: boolean
+ @@ivar asynchronous: Should event dispatch to local listeners be decoupled
+ from event receiving from the registry?
+ @@type asynchronous: boolean
@@ivar reg: Reference to the real, wrapped registry object
@@type reg: Accessibility.Registry
@@ivar dev: Reference to the device controller
@@ -111,25 +111,44 @@ def _set_registry (self, main_loop_type, app_name=None):
self.has_implementations = True
- self.async = False # not fully supported yet
+ self.asynchronous = False # not fully supported yet
self.started = False
self.event_listeners = dict()
+ def __getattr__(self, name):
+ """
+ For backwards compatibility with old API
+ """
+ if name == 'async':
+ return self.asynchronous
+ return object.__getattr__(self, name)
+
+ def __setattr__(self, name, value):
+ """
+ For backwards compatibility with old API
+ """
+ if name == 'async':
+ self.asynchronous = value
+ object.__setattr__(self, name, value)
+
def _set_default_registry (self):
self._set_registry (MAIN_LOOP_GLIB)
- def start(self, async=False, gil=True):
+ def start(self, asynchronous=False, gil=True, **kwargs):
"""
Enter the main loop to start receiving and dispatching events.
- @@param async: Should event dispatch be asynchronous (decoupled) from
- event receiving from the AT-SPI registry?
- @@type async: boolean
+ @@param asynchronous: Should event dispatch be asynchronous
+ (decoupled) from event receiving from the AT-SPI registry?
+ @@type asynchronous: boolean
@@param gil: Add an idle callback which releases the Python GIL for a few
milliseconds to allow other threads to run? Necessary if other threads
will be used in this process.
@@type gil: boolean
"""
+ if 'async' in kwargs:
+ # support previous API
+ asynchronous = kwargs['async']
if not self.has_implementations:
self._set_default_registry ()
self.started = True

View File

@ -7,7 +7,7 @@ CATEGORIES= archivers
MASTER_SITES= SF/sevenzip/LZMA%20SDK/
DISTNAME= lzma${PORTVERSION:S/.//g}
MAINTAINER= ndowens.fbsd@yandex.com
MAINTAINER= ndowens@yahoo.com
COMMENT= High-ratio LZMA compressor
CONFLICTS= lzmautils-[0-9]* xz-[0-9]*

View File

@ -14,10 +14,10 @@ COMMENT= Wrapper around Archive::Rar
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Archive-Any>=0:archivers/p5-Archive-Any \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Archive-Any>=0:archivers/p5-Archive-Any \
p5-Archive-Rar>=0:archivers/p5-Archive-Rar \
p5-lib-abs>=0.90:devel/p5-lib-abs
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= perl5
USE_PERL5= configure

View File

@ -14,11 +14,11 @@ LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= p5-Archive-Zip>=1.07:archivers/p5-Archive-Zip \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Archive-Zip>=1.07:archivers/p5-Archive-Zip \
p5-File-MMagic>=1.27:devel/p5-File-MMagic \
p5-MIME-Types>=1.16:mail/p5-MIME-Types \
p5-Module-Find>=0.05:devel/p5-Module-Find
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-Test-Perl-Critic>=0:textproc/p5-Test-Perl-Critic \
p5-Test-Warn>=0:devel/p5-Test-Warn

View File

@ -14,8 +14,8 @@ COMMENT= Generic archive extracting mechanism (using libarchive)
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Object-Tiny>=0:devel/p5-Object-Tiny
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Object-Tiny>=0:devel/p5-Object-Tiny
TEST_DEPENDS= p5-File-Slurp>=0:devel/p5-File-Slurp \
p5-Path-Class>=0:devel/p5-Path-Class \
p5-Test-Pod>=1.04:devel/p5-Test-Pod

View File

@ -14,10 +14,10 @@ COMMENT= Peek into archives without extracting them
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Archive-Zip>=0:archivers/p5-Archive-Zip \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Archive-Zip>=0:archivers/p5-Archive-Zip \
p5-Moose>=0:devel/p5-Moose \
p5-MooseX-Types-Path-Class>=0:devel/p5-MooseX-Types-Path-Class
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-Test-Pod>=1.14:devel/p5-Test-Pod
USES= perl5

View File

@ -14,9 +14,9 @@ COMMENT= Interface with the 'rar' command
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-IPC-Run>=0:devel/p5-IPC-Run \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-IPC-Run>=0:devel/p5-IPC-Run \
rar:archivers/rar
RUN_DEPENDS:= ${BUILD_DEPENDS}
NO_ARCH= yes
USES= perl5

View File

@ -14,9 +14,9 @@ COMMENT= Simple module for extract archives
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Archive-Rar>=2.02:archivers/p5-Archive-Rar \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Archive-Rar>=2.02:archivers/p5-Archive-Rar \
p5-Archive-Zip>=1.30:archivers/p5-Archive-Zip
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-Test-Pod>=0:devel/p5-Test-Pod \
p5-Test-Pod-Coverage>=0:devel/p5-Test-Pod-Coverage

View File

@ -13,10 +13,10 @@ COMMENT= API wrapper around the 'tar' utility
LICENSE= GPLv3+
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= p5-File-Which>=0:sysutils/p5-File-Which \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-File-Which>=0:sysutils/p5-File-Which \
p5-IPC-Run>=0:devel/p5-IPC-Run \
p5-Log-Log4perl>=0:devel/p5-Log-Log4perl
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-Dumbbench>=0.111:benchmarks/p5-Dumbbench
NO_ARCH= yes

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@ -13,11 +13,11 @@ COMMENT= Pure perl implementation of LZW
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Moo>=1.001000:devel/p5-Moo \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Moo>=1.001000:devel/p5-Moo \
p5-Type-Tiny>0:devel/p5-Type-Tiny \
p5-namespace-clean>0:devel/p5-namespace-clean \
p5-strictures>0:devel/p5-strictures
RUN_DEPENDS:= ${BUILD_DEPENDS}
NO_ARCH= yes
USES= perl5

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@ -13,9 +13,9 @@ COMMENT= Write lzf files / buffers
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Compress-LZF>=0:archivers/p5-Compress-LZF \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Compress-LZF>=0:archivers/p5-Compress-LZF \
p5-IO-Compress>=${PORTVERSION}:archivers/p5-IO-Compress
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-Test-Pod>=1:devel/p5-Test-Pod
NO_ARCH= yes

View File

@ -13,9 +13,9 @@ COMMENT= Write lzma files / buffers
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Compress-Raw-Lzma>=${PORTVERSION}:archivers/p5-Compress-Raw-Lzma \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Compress-Raw-Lzma>=${PORTVERSION}:archivers/p5-Compress-Raw-Lzma \
p5-IO-Compress>=${PORTVERSION}:archivers/p5-IO-Compress
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-IO-String>=0:devel/p5-IO-String \
p5-Test-Pod>=1:devel/p5-Test-Pod \
p7zip>=0:archivers/p7zip

View File

@ -13,9 +13,9 @@ COMMENT= Write lzop files / buffers
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Compress-LZO>=0:archivers/p5-Compress-LZO \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Compress-LZO>=0:archivers/p5-Compress-LZO \
p5-IO-Compress>=${PORTVERSION}:archivers/p5-IO-Compress
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-Test-Pod>=1:devel/p5-Test-Pod
NO_ARCH= yes

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@ -13,9 +13,9 @@ COMMENT= Perl5 compression modules (bzip2, deflate, gzip, zlib, zip)
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Compress-Raw-Bzip2>=${PORTVERSION}:archivers/p5-Compress-Raw-Bzip2 \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Compress-Raw-Bzip2>=${PORTVERSION}:archivers/p5-Compress-Raw-Bzip2 \
p5-Compress-Raw-Zlib>=${PORTVERSION}:archivers/p5-Compress-Raw-Zlib
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-Test-Pod>=1:devel/p5-Test-Pod
NO_ARCH= yes

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@ -14,9 +14,9 @@ LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= p5-Compress-Bzip2>=2.08:archivers/p5-Compress-Bzip2 \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Compress-Bzip2>=2.08:archivers/p5-Compress-Bzip2 \
p5-POE>=0.38:devel/p5-POE
RUN_DEPENDS:= ${BUILD_DEPENDS}
NO_ARCH= yes
USES= perl5

View File

@ -14,9 +14,9 @@ LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= p5-Compress-LZF>=1.51:archivers/p5-Compress-LZF \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Compress-LZF>=1.51:archivers/p5-Compress-LZF \
p5-POE>=0.38:devel/p5-POE
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= perl5
USE_PERL5= configure

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@ -14,9 +14,9 @@ LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= p5-Compress-LZO>=1.08:archivers/p5-Compress-LZO \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Compress-LZO>=1.08:archivers/p5-Compress-LZO \
p5-POE>=0.38:devel/p5-POE
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= perl5
USE_PERL5= configure

View File

@ -14,9 +14,9 @@ LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= p5-Compress-LZW>=0:archivers/p5-Compress-LZW \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Compress-LZW>=0:archivers/p5-Compress-LZW \
p5-POE>=0.38:devel/p5-POE
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= perl5
USE_PERL5= configure

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@ -14,8 +14,8 @@ LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= p5-POE>=0.38:devel/p5-POE
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-POE>=0.38:devel/p5-POE
USES= perl5
USE_PERL5= configure

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@ -14,8 +14,8 @@ COMMENT= Perl extension to provide a PerlIO layer to bzip2/bunzip2
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Compress-Bzip2>=0:archivers/p5-Compress-Bzip2
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Compress-Bzip2>=0:archivers/p5-Compress-Bzip2
USES= perl5
USE_PERL5= configure

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@ -3,7 +3,7 @@
PORTNAME= par2cmdline-tbb
PORTVERSION= 20100203
PORTREVISION= 15
PORTREVISION= 16
CATEGORIES= archivers
MASTER_SITES= http://chuchusoft.com/par2_tbb/
DISTNAME= par2cmdline-0.4-tbb-${PORTVERSION}

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@ -7,7 +7,7 @@ CATEGORIES= archivers python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= feld@FreeBSD.org
MAINTAINER= ports@FreeBSD.org
COMMENT= Fast C-based zipfile decryption for Python
LICENSE= PSFL

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@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= josm
PORTVERSION= 14178
PORTVERSION= 14289
CATEGORIES= astro java
MASTER_SITES= http://josm.openstreetmap.de/download/ \
http://mirror.amdmi3.ru/distfiles/

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@ -1,3 +1,3 @@
TIMESTAMP = 1535278956
SHA256 (josm-snapshot-14178.jar) = 19d8b2cf7d8408bccdb4242974e4215e67fb6a67a76d6ba3dfa8b1b591265621
SIZE (josm-snapshot-14178.jar) = 13221878
TIMESTAMP = 1538749972
SHA256 (josm-snapshot-14289.jar) = 4b6f570d8d42e7a20d0bcafe6bd47431e19b4648eb3271dc9f1aa74306bc4d80
SIZE (josm-snapshot-14289.jar) = 13308372

View File

@ -1,8 +1,7 @@
# $FreeBSD$
PORTNAME= kstars
DISTVERSION= 2.9.7
PORTREVISION= 1
DISTVERSION= 2.9.8
PORTEPOCH= 1
CATEGORIES= astro kde
MASTER_SITES= KDE/stable/${PORTNAME}

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@ -1,3 +1,3 @@
TIMESTAMP = 1533104584
SHA256 (kstars-2.9.7.tar.xz) = 4d80f5b5b5f38500f259c0272ba7f85bb4d1e877060bb3a1a0469a32573d0f53
SIZE (kstars-2.9.7.tar.xz) = 62657568
TIMESTAMP = 1538265420
SHA256 (kstars-2.9.8.tar.xz) = 95f36cae6cc84d5d745b13cf690b56ea8ba27012faef1f901191d89007232d7d
SIZE (kstars-2.9.8.tar.xz) = 62674968

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@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= mkgmap
PORTVERSION= r4240
PORTVERSION= r4244
CATEGORIES= astro converters java
MASTER_SITES= http://www.mkgmap.org.uk/download/ \
http://mirror.amdmi3.ru/distfiles/

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@ -1,3 +1,3 @@
TIMESTAMP = 1536078552
SHA256 (mkgmap-r4240.tar.gz) = c8812de76103a7a10221b2ea71438c1488ccc4a7ba66f60479028214db9ffcab
SIZE (mkgmap-r4240.tar.gz) = 3387357
TIMESTAMP = 1538587308
SHA256 (mkgmap-r4244.tar.gz) = 98b3e072c62bdca988e42a743174ab56302722173279054971b683c0ea7fc0ff
SIZE (mkgmap-r4244.tar.gz) = 3386451

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@ -13,8 +13,8 @@ COMMENT= OO Perl interface to the ADS abstract service
LICENSE= GPLv2+
BUILD_DEPENDS= p5-libwww>=0:www/p5-libwww
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-libwww>=0:www/p5-libwww
NO_ARCH= yes
USES= perl5

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@ -13,13 +13,13 @@ COMMENT= Forecast satellite visibility
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Astro-SIMBAD-Client>=0:astro/p5-Astro-SIMBAD-Client \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Astro-SIMBAD-Client>=0:astro/p5-Astro-SIMBAD-Client \
p5-Astro-satpass>=0.077:astro/p5-Astro-satpass \
p5-Clone>=0:devel/p5-Clone \
p5-File-HomeDir>=0.93:devel/p5-File-HomeDir \
p5-IPC-System-Simple>=0:devel/p5-IPC-System-Simple \
p5-Template-Toolkit>=2.21:www/p5-Template-Toolkit
RUN_DEPENDS:= ${BUILD_DEPENDS}
NO_ARCH= yes
USES= perl5

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@ -13,7 +13,8 @@ COMMENT= Generic stellar catalogue object
LICENSE= GPLv3
# p5-Astro-FITS-CFITSIO is a recommended dependency
BUILD_DEPENDS= p5-Astro-Coords>=0.12:astro/p5-Astro-Coords \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Astro-Coords>=0.12:astro/p5-Astro-Coords \
p5-Astro-FITS-CFITSIO>=1.03:astro/p5-Astro-FITS-CFITSIO \
p5-Astro-Flux>=0.01:astro/p5-Astro-Flux \
p5-Astro-Telescope>=0.50:astro/p5-Astro-Telescope \
@ -23,7 +24,6 @@ BUILD_DEPENDS= p5-Astro-Coords>=0.12:astro/p5-Astro-Coords \
p5-Number-Uncertainty>=0.1:math/p5-Number-Uncertainty \
p5-SOAP-Lite>=0:net/p5-SOAP-Lite \
p5-libwww>=5.53:www/p5-libwww
RUN_DEPENDS:= ${BUILD_DEPENDS}
NO_ARCH= yes
USES= localbase perl5

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@ -12,10 +12,10 @@ COMMENT= Class for handling astronomical coordinates
LICENSE= GPLv2+
BUILD_DEPENDS= p5-Astro-PAL>=0:astro/p5-Astro-PAL \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Astro-PAL>=0:astro/p5-Astro-PAL \
p5-Astro-Telescope>=0.71:astro/p5-Astro-Telescope \
p5-DateTime>=0.76:devel/p5-DateTime
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-Test-Number-Delta>=0:devel/p5-Test-Number-Delta \
p5-Test-Pod>=1:devel/p5-Test-Pod

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@ -13,8 +13,8 @@ COMMENT= OO interface to the 1st and 2nd Digital Sky Surveys
LICENSE= GPLv2+
BUILD_DEPENDS= p5-libwww>=0:www/p5-libwww
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-libwww>=0:www/p5-libwww
NO_ARCH= yes
USES= perl5

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@ -14,11 +14,11 @@ COMMENT= Class for handling astronomical flux quantities
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Astro-WaveBand>=0:astro/p5-Astro-WaveBand \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Astro-WaveBand>=0:astro/p5-Astro-WaveBand \
p5-DateTime>=0:devel/p5-DateTime \
p5-Misc-Quality>=0:astro/p5-Misc-Quality \
p5-Number-Uncertainty>=0:math/p5-Number-Uncertainty
RUN_DEPENDS:= ${BUILD_DEPENDS}
NO_ARCH= yes
USE_PERL5= configure

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@ -13,12 +13,12 @@ COMMENT= OO interface to SIMBAD4
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-HTTP-Message>=0:www/p5-HTTP-Message \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-HTTP-Message>=0:www/p5-HTTP-Message \
p5-SOAP-Lite>=0:net/p5-SOAP-Lite \
p5-URI>=0:net/p5-URI \
p5-XML-DoubleEncodedEntities>=1:textproc/p5-XML-DoubleEncodedEntities \
p5-libwww>=0:www/p5-libwww
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-YAML>=0:textproc/p5-YAML
USES= perl5

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@ -13,10 +13,10 @@ COMMENT= OO Perl interface to the SIMBAD astronomical database
LICENSE= GPLv2+
BUILD_DEPENDS= p5-HTML-Parser>=3.36:www/p5-HTML-Parser \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-HTML-Parser>=3.36:www/p5-HTML-Parser \
p5-HTML-Tree>=3.17:www/p5-HTML-Tree \
p5-libwww>=5.53:www/p5-libwww
RUN_DEPENDS:= ${BUILD_DEPENDS}
NO_ARCH= yes
USES= perl5

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@ -14,8 +14,8 @@ COMMENT= Class for obtaining telescope information
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Astro-PAL>=0.99:astro/p5-Astro-PAL
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Astro-PAL>=0.99:astro/p5-Astro-PAL
NO_ARCH= yes
USE_PERL5= modbuild

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@ -14,9 +14,9 @@ COMMENT= Perl interface to gpsbabel
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-File-Which>=0.05:sysutils/p5-File-Which \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-File-Which>=0.05:sysutils/p5-File-Which \
p5-Geo-Gpx>=0.25:graphics/p5-Geo-Gpx
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= perl5
USE_PERL5= configure

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@ -15,8 +15,8 @@ COMMENT= Perl interface to GPS receivers
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Device-SerialPort>=0.07:comms/p5-Device-SerialPort
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Device-SerialPort>=0.07:comms/p5-Device-SerialPort
USES= perl5
USE_PERL5= configure

View File

@ -14,9 +14,9 @@ COMMENT= Interface to the Starlink AST library
LICENSE= GPLv2 GPLv3
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Astro-FITS-CFITSIO>=0:astro/p5-Astro-FITS-CFITSIO \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Astro-FITS-CFITSIO>=0:astro/p5-Astro-FITS-CFITSIO \
p5-Astro-FITS-Header>=0:astro/p5-Astro-FITS-Header
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-Test-Number-Delta>=0:devel/p5-Test-Number-Delta
USES= perl5

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@ -14,9 +14,9 @@ COMMENT= Retrieve weather information from wunderground.com
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-HTML-Parser>=0:www/p5-HTML-Parser \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-HTML-Parser>=0:www/p5-HTML-Parser \
p5-libwww>=0:www/p5-libwww
RUN_DEPENDS:= ${BUILD_DEPENDS}
USE_PERL5= configure
USES= perl5

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@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= metpy
PORTVERSION= 0.9.1
PORTVERSION= 0.9.2
CATEGORIES= astro python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}

View File

@ -1,3 +1,3 @@
TIMESTAMP = 1535639725
SHA256 (MetPy-0.9.1.tar.gz) = 2dadf750ddb752da13f4ece9b5784587c79c6c86f9a7be8d0cae3d236e403498
SIZE (MetPy-0.9.1.tar.gz) = 2226789
TIMESTAMP = 1538591637
SHA256 (MetPy-0.9.2.tar.gz) = f1181cbbb82b892a0b0915a8899d95c61741520ba6feba3045c4619a139f0135
SIZE (MetPy-0.9.2.tar.gz) = 2226983

View File

@ -2,6 +2,7 @@
PORTNAME= cava
DISTVERSION= 0.6.1
PORTREVISION= 1
CATEGORIES= audio
MAINTAINER= tobik@FreeBSD.org
@ -10,6 +11,7 @@ COMMENT= Console-based Audio Visualizer for MPD, PulseAudio, and sndio
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= psf2bdf:x11-fonts/psftools
LIB_DEPENDS= libfftw3.so:math/fftw3 \
libiniparser.so:devel/iniparser
@ -18,11 +20,12 @@ USE_GITHUB= yes
GH_ACCOUNT= karlstav
GNU_CONFIGURE= yes
CONFIGURE_ENV= ac_cv_lib_asound_snd_pcm_open=no
CONFIGURE_ENV= ac_cv_lib_asound_snd_pcm_open=no \
FONT_DIR=${DATADIR}
INSTALL_TARGET= install-strip
PLIST_FILES= bin/cava
PLIST_FILES= bin/cava ${DATADIR}/cava.fnt
PORTDOCS= README.md
PORTEXAMPLES= config
@ -39,6 +42,10 @@ SNDIO_LIB_DEPENDS= libsndio.so:audio/sndio
pre-configure:
@${ECHO_CMD} ${DISTVERSION} > ${WRKSRC}/version
pre-build:
psf2bdf ${WRKSRC}/cava.psf > ${WRKSRC}/cava.bdf
vtfontcvt ${WRKSRC}/cava.bdf ${WRKSRC}/cava.fnt
post-install-DOCS-on:
@${MKDIR} ${STAGEDIR}${DOCSDIR}
${INSTALL_DATA} ${WRKSRC}/README.md ${STAGEDIR}${DOCSDIR}

View File

@ -2,17 +2,21 @@
does not recognize
- Do not install the Linux-only font
--- Makefile.am.orig 2018-09-10 08:31:56 UTC
--- Makefile.am.orig 2018-05-03 16:07:33 UTC
+++ Makefile.am
@@ -14,10 +14,8 @@ cava_LDADD = -liniparser
@@ -13,11 +13,12 @@ cava_SOURCES = cava.c
cava_LDADD = -liniparser
cava_LDFLAGS = -L/usr/local/lib -Wl,-rpath /usr/local/lib
cava_CPPFLAGS = -DPACKAGE=\"$(PACKAGE)\" -DVERSION=\"$(VERSION)\" \
-D_POSIX_SOURCE -D _POSIX_C_SOURCE=200809L
- -D_POSIX_SOURCE -D _POSIX_C_SOURCE=200809L
-cava_CFLAGS = -std=c99 -Wall -Wextra -Wno-unused-result -Wno-maybe-uninitialized
+ -D_POSIX_SOURCE -D _POSIX_C_SOURCE=200809L -DFONT_DIR=\"@FONT_DIR@\"
+
+cava_CFLAGS = -std=c99 -Wall -Wextra
-cava_font_dir = @FONT_DIR@
cava_font_dir = @FONT_DIR@
-cava_font__DATA = cava.psf
+cava_font__DATA = cava.fnt
if !SYSTEM_LIBINIPARSER
cava_SOURCES += iniparser/libiniparser.la

View File

@ -0,0 +1,15 @@
--- cava.c.orig 2018-10-04 05:51:51 UTC
+++ cava.c
@@ -341,8 +341,12 @@ as of 0.4.0 all options are specified in config file,
"/dev/console") == 0) inAtty = 1;
if (inAtty) {
+#ifdef __FreeBSD__
+ system("/usr/sbin/vidcontrol -f " FONT_DIR "/cava.fnt >/dev/null 2>&1");
+#else
system("setfont cava.psf >/dev/null 2>&1");
system("setterm -blank 0");
+#endif
}
}

View File

@ -0,0 +1,16 @@
--- output/terminal_ncurses.c.orig 2018-10-04 05:56:00 UTC
+++ output/terminal_ncurses.c
@@ -215,9 +215,13 @@ int flastd[200], int gradient) {
// general: cleanup
void cleanup_terminal_ncurses(void) {
echo();
+#ifdef __FreeBSD__
+ system("/usr/sbin/vidcontrol -f >/dev/null 2>&1");
+#else
system("setfont >/dev/null 2>&1");
system("setfont /usr/share/consolefonts/Lat2-Fixed16.psf.gz >/dev/null 2>&1");
system("setterm -blank 10");
+#endif
/*for(int i = 0; i < gradient_size; ++i) {
if(the_color_redefinitions[i].color) {
init_color(the_color_redefinitions[i].color,

View File

@ -18,7 +18,7 @@ LIB_DEPENDS= libjack.so:audio/jack \
libsndfile.so:audio/libsndfile \
liblo.so:audio/liblo
USES= gmake localbase:ldflags pkgconfig qt:5 shared-mime-info
USES= compiler:c++11-lang gl gmake localbase:ldflags pkgconfig qt:5 shared-mime-info
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --disable-alsa-midi
USE_QT= core gui widgets xml buildtools_build qmake_build

View File

@ -17,7 +17,7 @@ LIB_DEPENDS= libjack.so:audio/jack \
libsamplerate.so:audio/libsamplerate \
libsndfile.so:audio/libsndfile
USES= cmake:outsource pkgconfig
USES= cmake:outsource compiler:c++11-lang gnome pkgconfig
USE_GITHUB= yes
GH_ACCOUNT= openAVproductions
GH_PROJECT= openAV-Luppp

View File

@ -13,11 +13,9 @@ COMMENT= Realtime Lua as programmable glue in LV2
LICENSE= ART20
LICENSE_FILE= ${WRKSRC}/COPYING
BROKEN_powerpc64= fails to build: cc1: unrecognized command line option -std=gnu11
BUILD_DEPENDS= lv2>0:audio/lv2
USES= cmake:outsource pkgconfig
USES= cmake:outsource compiler:c++11-lang gl pkgconfig
USE_XORG= x11 xext
USE_GL= gl glu

View File

@ -13,12 +13,12 @@ COMMENT= Bunch of common helper classes for mpd
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Moose>=0.92:devel/p5-Moose \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Moose>=0.92:devel/p5-Moose \
p5-MooseX-Has-Sugar>=0:devel/p5-MooseX-Has-Sugar \
p5-MooseX-Types>=0:devel/p5-MooseX-Types \
p5-Readonly>=0:devel/p5-Readonly \
p5-String-Formatter>=0:devel/p5-String-Formatter
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= perl5
USE_PERL5= modbuild

View File

@ -15,7 +15,8 @@ LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= p5-Audio-MPD-Common>=0:audio/p5-Audio-MPD-Common \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Audio-MPD-Common>=0:audio/p5-Audio-MPD-Common \
p5-Getopt-Euclid>=0:devel/p5-Getopt-Euclid \
p5-List-AllUtils>=0:devel/p5-List-AllUtils \
p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \
@ -24,7 +25,6 @@ BUILD_DEPENDS= p5-Audio-MPD-Common>=0:audio/p5-Audio-MPD-Common \
p5-MooseX-SemiAffordanceAccessor>=0:devel/p5-MooseX-SemiAffordanceAccessor \
p5-MooseX-Types>=0:devel/p5-MooseX-Types \
p5-Proc-Daemon>=0:devel/p5-Proc-Daemon
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-Test-Corpus-Audio-MPD>=1.113282:audio/p5-Test-Corpus-Audio-MPD
NO_ARCH= yes

View File

@ -11,9 +11,9 @@ PKGNAMEPREFIX= p5-
MAINTAINER= perl@FreeBSD.org
COMMENT= Interface to Musepack file information and APE tag fields
BUILD_DEPENDS= p5-MP3-Info>=1.20:audio/p5-MP3-Info \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-MP3-Info>=1.20:audio/p5-MP3-Info \
p5-Audio-Scan>=0.85:audio/p5-Audio-Scan
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= perl5
USE_PERL5= configure

View File

@ -14,9 +14,9 @@ COMMENT= Perl interface to Last.fm and AudioScrobbler
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Config-IniFiles>=0:devel/p5-Config-IniFiles \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Config-IniFiles>=0:devel/p5-Config-IniFiles \
p5-libwww>=5:www/p5-libwww
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= perl5
USE_PERL5= configure

View File

@ -14,9 +14,9 @@ COMMENT= Perl modules for reading and writing Microsoft WAV files
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Inline>=0:devel/p5-Inline \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Inline>=0:devel/p5-Inline \
p5-Inline-C>=0:devel/p5-Inline-C
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= perl5
USE_PERL5= configure

View File

@ -14,8 +14,8 @@ COMMENT= Audio manipulation routines for perl
LICENSE= GPLv2 GPLv3
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Math-GSL>=0:math/p5-Math-GSL
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Math-GSL>=0:math/p5-Math-GSL
USES= perl5
USE_PERL5= configure

View File

@ -14,8 +14,8 @@ COMMENT= Search and sort MP3 files based on their ID3 tags
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-MP3-Info>=0:audio/p5-MP3-Info
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-MP3-Info>=0:audio/p5-MP3-Info
USES= perl5
USE_PERL5= configure

View File

@ -15,9 +15,9 @@ COMMENT= Assorted utilities for manipulating MP3 files via MP3::Tag
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-MP3-Tag>=1.13:audio/p5-MP3-Tag \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-MP3-Tag>=1.13:audio/p5-MP3-Tag \
p5-Text-NeatTemplate>=0.10.01:textproc/p5-Text-NeatTemplate
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= perl5 shebangfix
USE_PERL5= configure

View File

@ -12,9 +12,9 @@ COMMENT= Perl interface for the MusicBrainz libdiscid library
LICENSE= GPLv2
BUILD_DEPENDS= p5-Test-Pod>=0:devel/p5-Test-Pod
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Test-Pod>=0:devel/p5-Test-Pod
LIB_DEPENDS= libdiscid.so:audio/libdiscid
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= localbase pkgconfig perl5
USE_PERL5= configure

View File

@ -14,9 +14,9 @@ COMMENT= Get the CDID of an audio CD and query the FreeDB servers
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-CDDB-File>=0:audio/p5-CDDB-File \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-CDDB-File>=0:audio/p5-CDDB-File \
p5-Moo>=0:devel/p5-Moo
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= alias perl5
USE_PERL5= configure

View File

@ -13,11 +13,11 @@ COMMENT= Manipulate / fetch info from Ogg-Vorbis audio files
LICENSE= GPLv2 GPLv3
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Inline>=0:devel/p5-Inline \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Inline>=0:devel/p5-Inline \
p5-Inline-C>=0:devel/p5-Inline-C
LIB_DEPENDS= libogg.so:audio/libogg \
libvorbis.so:audio/libvorbis
RUN_DEPENDS:= ${BUILD_DEPENDS}
MAKE_JOBS_UNSAFE= yes
USES= perl5

View File

@ -11,10 +11,10 @@ PKGNAMEPREFIX= p5-
MAINTAINER= perl@FreeBSD.org
COMMENT= Automate launching of fake mdp for testing purposes
BUILD_DEPENDS= p5-File-ShareDir-PathClass>0:devel/p5-File-ShareDir-PathClass \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-File-ShareDir-PathClass>0:devel/p5-File-ShareDir-PathClass \
p5-Path-Class>=0:devel/p5-Path-Class \
p5-Readonly>=0:devel/p5-Readonly
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= perl5
USE_PERL5= modbuild

View File

@ -7,7 +7,7 @@ CATEGORIES= audio python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= feld@FreeBSD.org
MAINTAINER= ports@FreeBSD.org
COMMENT= Python Musicbrainz NGS site bindings
LICENSE= BSD2CLAUSE ISCL

View File

@ -8,7 +8,7 @@ CATEGORIES= audio python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= feld@FreeBSD.org
MAINTAINER= ports@FreeBSD.org
COMMENT= Bindings for Chromaprint acoustic fingerprinting and the Acoustid API
LICENSE= MIT

View File

@ -7,7 +7,7 @@ CATEGORIES= audio python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= feld@FreeBSD.org
MAINTAINER= ports@FreeBSD.org
COMMENT= Python interface to Last.fm and Libre.fm
LICENSE= APACHE20

View File

@ -3,7 +3,7 @@
PORTNAME= perftest
DISTVERSIONPREFIX= V
DISTVERSION= 4.2-0.8
DISTVERSION= 4.4-0.3
CATEGORIES= benchmarks
MAINTAINER= slavash@FreeBSD.org

View File

@ -1,3 +1,3 @@
TIMESTAMP = 1529065479
SHA256 (linux-rdma-perftest-V4.2-0.8_GH0.tar.gz) = 25e433e6ef13a634dfcf9c4b21e74cdc3bdcc5205b6fd88ee004d0671bcc82f4
SIZE (linux-rdma-perftest-V4.2-0.8_GH0.tar.gz) = 139323
TIMESTAMP = 1538562078
SHA256 (linux-rdma-perftest-V4.4-0.3_GH0.tar.gz) = 76cb6ae44e8bc1f29d1482ab4e5eb8df4d3cea29969598b2871f0d35512b37f7
SIZE (linux-rdma-perftest-V4.4-0.3_GH0.tar.gz) = 139473

View File

@ -3,7 +3,7 @@
PORTNAME= phoronix-test-suite
DISTVERSIONPREFIX= v
DISTVERSION= 8.0.1
DISTVERSION= 8.2.0
CATEGORIES= benchmarks
PKGNAMESUFFIX= ${PHP_PKGNAMESUFFIX}
@ -13,6 +13,8 @@ COMMENT= Phoronix Benchmarking Suite
LICENSE= GPLv3
LICENSE_FILE= ${WRKSRC}/COPYING
RUN_DEPENDS= sudo:security/sudo
USES= php:cli,build,flavors python
USE_GITHUB= yes
USE_PHP= curl dom gd json openssl pcntl posix simplexml zip zlib

View File

@ -1,3 +1,3 @@
TIMESTAMP = 1531758479
SHA256 (phoronix-test-suite-phoronix-test-suite-v8.0.1_GH0.tar.gz) = 8bfe972c601884f2bbbf4d5069c7691637e8a30af55d2a9597dbe53911b49081
SIZE (phoronix-test-suite-phoronix-test-suite-v8.0.1_GH0.tar.gz) = 846244
TIMESTAMP = 1538401066
SHA256 (phoronix-test-suite-phoronix-test-suite-v8.2.0_GH0.tar.gz) = cb92231040fd09a98a97d6620bc98758774731372f8a41b58b85357c0449904c
SIZE (phoronix-test-suite-phoronix-test-suite-v8.2.0_GH0.tar.gz) = 860755

View File

@ -131,7 +131,6 @@
SUBDIR += tRNAscan-SE
SUBDIR += t_coffee
SUBDIR += tabixpp
SUBDIR += tinker
SUBDIR += treepuzzle
SUBDIR += trimadap
SUBDIR += trimmomatic

View File

@ -3,6 +3,7 @@
PORTNAME= bowtie2
PORTVERSION= 2.3.3.1
DISTVERSIONPREFIX= v
PORTREVISION= 1
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org

View File

@ -2,56 +2,33 @@
# $FreeBSD$
PORTNAME= ncbi-toolkit
PORTVERSION= 2012.06.20 # containing BLAST v2.2.27
PORTREVISION= 1
DISTVERSION= 2017.01.06 # containing BLAST v2.2.27 (? is this true)
CATEGORIES= biology
MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
DISTNAME= ncbi
DIST_SUBDIR= ${PORTNAME}-${PORTVERSION}
MAINTAINER= ports@FreeBSD.org
MAINTAINER= yuri@FreeBSD.org
COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
LIB_DEPENDS= libpng.so:graphics/png
LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \
libgmp.so:math/gmp \
libgnutls.so:security/gnutls \
libhogweed.so:security/nettle \
libidn2.so:dns/libidn2 \
libnettle.so:security/nettle \
libp11-kit.so:security/p11-kit \
libpng.so:graphics/png \
libtasn1.so:security/libtasn1 \
libtspi.so:security/trousers \
libunistring.so:devel/libunistring \
libXp.so:x11/libXp
USES= iconv motif
MAKE_JOBS_UNSAFE= yes
USES= gettext-runtime iconv jpeg motif
USE_XORG= x11 xau xext xft xmu xrender xt
SUB_FILES= pkg-message
# These are the executables we install.
#
# We follow Debian in the separation of the port in three
# main categories and in the selection of programs that
# are installed in each case. This Makes Sense (TM).
# Thus, we drop a handful of programs that are useful only as tests
# or code examples
# (credit goes to Aaron Ucko, the Debian maintainer of the NCBI stuff)
# Right now the port installs all the executables below, this may
# change in the future with the addition of selectable knobs or
# new slave ports
TOOLKIT_EXE= asn2ff asn2gb asn2idx asn2xml asndhuff asntool cdscan \
checksub debruijn demo_regexp demo_regexp_grep dosimple \
entrcmd errhdr fa2htgs findspl gene2xml getmesh getpub \
gil2bin idfetch indexpub makeset ncbisort seqtest tbl2asn \
vecscreen
BLAST_EXE= bl2seq blastall blastcl3 blastclust blastpgp copymat \
fastacmd formatdb formatrpsdb impala makemat megablast \
rpsblast seedtop taxblast
X11_EXE= Nentrez Psequin ddv entrez2 sbtedit udv
# and these are the man pages we have
MAN_FILES= Psequin.1 asn2ff.1 asn2idx.1 asn2xml.1 asndhuff.1 \
asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 \
copymat.1 ddv.1 debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 \
fastacmd.1 findspl.1 formatdb.1 formatrpsdb.1 getmesh.1 \
getpub.1 gil2bin.1 idfetch.1 indexpub.1 makemat.1 \
taxblast.1 tbl2asn.1 udv.1 vecscreen.1
MAN_LINKS= bl2seq blastall blastcl3 blastpgp impala megablast \
seedtop rpsblast
OPTIONS_DEFINE= DOCS
post-patch:
@ -73,30 +50,25 @@ post-patch:
# and we use it
do-build:
cd ${WRKDIR}; ./${DISTNAME}/make/makedis.csh
@cd ${WRKDIR} && ./${DISTNAME}/make/makedis.csh
# the ncbi-toolkit does not provide an install target
# we thus roll our own
do-install:
(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${BLAST_EXE} \
${TOOLKIT_EXE} ${X11_EXE} ${STAGEDIR}${PREFIX}/bin)
cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} * ${STAGEDIR}${PREFIX}/bin
@${MKDIR} ${STAGEDIR}${PREFIX}/lib/${DISTNAME}
(cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a \
${STAGEDIR}${PREFIX}/lib/${DISTNAME})
cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a \
${STAGEDIR}${PREFIX}/lib/${DISTNAME}
@${MKDIR} ${STAGEDIR}${PREFIX}/include/${DISTNAME}/connect
(cd ${WRKSRC}/include && ${INSTALL_DATA} *.h \
${STAGEDIR}${PREFIX}/include/${DISTNAME})
(cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h \
${STAGEDIR}${PREFIX}/include/${DISTNAME}/connect)
(cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${MAN_FILES} \
${STAGEDIR}${MANPREFIX}/man/man1)
.for man in ${MAN_LINKS}
${LN} -s ${MANPREFIX}/man/man1/blast.1.gz \
${STAGEDIR}${PREFIX}/man/man1/${man}.1.gz
.endfor
cd ${WRKSRC}/include && ${INSTALL_DATA} *.h \
${STAGEDIR}${PREFIX}/include/${DISTNAME}
cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h \
${STAGEDIR}${PREFIX}/include/${DISTNAME}/connect
cd ${WRKSRC}/doc/man && ${INSTALL_MAN} * \
${STAGEDIR}${MANPREFIX}/man/man1
@${MKDIR} ${STAGEDIR}${DATADIR}
(cd ${WRKSRC}/data && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR})
cd ${WRKSRC}/data && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}
do-install-DOCS-on:
@${MKDIR} ${STAGEDIR}${DOCSDIR}

View File

@ -1,2 +1,3 @@
SHA256 (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 603c9a4ade2a6f2f8e412558b732924d78fae403d225706e2ac38d553b08073c
SIZE (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 68428744
TIMESTAMP = 1538934016
SHA256 (ncbi-toolkit-2017.01.06/ncbi.tar.gz) = 4b88aaad8f953b1b50bc7d06f3a5920f0d589d2c9a26c709199f8347905f5867
SIZE (ncbi-toolkit-2017.01.06/ncbi.tar.gz) = 155731358

View File

@ -1,11 +0,0 @@
--- corelib/ncbimisc.c.orig
+++ corelib/ncbimisc.c
@@ -1266,7 +1266,7 @@
if (len < 1) return NULL;
rsult = (Nlm_CharPtr) MemNew (len + 3);
- if (rsult == NULL) return;
+ if (rsult == NULL) return NULL;
tmp = rsult;
for (i = 0; /* local [i] != NULL */ i < numitems; i++) {

View File

@ -1,58 +0,0 @@
--- make/makenet.unx.orig 2008-12-11 00:23:29.000000000 +0300
+++ make/makenet.unx 2011-04-14 00:26:38.440426134 +0400
@@ -67,6 +67,7 @@
VIB =
VIBLIBS= -lXm -lXmu -lXt -lX11
VIBLIBS=
+USERLIBS = -lXft -lpng -ljpeg %%ICONV_LIB%%
SEQUIN_OPTS =
LIBCOPY = cp -p
SRCCOPY = ./ln-if-absent
@@ -934,17 +935,17 @@
$(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \
$(LIBCOMPADJ) $(LIB2) $(LIB1) \
- $(VIBLIBS) $(OTHERLIBS)
+ $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
udv : $(OBJUDV)
$(CC) -o udv $(LDFLAGS) $(OBJUDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \
$(LIB23) $(LIBCOMPADJ) $(LIB2) \
- $(LIB1) $(VIBLIBS) $(OTHERLIBS)
+ $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
Nentrez : entrez.c $(ULIB31)
$(CC) -o Nentrez $(LDFLAGS) entrez.c $(LIB41) $(LIB31) $(LIB30) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
- $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
+ $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
# left this in (Tentrez) for script backwards compatibility
Tentrez : entrez.c $(ULIB31)
@@ -1140,7 +1141,7 @@
entrez2 : entrez2.c
$(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB41) $(LIB6) $(LIB20) \
$(LIB61) $(LIB60) $(LIB22) $(LIB23) $(LIBCOMPADJ) \
- $(LIB2) $(LIB4) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
+ $(LIB2) $(LIB4) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
$(VIB_POST_LINK) entrez2
# demo program (spidey)
@@ -1421,7 +1422,7 @@
$(CC) -o Psequin -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSEQUIN) \
$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \
- $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
+ $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
$(VIB_POST_LINK) Psequin
# 'sbtedit' Submission Template Editor
@@ -1433,7 +1434,7 @@
$(CC) -o sbtedit -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSBTEDIT) \
$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \
- $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
+ $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
$(VIB_POST_LINK) sbtedit
# 'streamer' Sequinesque Stream Editor

View File

@ -16,4 +16,4 @@ From the README:
have found it a useful and stable basis for a number of tools and
applications.
WWW: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html
WWW: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html

View File

@ -6,14 +6,9 @@ bin/asn2idx
bin/asn2xml
bin/asndhuff
bin/asntool
bin/bl2seq
bin/blastall
bin/blastcl3
bin/blastclust
bin/blastpgp
bin/cdscan
bin/checksub
bin/copymat
bin/ddv
bin/debruijn
bin/demo_regexp
@ -23,27 +18,22 @@ bin/entrcmd
bin/entrez2
bin/errhdr
bin/fa2htgs
bin/fastacmd
bin/findspl
bin/formatdb
bin/formatrpsdb
bin/gene2xml
bin/getmesh
bin/getpub
bin/gil2bin
bin/idfetch
bin/impala
bin/indexpub
bin/makemat
bin/makeset
bin/megablast
bin/ncbisort
bin/rpsblast
bin/sbtedit
bin/seedtop
bin/seqtest
bin/taxblast
bin/tbl2asn
bin/test_regexp
bin/testcore
bin/testobj
bin/testval
bin/udv
bin/vecscreen
include/ncbi/FSpCompat.h
@ -186,7 +176,10 @@ include/ncbi/connect/ncbi_heapmgr.h
include/ncbi/connect/ncbi_host_info.h
include/ncbi/connect/ncbi_host_infop.h
include/ncbi/connect/ncbi_http_connector.h
include/ncbi/connect/ncbi_ipv6.h
include/ncbi/connect/ncbi_lb.h
include/ncbi/connect/ncbi_lbos.h
include/ncbi/connect/ncbi_lbosp.h
include/ncbi/connect/ncbi_lbsmd.h
include/ncbi/connect/ncbi_local.h
include/ncbi/connect/ncbi_memory_connector.h
@ -564,6 +557,7 @@ include/ncbi/xmlblast.h
lib/ncbi/libblast.a
lib/ncbi/libblastapi.a
lib/ncbi/libblastcompadj.a
lib/ncbi/libconnssl.a
lib/ncbi/libddvlib.a
lib/ncbi/libncbi.a
lib/ncbi/libncbiCacc.a
@ -586,41 +580,46 @@ lib/ncbi/libvibgif.a
lib/ncbi/libvibnet.a
lib/ncbi/libvibrant.a
man/man1/Psequin.1.gz
man/man1/asn2all.1.gz
man/man1/asn2asn.1.gz
man/man1/asn2ff.1.gz
man/man1/asn2fsa.1.gz
man/man1/asn2gb.1.gz
man/man1/asn2idx.1.gz
man/man1/asn2xml.1.gz
man/man1/asndhuff.1.gz
man/man1/asndisc.1.gz
man/man1/asnmacro.1.gz
man/man1/asntool.1.gz
man/man1/bl2seq.1.gz
man/man1/blast.1.gz
man/man1/blastall.1.gz
man/man1/asnval.1.gz
man/man1/blastcl3.1.gz
man/man1/blastclust.1.gz
man/man1/blastpgp.1.gz
man/man1/cdscan.1.gz
man/man1/checksub.1.gz
man/man1/copymat.1.gz
man/man1/cleanasn.1.gz
man/man1/ddv.1.gz
man/man1/debruijn.1.gz
man/man1/entrez2.1.gz
man/man1/errhdr.1.gz
man/man1/fa2htgs.1.gz
man/man1/fastacmd.1.gz
man/man1/findspl.1.gz
man/man1/formatdb.1.gz
man/man1/formatrpsdb.1.gz
man/man1/fmerge.1.gz
man/man1/gbseqget.1.gz
man/man1/gene2xml.1.gz
man/man1/getmesh.1.gz
man/man1/getpub.1.gz
man/man1/gil2bin.1.gz
man/man1/idfetch.1.gz
man/man1/impala.1.gz
man/man1/indexpub.1.gz
man/man1/makemat.1.gz
man/man1/megablast.1.gz
man/man1/rpsblast.1.gz
man/man1/seedtop.1.gz
man/man1/taxblast.1.gz
man/man1/insdseqget.1.gz
man/man1/makeset.1.gz
man/man1/nps2gps.1.gz
man/man1/sbtedit.1.gz
man/man1/sortbyquote.1.gz
man/man1/spidey.1.gz
man/man1/subfuse.1.gz
man/man1/tbl2asn.1.gz
man/man1/trna2sap.1.gz
man/man1/trna2tbl.1.gz
man/man1/udv.1.gz
man/man1/vecscreen.1.gz
%%PORTDOCS%%%%DOCSDIR%%/FAQ.txt
@ -629,26 +628,8 @@ man/man1/vecscreen.1.gz
%%PORTDOCS%%%%DOCSDIR%%/access.txt
%%PORTDOCS%%%%DOCSDIR%%/asn2gb.txt
%%PORTDOCS%%%%DOCSDIR%%/asn2gph.txt
%%PORTDOCS%%%%DOCSDIR%%/blast/bl2seq.html
%%PORTDOCS%%%%DOCSDIR%%/blast/blast.html
%%PORTDOCS%%%%DOCSDIR%%/blast/blastall.html
%%PORTDOCS%%%%DOCSDIR%%/blast/blastclust.html
%%PORTDOCS%%%%DOCSDIR%%/blast/blastdb.html
%%PORTDOCS%%%%DOCSDIR%%/blast/blastftp.html
%%PORTDOCS%%%%DOCSDIR%%/blast/blastpgp.html
%%PORTDOCS%%%%DOCSDIR%%/blast/fastacmd.html
%%PORTDOCS%%%%DOCSDIR%%/blast/filter.html
%%PORTDOCS%%%%DOCSDIR%%/blast/formatdb.html
%%PORTDOCS%%%%DOCSDIR%%/blast/formatrpsdb.html
%%PORTDOCS%%%%DOCSDIR%%/blast/history.html
%%PORTDOCS%%%%DOCSDIR%%/blast/impala.html
%%PORTDOCS%%%%DOCSDIR%%/blast/index.html
%%PORTDOCS%%%%DOCSDIR%%/blast/megablast.html
%%PORTDOCS%%%%DOCSDIR%%/blast/netblast.html
%%PORTDOCS%%%%DOCSDIR%%/blast/rpsblast.html
%%PORTDOCS%%%%DOCSDIR%%/blast/scoring.pdf
%%PORTDOCS%%%%DOCSDIR%%/blast/seedtop.html
%%PORTDOCS%%%%DOCSDIR%%/blast/web_blast.pl
%%PORTDOCS%%%%DOCSDIR%%/dispatcher.html
%%PORTDOCS%%%%DOCSDIR%%/fa2htgs/README
%%PORTDOCS%%%%DOCSDIR%%/fa2htgs/updateHtgsDoc
@ -761,12 +742,36 @@ man/man1/vecscreen.1.gz
%%DATADIR%%/LSURef_93.fasta.nhr
%%DATADIR%%/LSURef_93.fasta.nin
%%DATADIR%%/LSURef_93.fasta.nsq
%%DATADIR%%/LSU_chloro_rRNA.nhr
%%DATADIR%%/LSU_chloro_rRNA.nin
%%DATADIR%%/LSU_chloro_rRNA.nsq
%%DATADIR%%/LSU_mito_rRNA.nhr
%%DATADIR%%/LSU_mito_rRNA.nin
%%DATADIR%%/LSU_mito_rRNA.nsq
%%DATADIR%%/LSU_nomito-nochloro-noplastid.nhr
%%DATADIR%%/LSU_nomito-nochloro-noplastid.nin
%%DATADIR%%/LSU_nomito-nochloro-noplastid.nsq
%%DATADIR%%/LSU_plastid.nhr
%%DATADIR%%/LSU_plastid.nin
%%DATADIR%%/LSU_plastid.nsq
%%DATADIR%%/PAM250
%%DATADIR%%/PAM30
%%DATADIR%%/PAM70
%%DATADIR%%/SSU-mito-rRNA.nhr
%%DATADIR%%/SSU-mito-rRNA.nin
%%DATADIR%%/SSU-mito-rRNA.nsq
%%DATADIR%%/SSURef_93.fasta.nhr
%%DATADIR%%/SSURef_93.fasta.nin
%%DATADIR%%/SSURef_93.fasta.nsq
%%DATADIR%%/SSU_chloro_rRNA.nhr
%%DATADIR%%/SSU_chloro_rRNA.nin
%%DATADIR%%/SSU_chloro_rRNA.nsq
%%DATADIR%%/SSU_nomito_nochloro_noplastid.nhr
%%DATADIR%%/SSU_nomito_nochloro_noplastid.nin
%%DATADIR%%/SSU_nomito_nochloro_noplastid.nsq
%%DATADIR%%/SSU_plast_rRNA.nhr
%%DATADIR%%/SSU_plast_rRNA.nin
%%DATADIR%%/SSU_plast_rRNA.nsq
%%DATADIR%%/UniVec.nhr
%%DATADIR%%/UniVec.nin
%%DATADIR%%/UniVec.nsq
@ -775,6 +780,9 @@ man/man1/vecscreen.1.gz
%%DATADIR%%/UniVec_Core.nsq
%%DATADIR%%/asn2ff.prt
%%DATADIR%%/autofix.prt
%%DATADIR%%/bacteria-archea16SrRNA.nhr
%%DATADIR%%/bacteria-archea16SrRNA.nin
%%DATADIR%%/bacteria-archea16SrRNA.nsq
%%DATADIR%%/blast.prt
%%DATADIR%%/bstdt.prt
%%DATADIR%%/bstdt.val

View File

@ -14,8 +14,8 @@ COMMENT= Perl5 interface to the ACEDB genome database system
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Cache-Cache>=0:devel/p5-Cache-Cache
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Cache-Cache>=0:devel/p5-Cache-Cache
MAKE_JOBS_UNSAFE= yes
USES= perl5

View File

@ -16,8 +16,8 @@ LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= p5-BioPerl>=0:biology/p5-BioPerl
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-BioPerl>=0:biology/p5-BioPerl
NO_ARCH= yes
USES= perl5

View File

@ -14,8 +14,8 @@ LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= p5-BioPerl>=1.007000:biology/p5-BioPerl
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-BioPerl>=1.007000:biology/p5-BioPerl
NO_ARCH= yes
USE_PERL5= configure

View File

@ -14,10 +14,10 @@ COMMENT= Perl extension for the DAS (HTTP+XML) Protocol
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Readonly>=1.03:devel/p5-Readonly \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Readonly>=1.03:devel/p5-Readonly \
p5-libwww>=0:www/p5-libwww \
p5-WWW-Curl>=4.07:www/p5-WWW-Curl
RUN_DEPENDS:= ${BUILD_DEPENDS}
USES= perl5
USE_PERL5= modbuild

View File

@ -14,10 +14,10 @@ COMMENT= Client-side library for Distributed Genome Annotation System
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-BioPerl>=0:biology/p5-BioPerl \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-BioPerl>=0:biology/p5-BioPerl \
p5-HTML-Parser>=3:www/p5-HTML-Parser \
p5-libwww>=5:www/p5-libwww
RUN_DEPENDS:= ${BUILD_DEPENDS}
NO_ARCH= yes
USES= perl5

View File

@ -14,12 +14,12 @@ LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= p5-BioPerl>=0:biology/p5-BioPerl \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-BioPerl>=0:biology/p5-BioPerl \
p5-Tree-DAG_Node>=0:devel/p5-Tree-DAG_Node \
p5-URI>=0:net/p5-URI \
p5-XML-DOM>=0:textproc/p5-XML-DOM \
p5-XML-DOM-XPath>=0:textproc/p5-XML-DOM-XPath
RUN_DEPENDS:= ${BUILD_DEPENDS}
NO_ARCH= yes
USE_PERL5= configure

View File

@ -14,10 +14,10 @@ COMMENT= Fast low-level functions for parsing and formatting GFF3
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-File-ReadBackwards>=0:devel/p5-File-ReadBackwards \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-File-ReadBackwards>=0:devel/p5-File-ReadBackwards \
p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \
p5-URI>=0:net/p5-URI
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-IO-String>=0:devel/p5-IO-String
USES= perl5

View File

@ -11,8 +11,8 @@ PKGNAMEPREFIX= p5-
MAINTAINER= perl@FreeBSD.org
COMMENT= Perl Interface to G-language
BUILD_DEPENDS= p5-libwww>=5:www/p5-libwww
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-libwww>=5:www/p5-libwww
USES= perl5
USE_PERL5= configure

View File

@ -14,14 +14,14 @@ COMMENT= Generate GD Images of Bio::Seq Objects
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Bio-Coordinate>=1.007000:biology/p5-Bio-Coordinate \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Bio-Coordinate>=1.007000:biology/p5-Bio-Coordinate \
p5-Bio-SCF>=1.01:biology/p5-Bio-SCF \
p5-BioPerl>=1.007000:biology/p5-BioPerl \
p5-CGI>=0:www/p5-CGI \
p5-GD>=2.30:graphics/p5-GD \
p5-GD-SVG>=0.32:graphics/p5-GD-SVG \
p5-Statistics-Descriptive>=2.6:math/p5-Statistics-Descriptive
RUN_DEPENDS:= ${BUILD_DEPENDS}
NO_ARCH= yes
USES= perl5

View File

@ -13,7 +13,8 @@ COMMENT= Data model and utility API for the MAGE-TAB format
LICENSE= GPLv2
BUILD_DEPENDS= p5-Date-Manip>=5.44:devel/p5-Date-Manip \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Date-Manip>=5.44:devel/p5-Date-Manip \
p5-DateTime>=0.43.02:devel/p5-DateTime \
p5-DateTime-Format-DateManip>=0.04:devel/p5-DateTime-Format-DateManip \
p5-Email-Valid>=0.179:mail/p5-Email-Valid \
@ -24,7 +25,6 @@ BUILD_DEPENDS= p5-Date-Manip>=5.44:devel/p5-Date-Manip \
p5-Parse-RecDescent>=1.965.001:devel/p5-Parse-RecDescent \
p5-Text-CSV_XS>=0.32:textproc/p5-Text-CSV_XS \
p5-URI>=1.35:net/p5-URI
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-Test-Exception>=0.26:devel/p5-Test-Exception
USES= perl5

View File

@ -11,8 +11,8 @@ PKGNAMEPREFIX= p5-
MAINTAINER= perl@FreeBSD.org
COMMENT= Object-oriented Perl API for the NEXUS file format
BUILD_DEPENDS= p5-Clone-PP>=1.02:devel/p5-Clone-PP
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Clone-PP>=1.02:devel/p5-Clone-PP
TEST_DEPENDS= p5-Test-Deep>=0.106:devel/p5-Test-Deep \
p5-Test-Pod>=0:devel/p5-Test-Pod \

View File

@ -15,7 +15,8 @@ LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
LICENSE_FILE_ART10= ${WRKSRC}/COPYING
BUILD_DEPENDS= p5-Archive-Zip>=0:archivers/p5-Archive-Zip \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Archive-Zip>=0:archivers/p5-Archive-Zip \
p5-BioPerl>=0:biology/p5-BioPerl \
p5-GD>=0:graphics/p5-GD \
p5-Math-CDF>=0:math/p5-Math-CDF \
@ -29,7 +30,6 @@ BUILD_DEPENDS= p5-Archive-Zip>=0:archivers/p5-Archive-Zip \
p5-XML-Twig>=0:textproc/p5-XML-Twig \
p5-XML-XML2JSON>=0:textproc/p5-XML-XML2JSON \
p5-libxml>=0:textproc/p5-libxml
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-JSON>=0:converters/p5-JSON
NO_ARCH= yes

View File

@ -11,8 +11,8 @@ PKGNAMEPREFIX= p5-
MAINTAINER= wen@FreeBSD.org
COMMENT= Read and Update SCF Chromatographic Sequence Files
BUILD_DEPENDS= ${LOCALBASE}/include/io_lib/scf.h:biology/iolib
RUN_DEPENDS:= ${BUILD_DEPENDS}
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= ${LOCALBASE}/include/io_lib/scf.h:biology/iolib
CFLAGS+= -I${LOCALBASE}/include
LDFLAGS+= -L${LOCALBASE}/lib

View File

@ -15,7 +15,8 @@ LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
LICENSE_FILE_ART10= ${WRKSRC}/LICENSE
BUILD_DEPENDS= p5-Algorithm-Diff>=0:devel/p5-Algorithm-Diff \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Algorithm-Diff>=0:devel/p5-Algorithm-Diff \
p5-Bio-FeatureIO>=0:biology/p5-Bio-FeatureIO \
p5-BioPerl>=1.007000:biology/p5-BioPerl \
p5-Config-Any>=0:devel/p5-Config-Any \
@ -23,7 +24,6 @@ BUILD_DEPENDS= p5-Algorithm-Diff>=0:devel/p5-Algorithm-Diff \
p5-IO-String>=0:devel/p5-IO-String \
p5-IPC-Run>=0:devel/p5-IPC-Run \
p5-XML-Twig>=0:textproc/p5-XML-Twig
RUN_DEPENDS:= ${BUILD_DEPENDS}
CONFLICTS= p5-bioperl-run-1.[13579]*

View File

@ -14,7 +14,8 @@ COMMENT= Collection of Perl modules for bioinformatics
LICENSE= ART10 GPLv1+
LICENSE_COMB= dual
BUILD_DEPENDS= p5-Algorithm-Munkres>=0:math/p5-Algorithm-Munkres \
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= p5-Algorithm-Munkres>=0:math/p5-Algorithm-Munkres \
p5-Array-Compare>=0:misc/p5-Array-Compare \
p5-CGI>=0:www/p5-CGI \
p5-Clone>=0:devel/p5-Clone \
@ -51,7 +52,6 @@ BUILD_DEPENDS= p5-Algorithm-Munkres>=0:math/p5-Algorithm-Munkres \
p5-YAML>=0:textproc/p5-YAML \
p5-libwww>=0:www/p5-libwww \
p5-libxml>=0:textproc/p5-libxml
RUN_DEPENDS:= ${BUILD_DEPENDS}
TEST_DEPENDS= p5-Test-Most>=0:devel/p5-Test-Most \
p5-URI>=0:net/p5-URI

View File

@ -1,9 +1,9 @@
# $FreeBSD$
PORTNAME= biom-format
PORTVERSION= 2.1.6
PORTREVISION= 2
PORTVERSION= 2.1.7
CATEGORIES= biology python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= jrm@FreeBSD.org
@ -12,23 +12,21 @@ COMMENT= Biological Observation Matrix (BIOM) Format Project
LICENSE= BSD3CLAUSE
BUILD_DEPENDS= ${PYNUMPY}
RUN_DEPENDS= ${PYNUMPY} \
${PYTHON_PKGNAMEPREFIX}click>=6.6:devel/py-click@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}future>=0.15.2:devel/py-future@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}h5py>=2.6.0:science/py-h5py@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}scipy>=0.16.1:science/py-scipy@${PY_FLAVOR}
USE_GITHUB= yes
GH_ACCOUNT= biocore
RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>0:devel/py-click@${PY_FLAVOR} \
${PYNUMPY} \
${PYTHON_PKGNAMEPREFIX}future>=0.16.0:devel/py-future@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}scipy>=0.13.0:science/py-scipy@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pandas>=0.20.0:math/py-pandas@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}h5py>=2.2.0:science/py-h5py@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}six>=1.10.0:devel/py-six@${PY_FLAVOR}
USES= python
USE_PYTHON= autoplist distutils
USE_PYTHON= autoplist concurrent distutils
.include <bsd.port.pre.mk>
.if ${PYTHON_REL} < 3000
RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}pyqi>=0.2.0:devel/py-pyqi@${PY_FLAVOR}
RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}pyqi>0:devel/py-pyqi@${PY_FLAVOR}
.endif
post-extract:

View File

@ -1,3 +1,3 @@
TIMESTAMP = 1493465225
SHA256 (biocore-biom-format-2.1.6_GH0.tar.gz) = f2daddb634c540e10d04e4f71174da98f57d7f95472f02c358df4ca82e3f9921
SIZE (biocore-biom-format-2.1.6_GH0.tar.gz) = 11997159
TIMESTAMP = 1538769748
SHA256 (biom-format-2.1.7.tar.gz) = b47e54282ef13cddffdb00aea9183a87175a2372c91a915259086a3f444c42f4
SIZE (biom-format-2.1.7.tar.gz) = 11820666

View File

@ -1,69 +0,0 @@
# Created by: Glenn Johnson
# $FreeBSD$
PORTNAME= tinker
PORTVERSION= 7.1.3
PORTREVISION= 5
CATEGORIES= biology
MASTER_SITES= http://dasher.wustl.edu/tinker/downloads/
MAINTAINER= ports@FreeBSD.org
COMMENT= General purpose molecular modelling package
LICENSE= tinker
LICENSE_NAME= TINKER license agreement
LICENSE_FILE= ${WRKSRC}/doc/license.txt
LICENSE_PERMS= auto-accept
RESTRICTED= author requests no distribution except from his FTP site
OPTIONS_DEFINE= OPTIMIZED_FFLAGS DOCS EXAMPLES
OPTIMIZED_FFLAGS_DESC= compilation optimizations
WRKSRC= ${WRKDIR}/${PORTNAME}
BUILD_WRKSRC= ${WRKSRC}/source
INSTALL_WRKSRC= ${WRKSRC}/source
USES= fortran
MAKE_ENV= HAVE_G2C=yes
MAKEFILE= ${WRKSRC}/make/Makefile
ALL_TARGET= all
INSTALL_TARGET= rename
EXTRACT_AFTER_ARGS=--exclude fftw --exclude windows --exclude macosx
USE_HARDENING= pie:off relro:off
SUB_FILES= pkg-message
.include <bsd.port.options.mk>
.if ${PORT_OPTIONS:MOPTIMIZED_FFLAGS}
FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations
.if (${ARCH} == "i386")
FFLAGS+= -mfancy-math-387 -malign-double
.endif # i386
.endif
pre-build:
@${RM} ${BUILD_WRKSRC}/*.c
post-install:
${MKDIR} ${STAGEDIR}${DATADIR}
${MKDIR} ${STAGEDIR}${DATADIR}/bench
(cd ${WRKSRC}/bench && ${INSTALL_DATA} \
0README *.log *.key *.run *.xyz results* \
${STAGEDIR}${DATADIR}/bench)
${MKDIR} ${STAGEDIR}${DATADIR}/params
(cd ${WRKSRC}/params && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/params)
${MKDIR} ${STAGEDIR}${DATADIR}/test
(cd ${WRKSRC}/test && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/test)
post-install-DOCS-on:
${MKDIR} ${STAGEDIR}${DOCSDIR}
(cd ${WRKSRC}/doc && ${INSTALL_DATA} 0README *.pdf *.txt ${STAGEDIR}${DOCSDIR})
post-install-EXAMPLES-on:
${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
(cd ${WRKSRC}/example && ${INSTALL_DATA} \
0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.xyz \
${STAGEDIR}${EXAMPLESDIR})
.include <bsd.port.mk>

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@ -1,2 +0,0 @@
SHA256 (tinker-7.1.3.tar.gz) = c221459ac1ac423ed8c99c7ba67eaab09821c970333cd2841efb20ccbfd59095
SIZE (tinker-7.1.3.tar.gz) = 28655947

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@ -1,5 +0,0 @@
--- bench/bench1.run.orig 2015-05-08 20:57:45 UTC
+++ bench/bench1.run
@@ -1 +1 @@
-../bin/timer bench1 100 y
+timer bench1 1 y

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@ -1,5 +0,0 @@
--- bench/bench2.run.orig 2015-05-08 20:57:45 UTC
+++ bench/bench2.run
@@ -1 +1 @@
-../bin/timer bench2 1000 y
+timer bench2 1 y

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@ -1,5 +0,0 @@
--- bench/bench3.run.orig Wed Sep 5 14:00:09 2001
+++ bench/bench3.run Wed Sep 5 14:01:27 2001
@@ -1 +1 @@
-time ../bin/vibrate bench3 0
+time vibrate bench3 0

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@ -1,5 +0,0 @@
--- bench/bench4.run.orig 2014-12-16 05:17:53.000000000 +0200
+++ bench/bench4.run 2014-12-28 18:56:02.000000000 +0200
@@ -1 +1 @@
-time ../bin/dynamic bench4 1000 1.0 10.0 2 298.0
+time dynamic bench4 1000 1.0 10.0 2 298.0

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