UPDATE: textproc/py-yaml 3.12
Index: Makefile === RCS file: /cvs/ports/textproc/py-yaml/Makefile,v retrieving revision 1.14 diff -u -p -r1.14 Makefile --- Makefile9 Dec 2015 18:26:47 - 1.14 +++ Makefile13 Nov 2016 05:15:05 - @@ -2,10 +2,9 @@ COMMENT= YAML parser and emitter in Python -MODPY_EGG_VERSION=3.11 +MODPY_EGG_VERSION=3.12 DISTNAME= PyYAML-${MODPY_EGG_VERSION} PKGNAME= py-yaml-${MODPY_EGG_VERSION} -REVISION= 1 CATEGORIES=textproc HOMEPAGE= http://pyyaml.org/wiki/PyYAML Index: distinfo === RCS file: /cvs/ports/textproc/py-yaml/distinfo,v retrieving revision 1.4 diff -u -p -r1.4 distinfo --- distinfo19 Aug 2014 14:25:11 - 1.4 +++ distinfo13 Nov 2016 05:15:12 - @@ -1,2 +1,2 @@ -SHA256 (PyYAML-3.11.tar.gz) = w2yTiocuX/SUk4szsUqqFWy0OexnVI/Ks1Nbt4sIRug= -SIZE (PyYAML-3.11.tar.gz) = 248685 +SHA256 (PyYAML-3.12.tar.gz) = WSdmxjAyB6IO/ERVh3eDItf3OxYb2ZTyJ62qNBuiEqs= +SIZE (PyYAML-3.12.tar.gz) = 253011 Index: patches/patch-lib3_yaml_scanner_py === RCS file: patches/patch-lib3_yaml_scanner_py diff -N patches/patch-lib3_yaml_scanner_py --- patches/patch-lib3_yaml_scanner_py 1 Dec 2014 09:24:46 - 1.1 +++ /dev/null 1 Jan 1970 00:00:00 - @@ -1,17 +0,0 @@ -$OpenBSD: patch-lib3_yaml_scanner_py,v 1.1 2014/12/01 09:24:46 jasper Exp $ - -Security fix for CVE-2014-9130 -http://marc.info/?l=oss-security=141720508007010=2 - lib3/yaml/scanner.py.orig Mon Dec 1 10:14:54 2014 -+++ lib3/yaml/scanner.py Mon Dec 1 10:15:21 2014 -@@ -299,7 +299,8 @@ class Scanner: - - # A simple key is required only if it is the first token in the current - # line. Therefore it is always allowed. --assert self.allow_simple_key or not required -+# http://marc.info/?l=oss-security=141720508007010=2 -+#assert self.allow_simple_key or not required - - # The next token might be a simple key. Let's save it's number and - # position. Index: patches/patch-lib_yaml_scanner_py === RCS file: patches/patch-lib_yaml_scanner_py diff -N patches/patch-lib_yaml_scanner_py --- patches/patch-lib_yaml_scanner_py 1 Dec 2014 09:24:46 - 1.1 +++ /dev/null 1 Jan 1970 00:00:00 - @@ -1,17 +0,0 @@ -$OpenBSD: patch-lib_yaml_scanner_py,v 1.1 2014/12/01 09:24:46 jasper Exp $ - -Security fix for CVE-2014-9130 -http://marc.info/?l=oss-security=141720508007010=2 - lib/yaml/scanner.py.orig Wed Mar 26 19:54:13 2014 -+++ lib/yaml/scanner.pyMon Dec 1 10:15:36 2014 -@@ -299,7 +299,8 @@ class Scanner(object): - - # A simple key is required only if it is the first token in the current - # line. Therefore it is always allowed. --assert self.allow_simple_key or not required -+# http://marc.info/?l=oss-security=141720508007010=2 -+#assert self.allow_simple_key or not required - - # The next token might be a simple key. Let's save it's number and - # position.
UPDATE: textproc/lua-yaml 6.1
Index: Makefile === RCS file: /cvs/ports/textproc/lua-yaml/Makefile,v retrieving revision 1.2 diff -u -p -r1.2 Makefile --- Makefile16 Oct 2016 23:21:23 - 1.2 +++ Makefile13 Nov 2016 05:12:28 - @@ -1,7 +1,7 @@ # $OpenBSD: Makefile,v 1.2 2016/10/16 23:21:23 jca Exp $ COMMENT = Lua library for parsing and emitting YAML -V =6.0 +V =6.1 PKGNAME = lua-yaml-${V} Index: distinfo === RCS file: /cvs/ports/textproc/lua-yaml/distinfo,v retrieving revision 1.1.1.1 diff -u -p -r1.1.1.1 distinfo --- distinfo24 Apr 2016 02:36:45 - 1.1.1.1 +++ distinfo13 Nov 2016 05:12:40 - @@ -1,2 +1,2 @@ -SHA256 (lyaml-release-v6.0.tar.gz) = nXz3TXdpmf9vdYxWnVIC/12h8wPG9CKdO0H3HNOj56c= -SIZE (lyaml-release-v6.0.tar.gz) = 475288 +SHA256 (lyaml-release-v6.1.tar.gz) = cGPlDfzuJfh/Gin8LXXRLl2P2DUiqZk21RhBw/N0hRo= +SIZE (lyaml-release-v6.1.tar.gz) = 476721
UPDATE: devel/libyaml 0.1.7
https://bitbucket.org/xi/libyaml/raw/6d5f97d2330147c286839bacfa0c66fac3992faf/announcement.msg * Fixed segfault in yaml_string_write_handler. * Fixed invalid simple key assertion. * Fixed error handling in some examples (thank to Mathias Svensson). * Removed obsolete VS project files. Index: Makefile === RCS file: /cvs/ports/devel/libyaml/Makefile,v retrieving revision 1.11 diff -u -p -r1.11 Makefile --- Makefile11 Mar 2016 19:59:13 - 1.11 +++ Makefile13 Nov 2016 04:58:16 - @@ -2,8 +2,7 @@ COMMENT= YAML 1.1 parser and emitter written in C -DISTNAME= yaml-0.1.6 -REVISION= 1 +DISTNAME= yaml-0.1.7 PKGNAME= lib${DISTNAME} CATEGORIES=devel Index: distinfo === RCS file: /cvs/ports/devel/libyaml/distinfo,v retrieving revision 1.5 diff -u -p -r1.5 distinfo --- distinfo30 Mar 2014 06:59:49 - 1.5 +++ distinfo13 Nov 2016 04:59:16 - @@ -1,2 +1,2 @@ -SHA256 (yaml-0.1.6.tar.gz) = faaXG0vQipht0qYTU7xCI2K9DtzGfX66rGjJX3QYJ0k= -SIZE (yaml-0.1.6.tar.gz) = 503012 +SHA256 (yaml-0.1.7.tar.gz) = gIjkVyZKmLpFGpC4Zh/LT51vR49yZdSDIqGWzsJIByk= +SIZE (yaml-0.1.7.tar.gz) = 527518 Index: patches/patch-src_scanner_c === RCS file: patches/patch-src_scanner_c diff -N patches/patch-src_scanner_c --- patches/patch-src_scanner_c 1 Dec 2014 08:48:51 - 1.4 +++ /dev/null 1 Jan 1970 00:00:00 - @@ -1,21 +0,0 @@ -$OpenBSD: patch-src_scanner_c,v 1.4 2014/12/01 08:48:51 jasper Exp $ - -Security fix for CVE-2014-9130 -https://marc.info/?l=oss-security=141715462623662=2 - src/scanner.c.orig Thu Mar 27 05:54:02 2014 -+++ src/scanner.c Sat Nov 29 16:10:33 2014 -@@ -1106,13 +1106,6 @@ yaml_parser_save_simple_key(yaml_parser_t *parser) - && parser->indent == (ptrdiff_t)parser->mark.column); - - /* -- * A simple key is required only when it is the first token in the current -- * line. Therefore it is always allowed. But we add a check anyway. -- */ -- --assert(parser->simple_key_allowed || !required);/* Impossible. */ -- --/* - * If the current position may start a simple key, save it. - */ -
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: juan...@cvs.openbsd.org 2016/11/12 19:30:23 Modified files: archivers/zstd : Makefile distinfo archivers/zstd/patches: patch-tests_playTests_sh Log message: Update to zstd 1.1.1.
Re: UPDATE: devel/doxygen
Nigel Taylorwrites: > On 10/22/16 16:42, Rafael Sadowski wrote: >> On Tue Sep 20, 2016 at 01:33:34AM +0100, Stuart Henderson wrote: >>> These plist changes for every update are getting silly, I think I'd >>> rather disable doxygen in those ports.. >>> >> >> Other opinions or agreements? >> > > I don't build qt5/kde4/kde5 for amd64. > > From what I see, the -gui and hence inclusion qt5 has no point it > doesn't appear to be used in other ports. If no one actually uses the > -gui spending a lot of time building qt5 / and -gui for nothing. > > Because of the size of qt5 this should be split into two ports, rather > than using the PSEUDO_FLAVOR otherwise all the ports listed will be > waiting on the qt5 build to complete when using dpb. > > qt5 itself needs splitting using the separate source files provided, > rather then the combined file with everything needed or not. > > As is I will be just removing -gui / PSEUDO_FLAVOR from the port for myself. Instead of people having to maintain local patches, wouldn't it be better to remove qt5 from this build path? That can surely be done without killing the -gui package. > The same way I have removed kde4 from editors/libreoffice, qt, qt4, qt5 > from print/poppler. > The PLIST issue is gnerating html documentation with changed scripts, > images, with the same names > > > also as far as I can see there is an option to force the use of Qt4 if > Qt5 is present. > > From doxygen install document it says... > > Qt Software's GUI toolkit > http://qt-project.org/;>Qt > \addindex Qt > version 4.3 or higher (but currently, Qt 5.x is not yet supported). > This is needed to build the GUI front-end doxywizard. > > I searched the changelog not a single mention of a switch to Qt5 > > This looks like we are switching to Qt5 because it being built / test on > a machine with Qt5 installed else the switch to Qt5 hasn't been documented. > > So why is this even using Qt5. Upstream made the choice of introducing Qt5 compatibility in this release, and to use Qt5 by default. doxywizard runs fine here. To me it looks like a case of slightly outdated information on the website. Note that this diff has been floating on the mailing-list since some time already, you could have voiced objections earlier. ;) -- jca | PGP : 0x1524E7EE / 5135 92C1 AD36 5293 2BDF DDCC 0DFA 74AE 1524 E7EE
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: j...@cvs.openbsd.org2016/11/12 14:18:05 Modified files: net/openvpn-auth-ldap: Makefile Log message: Enable tests.
Re: UPDATE: devel/doxygen
On 10/22/16 16:42, Rafael Sadowski wrote: > On Tue Sep 20, 2016 at 01:33:34AM +0100, Stuart Henderson wrote: >> These plist changes for every update are getting silly, I think I'd >> rather disable doxygen in those ports.. >> > > Other opinions or agreements? > I don't build qt5/kde4/kde5 for amd64. >From what I see, the -gui and hence inclusion qt5 has no point it doesn't appear to be used in other ports. If no one actually uses the -gui spending a lot of time building qt5 / and -gui for nothing. Because of the size of qt5 this should be split into two ports, rather than using the PSEUDO_FLAVOR otherwise all the ports listed will be waiting on the qt5 build to complete when using dpb. qt5 itself needs splitting using the separate source files provided, rather then the combined file with everything needed or not. As is I will be just removing -gui / PSEUDO_FLAVOR from the port for myself. The same way I have removed kde4 from editors/libreoffice, qt, qt4, qt5 from print/poppler. The PLIST issue is gnerating html documentation with changed scripts, images, with the same names also as far as I can see there is an option to force the use of Qt4 if Qt5 is present. >From doxygen install document it says... Qt Software's GUI toolkit http://qt-project.org/;>Qt \addindex Qt version 4.3 or higher (but currently, Qt 5.x is not yet supported). This is needed to build the GUI front-end doxywizard. I searched the changelog not a single mention of a switch to Qt5 This looks like we are switching to Qt5 because it being built / test on a machine with Qt5 installed else the switch to Qt5 hasn't been documented. So why is this even using Qt5. >> >> >> On 2016/09/19 21:38, Rafael Sadowski wrote: >>> Hi ports@ >>> >>> updated again. Doxygen port changes: >>> >>> - Switch to qt5 >>> -- Build doxyapp, doxyindexer applications (Tested @amd64) >>> - Some patches are no longer needed (committed upstream) >>> - Take Maintainer >>> >>> I checked all ports with doxygen usage: >>> >>> devel/libmtpREVISION bump and updated plist >>> devel/qjson REVISION bump and updated plist >>> geo/geosREVISION bump and updated plist, switch >>> HOMEPAGE to HTTPS >>> graphics/lensfunREVISION bump and updated plist >>> multimedia/libquicktime REVISION bump and updated plist >>> x11/dbusmenu-qt REVISION bump and updated plist >>> x11/ede/lib REVISION bump and updated plist >>> net/ortpREVISION bump and updated plist >>> >>> databases/soprano none plist changes >>> devel/kf5/kapidox none plist changes >>> devel/libidnnone plist changes >>> devel/simulavr none plist changes >>> devel/tclap none plist changes >>> graphics/digikam-kde4 none plist changes >>> graphics/opencv none plist changes >>> math/ginac none plist changes >>> net/libktorrent none plist changes >>> net/libmygpo-qt none plist changes >>> productivity/kmymoney none plist changes >>> productivity/libalkimia none plist changes >>> x11/awesome none plist changes >>> x11/gtk3mm none plist changes >>> x11/kde4/nepomuk-core none plist changes >>> x11/kde4/runtimenone plist changes >>> >>> devel/cppunit/Makefile disable-doxygen >>> devel/kyua-cli without-doxygen >>> devel/kyua-testers without-doxygen >>> devel/libhidw without-doxygen >>> devel/rapidsvn with-doxygen=no >>> graphics/geeqie disable-doxygen-doc >>> graphics/libpgf Force disabling documentation >>> generation through doxygen >>> multimedia/libbluraydisable-doxygen-doc >>> multimedia/libv4l disable-doxygen-doc >>> net/avahi disable-doxygen-doc >>> net/meanwhile enable-doxygen=no >>> net/pidgin disable-doxygen >>> productivity/gnucashdisable-doxygen >>> sysutils/inotify-tools disable-doxygen >>> x11/dbusdisable-doxygen-docs >>> x11/libxdg-basedir disable-doxygen-doc >>> x11/xkbcommon without-doxygen >>> >>> Tested only on amd64. I am looking forward about your feedback and I hope we >>> will see 1.8.12 quickly in the tree. >>> >>> Kind regards, >>> >>> Rafael Sadowski >>> >>> >>> >>> Index: devel/doxygen/Makefile >>> === >>> RCS file: /cvs/ports/devel/doxygen/Makefile,v >>> retrieving revision 1.35 >>> diff -u -p -u -p -r1.35 Makefile >>> --- devel/doxygen/Makefile 28 Apr 2016 17:55:27 - 1.35 >>> +++ devel/doxygen/Makefile 18 Sep 2016 15:13:38 - >>> @@
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: j...@cvs.openbsd.org2016/11/12 14:17:02 Modified files: net/openvpn-auth-ldap: Makefile Added files: net/openvpn-auth-ldap/patches: patch-src_Makefile_in patch-tests_Makefile_in Log message: Ensure that we link against libobjc.so from base. Newer libobjc from ports isn't compatible. Problem reported by Sebastien Leclerc.
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: j...@cvs.openbsd.org2016/11/12 13:59:18 Modified files: devel/doxygen : Makefile Log message: Don't try to build the gui on powerpc, qt5 doesn't build there.
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: j...@cvs.openbsd.org2016/11/12 13:54:09 Modified files: geo/geos : Makefile Log message: Switch HOMEPAGE to https:// >From Rafael Sadowski, as part of a larger diff.
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: j...@cvs.openbsd.org2016/11/12 13:50:41 Modified files: audio/libnjb : Makefile audio/libnjb/pkg: PLIST devel/doxygen : Makefile distinfo devel/doxygen/patches: patch-addon_doxywizard_CMakeLists_txt patch-libmd5_libmd5_pro_in patch-qtools_qtools_pro_in patch-src_CMakeLists_txt patch-src_dirdef_cpp devel/doxygen/pkg: PLIST-main devel/libmtp : Makefile devel/libmtp/pkg: PLIST devel/qjson: Makefile devel/qjson/pkg: PLIST geo/geos : Makefile geo/geos/pkg : PLIST graphics/lensfun: Makefile graphics/lensfun/pkg: PLIST multimedia/libquicktime: Makefile multimedia/libquicktime/pkg: PLIST net/ortp : Makefile net/ortp/pkg : PLIST x11/dbusmenu-qt: Makefile x11/dbusmenu-qt/pkg: PLIST x11/ede/lib: Makefile x11/ede/lib/pkg: PLIST Log message: Update to doxygen-1.8.12 and switch the gui to Qt5 >From Rafael Sadowski, who takes maintainership.
Re: New: biology/hmmer
On Sat, 12 Nov 2016, Jeremie Courreges-Anglas wrote: > Senthil Kumar Mwrites: > > > Hello ports, > > > > HMMER is used for searching sequence databases for sequence homologs, > > and for making sequence alignments. It implements methods using > > probabilistic models called profile hidden Markov models (profile > > HMMs). (http://hmmer.org) > > > > The latest version 3.1b2 compiles and builds without any additional > > patches/errors on OpenBSD, unlike previous versions (see: `h104' > > on: > > https://raw.githubusercontent.com/EddyRivasLab/hmmer/master/documentation/bugs/BUGTRAX > > . > > > > HMMER is an indispensable tool for bioinformatics research and it > > would be neat to have it available on OpenBSD. > > > > I have tested this on amd64, additional tests, comments are welcome. > > Here's a updated tarball with the following changes: > - more spacing in Makefile > - move PKGNAME to hmmer-3.1beta2, per packages-specs(7) > - I added your name to the mail address in MAINTAINER > - "License GPLv3 only": "GPLv3" is enough, else it would be "GPLv3+" > - make V=1 to show build commands > - disable sse(2) except on amd64 > - kill last paragraph in DESCR, trim the third one and merge it with the > first one. Those bits didn't seem particularly relevant for a package > description > > Looks good to me as is. Are the executables in this package useful > alone, or do you use it only for the library? > > Hi Jeremie, Thank you so much for taking time to look into this and your inputs. I checked the updated tarball on amd64 (running Nov. 9 snapshot) and it works (installs and runs) as expected. The executables in this package are useful by themselves. Senthil
NEW: math/py-bottleneck 1.2.0
Hi, ok to import? DESCR: Bottleneck is a collection of fast NumPy array functions written in C. -- Alexandr Shadchin py-bottleneck.tgz Description: application/tar-gz
update devel/cargo to 0.14.0
Hi, The problem of crates.io has been resolved by upstream (problematic commit has been reverted), so we are free to remove BROKEN now. While here, upgrade cargo :) Regarding the diff, a license clarification has been done: hamcrest part is MIT/Apache 2.0, and a new release (with proper license) has been released. So I updated the license indications and PERMIT_DISTFILES_FTP. Same as rust, I would like to take back the maintenership. Thanks. -- Sebastien Marie Index: Makefile === RCS file: /cvs/ports/devel/cargo/Makefile,v retrieving revision 1.5 diff -u -p -r1.5 Makefile --- Makefile12 Nov 2016 08:53:11 - 1.5 +++ Makefile12 Nov 2016 19:08:40 - @@ -1,21 +1,19 @@ # $OpenBSD: Makefile,v 1.5 2016/11/12 08:53:11 landry Exp $ COMMENT = package manager for Rust language -BROKEN = crates.io requires Accept: HTTP header - # cargo version -CARGO_VERSION =0.13.0 +CARGO_VERSION =0.14.0 # rust-install submodule version in cargo/src/rust-installer # see https://github.com/rust-lang/cargo/tree/${CARGO_VERSION}/src -RUSTINSTALL_INDEX =c37d3747da75c280237dc2d6b925078e69555499 +RUSTINSTALL_INDEX =4f994850808a572e2cc8d43f968893c8e942e9bf # crates.io commit for CARGO_VERSION # see https://github.com/rust-lang/crates.io-index/commits/master/ca/rg/cargo -CRATESIO_INDEX = 2e1f891403b2d057f0ea21475b1bb99800aa14b6 +CRATESIO_INDEX = 9f8c3a65f70b2a5723e0d9cc0a32d531ea42da67 # cargo version used for bootstrapping -BOOTSTRAP_VERSION =0.12.0-20160821 +BOOTSTRAP_VERSION =0.14.0-20161112 # registry index # see ${WRKDIR}/cargo-home/registry/index/github.com-${REGISTRY_INDEX} @@ -27,19 +25,15 @@ CATEGORIES =devel HOMEPAGE = https://doc.crates.io/ +MAINTAINER = Sebastien Marie <sema...@online.fr> + # cargo is dual licensed MIT/Apache-2.0 # third-parties (detail below): # - MIT # - Unlicense/MIT # - MIT/Apache-2.0 -# - MPL-2.0 -# - one with no indication of licence (hamcrest) -# -# hamcrest is used only for the testsuite, and isn't builded with cargo. -# so the package doesn't contain it. # PERMIT_PACKAGE_CDROM = Yes -PERMIT_DISTFILES_FTP = No as hamcrest has no license information WANTLIB = c crypto curl m pthread ssh2 ssl z @@ -52,55 +46,57 @@ DISTFILES +=crates.io-index-${CRATESIO_ # look at ${WRKDIR}/cargo-home/registry/src/github.com-${REGISTRY_INDEX} # for the list CRATES += advapi32-sys-0.2.0 # MIT -CRATES += aho-corasick-0.5.2 # Unlicense/MIT +CRATES += aho-corasick-0.5.3 # Unlicense/MIT CRATES += bitflags-0.1.1 # MIT/Apache-2.0 CRATES += bitflags-0.7.0 # MIT/Apache-2.0 +CRATES += bufstream-0.1.2 # MIT/Apache-2.0 (test) CRATES += cfg-if-0.1.0# MIT/Apache-2.0 CRATES += cmake-0.1.17# MIT/Apache-2.0 CRATES += crossbeam-0.2.9 # MIT/Apache-2.0 -CRATES += curl-0.3.2 # MIT -CRATES += curl-sys-0.2.1 # MIT +CRATES += curl-0.3.9 # MIT +CRATES += curl-sys-0.2.4 # MIT CRATES += docopt-0.6.82 # Unlicense/MIT CRATES += env_logger-0.3.4# MIT/Apache-2.0 CRATES += filetime-0.1.10 # MIT/Apache-2.0 CRATES += flate2-0.2.14 # MIT/Apache-2.0 CRATES += fs2-0.2.5 # MIT/Apache-2.0 -CRATES += gcc-0.3.32 # MIT/Apache-2.0 +CRATES += gcc-0.3.35 # MIT/Apache-2.0 CRATES += git2-0.4.4 # MIT/Apache-2.0 CRATES += git2-curl-0.5.0 # MIT/Apache-2.0 CRATES += glob-0.2.11 # MIT/Apache-2.0 -CRATES += hamcrest-0.1.0 # no license indication (test only) +CRATES += hamcrest-0.1.1 # MIT/Apache-2.0 (test) CRATES += idna-0.1.0 # MIT/Apache-2.0 CRATES += kernel32-sys-0.2.2 # MIT CRATES += lazy_static-0.2.1 # MIT -CRATES += libc-0.2.15 # MIT/Apache-2.0 +CRATES += libc-0.2.17 # MIT/Apache-2.0 CRATES += libgit2-sys-0.4.5 # MIT/Apache-2.0 -CRATES += libssh2-sys-0.1.38 # MIT/Apache-2.0 -CRATES += libz-sys-1.0.5 # MIT/Apache-2.0 +CRATES += libssh2-sys-0.1.39 # MIT/Apache-2.0 +CRATES += libz-sys-1.0.6 # MIT/Apache-2.0 CRATES += log-0.3.6 # MIT/Apache-2.0 CRATES += matches-0.1.2 # MIT CRATES += memchr-0.1.11 # Unlicense/MIT CRATES += miniz-sys-0.1.7 # MIT/Apache-2.0 CRATES += miow
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: shadc...@cvs.openbsd.org2016/11/12 11:12:31 Modified files: devel/py-test : Makefile distinfo Log message: Update to py-test 3.0.4
Re: New: biology/hmmer
Senthil Kumar Mwrites: > Hello ports, > > HMMER is used for searching sequence databases for sequence homologs, > and for making sequence alignments. It implements methods using > probabilistic models called profile hidden Markov models (profile > HMMs). (http://hmmer.org) > > The latest version 3.1b2 compiles and builds without any additional > patches/errors on OpenBSD, unlike previous versions (see: `h104' > on: > https://raw.githubusercontent.com/EddyRivasLab/hmmer/master/documentation/bugs/BUGTRAX > . > > HMMER is an indispensable tool for bioinformatics research and it > would be neat to have it available on OpenBSD. > > I have tested this on amd64, additional tests, comments are welcome. Here's a updated tarball with the following changes: - more spacing in Makefile - move PKGNAME to hmmer-3.1beta2, per packages-specs(7) - I added your name to the mail address in MAINTAINER - "License GPLv3 only": "GPLv3" is enough, else it would be "GPLv3+" - make V=1 to show build commands - disable sse(2) except on amd64 - kill last paragraph in DESCR, trim the third one and merge it with the first one. Those bits didn't seem particularly relevant for a package description Looks good to me as is. Are the executables in this package useful alone, or do you use it only for the library? hmmer.tgz Description: Binary data -- jca | PGP : 0x1524E7EE / 5135 92C1 AD36 5293 2BDF DDCC 0DFA 74AE 1524 E7EE
Re: [NEW] www/tbb improved, updated
[Sorry for duplicate email to anyone who got one, my bad -A] Landry Breuilwrites: > On Wed, Nov 02, 2016 at 09:55:17AM -0600, attila wrote: n>> >> Landry Breuil writes: >> >> > On Tue, Oct 18, 2016 at 11:07:22AM -0500, attila wrote: >> >> >> >> attila writes: >> >> >> >> > attila writes: >> >> > >> >> >> Hi ports@, >> >> >> >> >> > Feedback, comments, most welcome. >> >> > >> >> > Pax, -A >> >> >> >> Ping. Ports attached for convenience. >> > >> > Fwiw, i've built the git tip of https://github.com/torbsd/openbsd-ports >> > on current, and they build fine. >> >> I just pushed a couple of times to address your concerns; updated >> tarball attached for convenience. > > So, more nits portswise only: Thanks a lot for this feedback. Attached is a tarball that attempts to address both your and danj@'s concerns. > - meta/tbb/pkg/DESCR could use some more wording, as > www/tbb/tor-browser/pkg/DESCR. All of the COMMENTs and pkg/DESCR files have been updated. > - i dont see a README anywhere installed in the pkgs (could go to > meta/tbb/pkg/README, with the added line to the corresponding PLIST) > explaining the end-user how that whole stuff works, without having to > refer to the website... There is now a meta/tor-browser/pkg/README > - www/tbb/Makefile -> that .if !defined(ADDONS_ONLY) block should go away Done. > - no need to cargo-cult BROKEN-sparc64 nor the MODGCC4 stuff for archs > where it wont build (yeah i know, i need to clean firefox Makefile..) Removed. > - the dependency on gettext looks fishy. BUILD_DEPENDS + LIB_DEPENDS + > RUN_DEPENDS ? i dont think so, that also looks like cargoculting. Fixed. > - CONFIGURE_STYLE=autoheader ? I have "autoconf no-autoheader", which I think is correct in this case. However there was an issue with make configure that I'm not sure I solved well. The issue is that the "test -f $$d/configure" in gnu.port.mk fails because Tor Browser does not have a configure at toplevel, only a configure.in. I presume there's a reason why the test is not: -f $$d/configure.in -o -f $$d/configure.ac but I don't understand what it is... ? My hack was to prepend . to MOZILLA_AUTOCONF_DIRS, since you already have a pre-configure hook in mozilla.port.mk (which is where I would've put the "extra" call to autoconf anyway). This has the desired effect. If there's a better, more generic way to deal with autoconf'd projects that don't ship a top-level configure I would like to be enlightened. > - since all extensions are installed *only* for tbb, it should be > stressed in their COMMENT/DESCR, so that ppl dont think that > installing 'https-everywhere' package will magically enabled httpse for > their firefox.. My munging of PKGNAMEs attempts to address this as well as explicit text in */pkg/DESCR and COMMENTs. I put a tb- prefix in the PKGNAMEs for www/tor-browser/{browser,noscript,https-everywhere}, so the full list of PKGNAMEs is: tor-browser# meta package tb-browser # firefox esr fork torbutton tor-launcher tb-noscript tb-https-everywhere > And there are probably other nits... :) I have a question that might turn into a nit: portcheck complains thus in www/tor-browser/browser: stdc++ in WANTLIB when gcc4 is in MODULES; run port-lib-depends-check and if stdc++ is still there, check actual build thoroughly, it's broken port-lib-depends-check says: ... tb-browser-6.0.5(www/tor-browser/browser): Extra: stdc++.57 I built www/firefox-esr to see what port-lib-depends-check says there and it's the same. I take it this is due to the way that Mozilla does dynamic loading and there's nothing to be done about it? This has always been the case for TB but I forgot to ask until now. > Landry Again, thanks a lot for your time. Pax, -A -- http://haqistan.net/~attila | att...@stalphonsos.com | 0x62A729CF tbb605-is.tgz Description: updated tor browser ports
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: d...@cvs.openbsd.org2016/11/12 09:42:24 Modified files: lang/rust : Makefile distinfo lang/rust/patches: patch-configure patch-src_librustdoc_test_rs patch-src_libstd_sys_unix_ext_net_rs patch-src_tools_compiletest_src_runtest_rs lang/rust/pkg : PLIST-doc PLIST-main Log message: Update to rust-1.13.0, from semarie who takes maintainership again ok aja@
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: j...@cvs.openbsd.org2016/11/12 09:29:16 Modified files: net/knot : Makefile Log message: Tell portroach to skip 1.99.1, for it is not an LTS version.
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: ajacou...@cvs.openbsd.org 2016/11/12 09:27:58 Modified files: x11/gnome/builder: Makefile x11/gnome/builder/patches: patch-plugins_terminal_gb-terminal-view_c Added files: x11/gnome/builder/patches: patch-libide_subprocess_ide-subprocess-launcher_c Log message: Sync with what's been committed upstream.
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: ajacou...@cvs.openbsd.org 2016/11/12 09:26:46 Modified files: cad/gtkwave: Makefile distinfo Log message: Update to gtkwave-3.3.78.
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: st...@cvs.openbsd.org 2016/11/12 09:15:31 Modified files: net/wireshark : Makefile net/wireshark/pkg: PLIST-text Log message: Add hidden dep (security/libssh) to Wireshark, noticed by naddy. This enables building sshdump and ciscodump providing an interface to run remote captures.
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: st...@cvs.openbsd.org 2016/11/12 08:55:22 Modified files: lang/lucee : Makefile distinfo Log message: update to Lucee 4.5.3.020
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: st...@cvs.openbsd.org 2016/11/12 08:37:32 Modified files: mail/dovecot : Makefile mail/dovecot/pkg: PLIST-ldap PLIST-server Log message: move include/dovecot/ldap-client.h to PLIST-ldap, reported by brad and dhill, based on a diff from dhill
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: shadc...@cvs.openbsd.org2016/11/12 07:31:53 Modified files: net: Makefile Log message: +py-boto,python3
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: shadc...@cvs.openbsd.org2016/11/12 07:30:41 Modified files: net/py-boto: Makefile net/py-boto/pkg: PLIST Added files: net/py-boto/pkg: PFRAG.no-python3 Log message: Add py3 flavor for py-boto (only package, without utilities) ok ajacoutot@
Re: add py3 flavor for py-boto
On Sat, Nov 12, 2016 at 06:35:56PM +0500, Alexandr Shadchin wrote: > On Fri, Nov 11, 2016 at 01:01:21PM +0100, Antoine Jacoutot wrote: > > On Fri, Nov 11, 2016 at 03:05:14PM +0500, Alexandr Shadchin wrote: > > > On Fri, Nov 11, 2016 at 10:46:16AM +0100, Antoine Jacoutot wrote: > > > > On Fri, Nov 11, 2016 at 02:43:51PM +0500, Alexandr Shadchin wrote: > > > > > Add py3 flavor for py-boto. OK ? > > > > > > > > Hmm, not a super fan of it. > > > > Why is it needed for? > > > > > > > > > > I work on py-pandas. For docs and test need py-boto. > > > > > > It not critical. I just decided to propose. > > > > > > For docs need more depends, which not in tree. > > > I'm inclined to disable the documentation. > > > > > > For test - if not exists py-boto then test will skipped. > > > > I usually don't mind adding python3 FLAVOR to python ports, but I don't > > really like it when they ship utilities and not just libs/modules. > > That's the reason I did not create a sysutils/awscli python3 FLAVOR either. > > Also I'm aware of external scripts using things like s3put... which will > > break if one only installs the python3 FLAVOR. > > > > What I propose you do is to only package the utilities for !python3. > > rm them when building -python3 and add a PFRAG for !python3. > > > > Hope that makes sense ;-) > > > > > > Hmm, but I like this idea :-) > Update diff. Cool, OK aja :-) > -- > Alexandr Shadchin > > Index: Makefile > === > RCS file: /cvs/ports/net/py-boto/Makefile,v > retrieving revision 1.21 > diff -u -p -r1.21 Makefile > --- Makefile 18 Oct 2016 07:26:26 - 1.21 > +++ Makefile 12 Nov 2016 13:28:30 - > @@ -4,7 +4,8 @@ COMMENT= python interface to amazon web > > MODPY_EGG_VERSION= 2.43.0 > DISTNAME=boto-${MODPY_EGG_VERSION} > -PKGNAME= py-${DISTNAME} > +PKGNAME= py-${DISTNAME} > +REVISION=0 > > CATEGORIES= net > > @@ -20,9 +21,12 @@ MODULES= lang/python > MODPY_PI=Yes > MODPY_SETUPTOOLS=Yes > > -RUN_DEPENDS= security/py-paramiko \ > - textproc/py-yaml \ > - www/py-requests > +RUN_DEPENDS= security/py-paramiko${MODPY_FLAVOR} \ > + textproc/py-yaml${MODPY_FLAVOR} \ > + www/py-requests${MODPY_FLAVOR} > + > +FLAVORS= python3 > +FLAVOR?= > > # requires an AWS account > TEST_IS_INTERACTIVE= Yes > Index: pkg/PFRAG.no-python3 > === > RCS file: pkg/PFRAG.no-python3 > diff -N pkg/PFRAG.no-python3 > --- /dev/null 1 Jan 1970 00:00:00 - > +++ pkg/PFRAG.no-python3 12 Nov 2016 13:28:30 - > @@ -0,0 +1,22 @@ > +@comment $OpenBSD$ > +bin/asadmin > +bin/bundle_image > +bin/cfadmin > +bin/cq > +bin/cwutil > +bin/dynamodb_dump > +bin/dynamodb_load > +bin/elbadmin > +bin/fetch_file > +bin/glacier > +bin/instance_events > +bin/kill_instance > +bin/launch_instance > +bin/list_instances > +bin/lss3 > +bin/mturk > +bin/pyami_sendmail > +bin/route53 > +bin/s3put > +bin/sdbadmin > +bin/taskadmin > Index: pkg/PLIST > === > RCS file: /cvs/ports/net/py-boto/pkg/PLIST,v > retrieving revision 1.8 > diff -u -p -r1.8 PLIST > --- pkg/PLIST 20 Mar 2016 11:18:11 - 1.8 > +++ pkg/PLIST 12 Nov 2016 13:28:30 - > @@ -1,25 +1,5 @@ > @comment $OpenBSD: PLIST,v 1.8 2016/03/20 11:18:11 ajacoutot Exp $ > -bin/asadmin > -bin/bundle_image > -bin/cfadmin > -bin/cq > -bin/cwutil > -bin/dynamodb_dump > -bin/dynamodb_load > -bin/elbadmin > -bin/fetch_file > -bin/glacier > -bin/instance_events > -bin/kill_instance > -bin/launch_instance > -bin/list_instances > -bin/lss3 > -bin/mturk > -bin/pyami_sendmail > -bin/route53 > -bin/s3put > -bin/sdbadmin > -bin/taskadmin > +!%%python3%% > lib/python${MODPY_VERSION}/site-packages/boto/ > > lib/python${MODPY_VERSION}/site-packages/boto-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/ > > lib/python${MODPY_VERSION}/site-packages/boto-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/PKG-INFO > @@ -27,816 +7,882 @@ lib/python${MODPY_VERSION}/site-packages > > lib/python${MODPY_VERSION}/site-packages/boto-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/dependency_links.txt > > lib/python${MODPY_VERSION}/site-packages/boto-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/top_level.txt > lib/python${MODPY_VERSION}/site-packages/boto/__init__.py > -lib/python${MODPY_VERSION}/site-packages/boto/__init__.pyc > +${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/boto/${MODPY_PYCACHE}/ > +lib/python${MODPY_VERSION}/site-packages/boto/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc > +lib/python${MODPY_VERSION}/site-packages/boto/${MODPY_PYCACHE}auth.${MODPY_PYC_MAGIC_TAG}pyc >
Re: add py3 flavor for py-boto
On Fri, Nov 11, 2016 at 01:01:21PM +0100, Antoine Jacoutot wrote: > On Fri, Nov 11, 2016 at 03:05:14PM +0500, Alexandr Shadchin wrote: > > On Fri, Nov 11, 2016 at 10:46:16AM +0100, Antoine Jacoutot wrote: > > > On Fri, Nov 11, 2016 at 02:43:51PM +0500, Alexandr Shadchin wrote: > > > > Add py3 flavor for py-boto. OK ? > > > > > > Hmm, not a super fan of it. > > > Why is it needed for? > > > > > > > I work on py-pandas. For docs and test need py-boto. > > > > It not critical. I just decided to propose. > > > > For docs need more depends, which not in tree. > > I'm inclined to disable the documentation. > > > > For test - if not exists py-boto then test will skipped. > > I usually don't mind adding python3 FLAVOR to python ports, but I don't > really like it when they ship utilities and not just libs/modules. > That's the reason I did not create a sysutils/awscli python3 FLAVOR either. > Also I'm aware of external scripts using things like s3put... which will > break if one only installs the python3 FLAVOR. > > What I propose you do is to only package the utilities for !python3. > rm them when building -python3 and add a PFRAG for !python3. > > Hope that makes sense ;-) > > Hmm, but I like this idea :-) Update diff. -- Alexandr Shadchin Index: Makefile === RCS file: /cvs/ports/net/py-boto/Makefile,v retrieving revision 1.21 diff -u -p -r1.21 Makefile --- Makefile18 Oct 2016 07:26:26 - 1.21 +++ Makefile12 Nov 2016 13:28:30 - @@ -4,7 +4,8 @@ COMMENT=python interface to amazon web MODPY_EGG_VERSION= 2.43.0 DISTNAME= boto-${MODPY_EGG_VERSION} -PKGNAME= py-${DISTNAME} +PKGNAME= py-${DISTNAME} +REVISION= 0 CATEGORIES=net @@ -20,9 +21,12 @@ MODULES= lang/python MODPY_PI= Yes MODPY_SETUPTOOLS= Yes -RUN_DEPENDS= security/py-paramiko \ - textproc/py-yaml \ - www/py-requests +RUN_DEPENDS= security/py-paramiko${MODPY_FLAVOR} \ + textproc/py-yaml${MODPY_FLAVOR} \ + www/py-requests${MODPY_FLAVOR} + +FLAVORS= python3 +FLAVOR?= # requires an AWS account TEST_IS_INTERACTIVE= Yes Index: pkg/PFRAG.no-python3 === RCS file: pkg/PFRAG.no-python3 diff -N pkg/PFRAG.no-python3 --- /dev/null 1 Jan 1970 00:00:00 - +++ pkg/PFRAG.no-python312 Nov 2016 13:28:30 - @@ -0,0 +1,22 @@ +@comment $OpenBSD$ +bin/asadmin +bin/bundle_image +bin/cfadmin +bin/cq +bin/cwutil +bin/dynamodb_dump +bin/dynamodb_load +bin/elbadmin +bin/fetch_file +bin/glacier +bin/instance_events +bin/kill_instance +bin/launch_instance +bin/list_instances +bin/lss3 +bin/mturk +bin/pyami_sendmail +bin/route53 +bin/s3put +bin/sdbadmin +bin/taskadmin Index: pkg/PLIST === RCS file: /cvs/ports/net/py-boto/pkg/PLIST,v retrieving revision 1.8 diff -u -p -r1.8 PLIST --- pkg/PLIST 20 Mar 2016 11:18:11 - 1.8 +++ pkg/PLIST 12 Nov 2016 13:28:30 - @@ -1,25 +1,5 @@ @comment $OpenBSD: PLIST,v 1.8 2016/03/20 11:18:11 ajacoutot Exp $ -bin/asadmin -bin/bundle_image -bin/cfadmin -bin/cq -bin/cwutil -bin/dynamodb_dump -bin/dynamodb_load -bin/elbadmin -bin/fetch_file -bin/glacier -bin/instance_events -bin/kill_instance -bin/launch_instance -bin/list_instances -bin/lss3 -bin/mturk -bin/pyami_sendmail -bin/route53 -bin/s3put -bin/sdbadmin -bin/taskadmin +!%%python3%% lib/python${MODPY_VERSION}/site-packages/boto/ lib/python${MODPY_VERSION}/site-packages/boto-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/ lib/python${MODPY_VERSION}/site-packages/boto-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/PKG-INFO @@ -27,816 +7,882 @@ lib/python${MODPY_VERSION}/site-packages lib/python${MODPY_VERSION}/site-packages/boto-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/dependency_links.txt lib/python${MODPY_VERSION}/site-packages/boto-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info/top_level.txt lib/python${MODPY_VERSION}/site-packages/boto/__init__.py -lib/python${MODPY_VERSION}/site-packages/boto/__init__.pyc +${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/boto/${MODPY_PYCACHE}/ +lib/python${MODPY_VERSION}/site-packages/boto/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc +lib/python${MODPY_VERSION}/site-packages/boto/${MODPY_PYCACHE}auth.${MODPY_PYC_MAGIC_TAG}pyc +lib/python${MODPY_VERSION}/site-packages/boto/${MODPY_PYCACHE}auth_handler.${MODPY_PYC_MAGIC_TAG}pyc +lib/python${MODPY_VERSION}/site-packages/boto/${MODPY_PYCACHE}compat.${MODPY_PYC_MAGIC_TAG}pyc +lib/python${MODPY_VERSION}/site-packages/boto/${MODPY_PYCACHE}connection.${MODPY_PYC_MAGIC_TAG}pyc +lib/python${MODPY_VERSION}/site-packages/boto/${MODPY_PYCACHE}exception.${MODPY_PYC_MAGIC_TAG}pyc
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: j...@cvs.openbsd.org2016/11/12 03:33:04 Modified files: devel/boehm-gc : Makefile distinfo devel/boehm-gc/patches: patch-include_private_gcconfig_h devel/boehm-gc/pkg: PLIST-main Log message: Update to gc-7.6.0 and libatomic_ops-7.4.4 Maintenance only update for libatomic_ops. Bulk build and ok ajacoutot@
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: ajacou...@cvs.openbsd.org 2016/11/12 03:32:28 Modified files: meta/gnome : Makefile meta/gnome/pkg : README-main Log message: Extend GDM configuration and add a note that changing the GDM kbd layout is not possible due to the lack of systemd-localed support.
Re: [update] lang/rust 1.13.0
On Sat, 12 Nov 2016 10:00:45 +0100, Sebastien Mariewrote: > Here an update for lang/rust to 1.13.0 It's ok danj@ (I'm not really quick, I got premium access to the diff ;)). Cheers, Daniel
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: lan...@cvs.openbsd.org 2016/11/12 01:53:11 Modified files: devel/cargo: Makefile Log message: Mark temporarly BROKEN, crates.io requires Accept: HTTP header, cf https://github.com/rust-lang/crates.io/issues/466
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: ajacou...@cvs.openbsd.org 2016/11/12 01:41:38 Modified files: sysutils/awscli: Makefile distinfo Log message: Update to awscli-1.11.14.
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: ajacou...@cvs.openbsd.org 2016/11/12 01:41:22 Modified files: net/py-botocore: Makefile distinfo Log message: Update to py-botocore-1.4.71.
CVS: cvs.openbsd.org: ports
CVSROOT:/cvs Module name:ports Changes by: ajacou...@cvs.openbsd.org 2016/11/12 01:32:48 Modified files: graphics/graphite2: Makefile distinfo Log message: Update to graphite2-1.3.9.