FreshPorts -- science/openbabel: Chemical toolbox designed to speak the many languages of chemical data

openbabel
ABI	latest	quarterly
FreeBSD:11:aarch64	2.4.1_1	2.4.1_5
FreeBSD:11:amd64	3.1.1	2.4.1_6
FreeBSD:11:armv6	2.3.2_2	-
FreeBSD:11:i386	3.1.1	2.4.1_6
FreeBSD:11:mips	2.3.2_2	-
FreeBSD:11:mips64	-	-
FreeBSD:12:aarch64	2.4.1_1	-
FreeBSD:12:amd64	3.1.1	2.4.1_6
FreeBSD:12:armv6	2.4.1_1	-
FreeBSD:12:armv7	2.4.1_1	-
FreeBSD:12:i386	3.1.1	2.4.1_6
FreeBSD:12:mips	-	-
FreeBSD:12:mips64	-	-
FreeBSD:12:powerpc64	-	2.4.1_6
FreeBSD:13:aarch64	-	-
FreeBSD:13:amd64	3.1.1	-
FreeBSD:13:armv6	-	-
FreeBSD:13:armv7	-	-
FreeBSD:13:i386	3.1.1	-
FreeBSD:13:mips	-	-
FreeBSD:13:mips64	-	-
FreeBSD:13:powerpc64	-	-

- Upgrade math/eigen3 to 3.3.8; - Add some dependencies which might be detected by Find_Package but not registered; - Bump PORTREVISION of consumers. PR: 250833 Submitted by: /me Approved by: tcberner@ (KDE / maintainer) + exp-run

Bump PORTREVISION for ports depending on the canonical version of GCC as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3 to GCC 9.1 under most circumstances now after revision 507371. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, everything INDEX-11 shows with a dependency on lang/gcc9 now. PR: 238330

Prepare for powerpc-on-clang by deleting hard-coded tests for libstdc++.so as a stand-in for "are we running on gcc". For people already testing powerpc on clang, it is possible that they already have both compilers in base. Thus, the assumption that "gcc is in base" (e.g. libstdc++.so exists) always means "force use of GCC" is already broken. It will be for everyone on -CURRENT once the switch is made. While here, standardize on compiler:c++11-lang instead of -lib (they are equivalent these days), pet portlint, and do some other cleanup. Approved by: portmgr (tier-2 blanket)

Change cmake default behaviour to outsource. Ports that build out of source now simply can use "USES=cmake" instead of "USES=cmake:outsource". Ports that fail to build out of source now need to specify "USES=cmake:insource". I tried to only set insource where explictely needed. PR: 232038 Exp-run by: antoine

Bump PORTREVISION for ports depending on the canonical version of GCC defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t GCC 8.2 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, as a double check, everything INDEX-11 showed depending on lang/gcc7. PR: 231590

New USES=eigen Usage: USES=eigen:<version>[,<type>] version: 2 or 3 (required) type: build (default), run For example: USES=eigen:2,build,run will add a BUILD- and RUN_DEPENDS on math/eigen2, and USES=eigen:3 will add a BUILD_DEPENDS on math/eigen3. * Convert the existing ports to use it - biology/iqtree: remove run time dependency (seemed not to be needed) - graphics/movit: remove run time dependency (seemed not to be needed) - science/avogadro: add run time dependeny (installed cmake file requires it to be present) Reviewed by: rakuco, mat Differential Revision: https://reviews.freebsd.org/D13702

science/openbabel: Update to 2.4.1 Patches removed: patch-git_c3abbdda, patch-gcc5-support (Integrated upstream) patch-scripts__CMakeLists.txt (Builds without it) While here, set LICENSE and simplify BUILD_DEPENDS. Changes: https://github.com/openbabel/openbabel/releases PR: 219382 Submitted by: Yuri Victorovich <yuri@rawbw.com> Approved by: garga (mentor) Differential Revision: https://reviews.freebsd.org/D10837

Reassign makc's ports back to the pool. See "Maintainer Reset" in https://www.freebsd.org/portmgr/policies_contributors.html. makc's last commit was in March 31st (r412218), and his ports have been timing out since at least July (r418155). I also emailed him 2 weeks ago and have received no response so far.

science/openbabel: Support gcc5 (taken from upstream) This was really painful. I consolidated numerous shared_ptr (TR1) patches to a single big patch (including moving part of an existing patch to it because the target needed yet another change). Tested on FreeBSD 8/i386 and FreeBSD 10/amd64. This was previously built on DragonFly with gcc 4.7, but libstdc++ incompatibilities caused avogadro to break which eventually broken kde4 metapackage. Those openbabel guys are long overdue for a new release, this was a bit absurd although maybe some clever sed'ding could have reduced the patch count. Approved by: blanket (gcc5 & DF breakage)

The FreeBSD x11@ and graphics team proudly presents a zeising, kwm production, with help from dumbbell, bdrewery: NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE This update switches over to use the new xorg stack by default on FreeBSD 9 and 10 stable, on osversions where vt(9) is available. It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in /etc/make.conf . FreeBSD 8-STABLE and released versions of FreeBSD still use the old version. A package repository with binary packages for new xorg will be available soon. This patch also contains updates of libxcb and related ports, pixman, as well

science/openbabel: - Update openbabel to 2.3.2 - Switch to CMake build system - Add PYTHON and CAIRO options - Don't rename babel binary, mark conflict with ancient biology/babel science/py-openbabel: - Merge py-openbabel to openbabel other: - chase openbabel update

-Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22. -Update libtool and libltdl to 2.2.6a. -Remove devel/libtool15 and devel/libltdl15. -Fix ports build with libtool22/libltdl22. -Bump ports that depend on libltdl22 due to shared library version change. -Explain what to do update in the UPDATING. It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop and applications in the runtime. With help: marcus and kwm Pointyhat-exp: a few times by pav Tested by: pgollucci, "Romain TartiÃ¨re" <romain@blogreen.org>, and a few MarcusCom CVS users. Also, I might have missed a few. Repocopy by: marcus Approved by: portmgr

- Update boost to 1.39 - Split boost port to separate components, with boost-all metaport PR: ports/137054 Submitted by: Alexander Churanov <churanov.port.maintainer@gmail.com> (maintainer)

- Set --mandir and --infodir in CONFIGURE_ARGS if the configure script supports them. This is determined by running ``configure --help'' in do-configure target and set the shell variable _LATE_CONFIGURE_ARGS which is then passed to CONFIGURE_ARGS. - Remove --mandir and --infodir in ports' Makefile where applicable Few ports use REINPLACE_CMD to achieve the same effect, remove them too. - Correct some manual pages location from PREFIX/man to MANPREFIX/man - Define INFO_PATH where necessary - Document that .info files are installed in a subdirectory relative to PREFIX/INFO_PATH and slightly change add-plist-info to use INFO_PATH and subdirectory detection. PR: ports/111470 Approved by: portmgr Discussed with: stas (Mk/*), gerald (info related stuffs) Tested by: pointyhat exp run

- s,INSTALLS_SHLIB,USE_LDCONFIG,g - these include misc/ multimedia/ net/ net-mgmt/ net-im/ net-p2p/ palm/ print/ science/ maintained by ports@ PR: ports/101916 Submitted by: Gea-Suan Lin <gslin_AT_gslin dot org>

Mass-conversion to the USE_AUTOTOOLS New World Order. The code present in bsd.autotools.mk essentially makes this a no-op given that all the old variables set a USE_AUTOTOOLS_COMPAT variable, which is parsed in exactly the same way as USE_AUTOTOOLS itself. Moreover, USE_AUTOTOOLS has already been extensively tested by the GNOME team -- all GNOME 2.12.x ports use it. Preliminary documentation can be found at: http://people.FreeBSD.org/~ade/autotools.txt which is in the process of being SGMLized before introduction into the Porters Handbook. Light blue touch-paper. Run.

science/openbabel and biology/babel binary names conflict renamed the binaries and manpages of science/openbabel to openbabel instead of babel. PR: ports/47109 Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>

Current status