lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms), part II.
The first part covered ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.
This adds ports with USES=fortran and ports using Mk/bsd.octave.mk
which in turn has USES=fortran.
PR: 214965
Reported by: thierry
The only reason to use post-stage is because the port needs to do
"things" at a later time, like some plist manipulation.
While there, fold post-install in do-install targets when they are
defined.
PR: 214780
Submitted by: mat
Exp-run by: antoine
Sponsored by: Absolight
Correct LICENSE and set LICENSE_FILE
Upstream changelog:
- support for gzip compressed files containing multiple gzip streams
- support for the BLAST pairwise format (option -f 0)
- slightly improved sensitivity
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D8652
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms).
In particular that is ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.
- Blixem: Features can now be added to multiple different groups/filters.
- Belvu: Fix a problem where column highlighting can get out of sync
with the text.
- Update to version 4.9c
- Set LICENSE=GPLv3
- Use the variable PORTDOCS to automate the generation of the DOCS plist (as
suggested by mat@).
- Install dat/ examples/ and Technical/ directories as well as files in the root
directory of the distribution tarball.
- Fix broken permissions.
- Delete Windows executables.
- Build and install useful binaries not built by upstream's Makefile.
- Update pkg-descr.
Reviewed by: swills (mentor)
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8040
- If a port has another upstream, remove GOOGLE_CODE
- If a port only has GOOGLE_CODE mark it BROKEN
Some ports have a local mirror configured but for security reasons, it
is not considered upstream.
Sponsored by: Absolight
hide actual commands executed and only show short summary line (like
"CC foo.c"). CMake and ninja enable this by default, some autotools
using ports do as well. This is unacceptable because we need complete
build logs at any time, so we now switch to verbose build logs
unconditionally. Note that this change deliberately affects ALL
builds and not only package builds on cluster, because we need to
be sure that user experiencing failure can always provide informative
build log regardless of settings and without rerunning the build.
Change summary:
- Always do verbose builds for cmake, ninja and GNU configure (the
latter includes check if --disable-silent-rules is actually supported
by the configure script; there are isolated cases when it's not true)
- Remove CMAKE_VERBOSE, NINJA_VERBOSE and
CONFIGURE_ARGS=--disable-silent-rules from all ports which set them
for this is no longer needed
- Revert hacks for --disable-silent-rules support priorly committed
to biology/ncbi-blast+ and net-p2p/mldonkey - no longer needed as well
Submitted by: amdmi3
Reviewed by: mat
Exp-run by: antoine
Approved by: portmgr (mat, antoine)
Differential Revision: D7534
Mk/Uses/linux.mk.
- Replace USE_LINUX=yes with USES+=linux and USE_LINUX=(.*) with
USES+=linux:\1 in all ports.
- Replace USE_LINUX_APPS with USE_LINUX in all ports.
- Use INSTALL_SCRIPT instead of INSTALL_PROGRAM to install scripts in some
ports.
- When USE_LINUX_RPM is defined, simplify the way DISTFILES and EXTRACT_ONLY
are defined.
- Remove BRANDELF_DIRS and BRANDELF_FILES handling. In the very rare cases
that it is still necessary ports can run ${BRANDELF} from post-patch.
- Remove AUTOMATIC_PLIST handling. Only one port used it.
- Fix Linux MASTER_SITES.
- Replace OVERRIDE_LINUX_BASE_PORT and OVERRIDE_LINUX_NONBASE_PORTS with
default versions framework.
- bsd.port.mk:
- Move Linux related bits to Uses/linux.mk, except USE_LINUX_PREFIX.
- Put USE_LINUX_PREFIX handling after USES processing.
- Define DOCSDIR, DATADIR, etc. after handling USE_LINUX_PREFIX so it can
give these variables a different default value.
- When a package needs to run Linux ldconfig check before installation if
Linux support is enabled.
- emulators/linux_base-*:
- Use USES=linux and remove duplication.
- Remove files/lp. FreeBSD or CUPS lp(1) should work.
- Remove files/yp.conf. No longer seems to be used.
- Remove pkg-deinstall and move pkg-install into pkg-plist.
- Update pkg-descr and pkg-message.
- Fix handling of ldconfig cache in pkg-plist.
- devel/fb-adb: Use a Linux shell to run a Linux script but patch the script
to use FreeBSD mkdir so mkdir -p $path creates $path and not
/compat/linux/$path.
PR: 211645
Exp-run by: antoine
Approved by: portmgr (antoine)
- Adds editable text fields that are longer than the visible string
and introduces a new way of selecting a range of amino acids.
- introduces interfaces to the open source packages openbabel and pharmer.
Openbabel is used to create 2D images of the molecules in a .sdf
file. It is also used to do 2D fingerprint searching.
Pharmer is used to pharmacophore (3D) searching against indexed
databases of .sdf files.
- Regenerate patches with `make makepatch`
- Mark WXGTK option broken: does not build: src/convErr/gc_errhandling.cpp:75:12: error: cannot initialize return object of type 'const char *' with an rvalue of type 'const wxChar *' (aka 'const wchar_t *')
