biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage
UPDATING: document SeqAn updates and seqan1 port for legacy usage
PR: 204127
Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
Due to questionable c++, GCC 4.9 and newer cannot build seqan. An update
has been in the works that will enable clang compilers and all versions
of GCC to build seqan, but it is not quite ready yet. While waiting for
it, limit the version of GCC used to 4.8.
PR: 196851
GCC 4.6.4 to GCC 4.7.3. This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.
Part II, Bump PORTREVISIONs.
PR: 182136
Supported by: Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by: bdrewery (two -exp runs)
- Switched to automake 1.11.6, see CVE-2012-3386.
- #14669: Fixed extraction of CC from gmp.h.
- Fixed case of intermediate zero real or imaginary part in mpc_fma,
found by hydra with GMP_CHECK_RANDOMIZE=1346362345.
This is on top of the following changes from version 1.0
- Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
invariant sections) for the documentation.
- 100% of all lines are covered by tests
- Renamed functions
. mpc_mul_2exp to mpc_mul_2ui
. mpc_div_2exp to mpc_div_2ui
- 0^0, which returned (NaN,NaN) previously, now returns (1,+0).
- Removed compatibility with K&R compilers, which was untestable due
to lack of such compilers.
- New functions
. mpc_log10
. mpc_mul_2si, mpc_div_2si
- Speed-ups
. mpc_fma
- Bug fixes
. mpc_div and mpc_norm now return a value indicating the effective
rounding direction, as the other functions.
. mpc_mul, mpc_sqr and mpc_norm now return correct results even if
there are over- or underflows during the computation.
. mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has
infinite part and equals output variable is corrected.
. mpc_fr_sub: Wrong return value for imaginary part is corrected.
Convert to the new LIB_DEPENDS standard and remove hard-coded
.so versions from a couple of dependent ports.
Bump PORTREVISIONS of all dependent ports.
PR: 183141
Approved by: portmgr (bdrewery)
Right now this is a noop in the former case and a noop in the latter
case unless lang/gcc44 has been installed explicitly.
This puts a bit more emphasis on standardizing on a canonical version
"current" GCC and makes it easier to update that canonical version
by changing the default in Mk/bsd.gcc.mk and updating the lang/gcc port.
That is, USE_GCC=yes means "use a decent/modern version of GCC" without
having to worry about details.
Approved by: portmgr (bdrewery)
and data structures for the analysis of sequences with the
focus on biological data. The library is licensed under the
3-clause BSD license except the applications which are GPL.
WWW: http://www.seqan.de/
PR: 167571
Submitted by: Hannes <h2+fbsdports@fsfe.org>
