1.72 2016-09-02 06:50:53-05:00 America/Chicago
* Full release (no changes from 1.71 beyond version)
1.71 2016-09-01 22:57:25-05:00 America/Chicago (TRIAL RELEASE)
* Minor bump for impending BioPerl 1.7 release.
* #2 : 'Unescaped left brace in regex is deprecated' with newer versions of perl
fixed [fjossandon]
Add p5-Text-Diff as test dependency.
1.7.2 - "Entebbe"
[Bugs]
* #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
* #245 - Code coverage fixes [zmughal,cjfields]
* #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
* #238 - Use a Travis cron job for network tests [zmughal,cjfields]
* #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
* #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
* #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
* #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
* #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
* #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
* #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
* #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
[Code changes]
* PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
MASTER_SITES= site1 \
site2
style continuation lines to be simple repeated
MASTER_SITES+= site1
MASTER_SITES+= site2
lines. As previewed on tech-pkg. With thanks to rillig for fixing pkglint
accordingly.
Upstream changes:
1.7.1 - "Election"
[Bugs]
* Minor release to incorporate fix for CPAN indexing, which
prevented proper updates [cjfields]
* Fix problem in managing Target attribute for gff3 [Jukes34]
* Minor bug fixes related to NCBI HTTPS support [cjfields]
1.7.0 - "Disney"
[New site]
* We have migrated to Github Pages. This was actually planned, but the
recent OBF server compromise forced our hand.
Brian Osborne [bosborne] took this under his wing to move docs and has
done a tremendous amount of work formatting the site and working out some
of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
Cantalupo and Franscison Ossandon also helped. Kudos!!
* Similarly, the official issue tracker is now Github Issues. This has
been updated in the relevant documentation bits (we hope!)
[Code changes]
* Previously deprecated modules removed
* Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
* Bio::DB::SeqHound has been removed due to the service no longer being
available
* Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
reasons due to the server no longer having a valid cert
* Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
* Bio::Coordinate, Bio::SearchIO::blastxml,
Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
added on CPAN
[New features]
* Docker instances of tagged releases are available! [hlapp]
* NCBI HTTPS support [mjohnson and others]
* Bio::SearchIO::infernal
- Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
* Bio::Search::HSP::ModelHSP
- Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
reports [pcantalupo]
* Bio::Search::Result::INFERNALResult
- Added new module to represent features of Infernal reports [pcantalupo]
* Bio::DB::Taxonomy SQLite option [cjfields]
* WrapperBase quoted option values [majensen]
* Various documentation fixes and updates [bosborne]
[Bug Fixes]
* Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
* Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
* NeXML parser fixes [fjossandon]
* Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
* RT 103272 : SeqFeature database deletion skipped features with a decimal -
Joshua Fortriede (Xenbase)
* RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
* Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
* Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
* Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
* Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
* Issue #84: EMBL format wrapping problem [nyamned]
* Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
* Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
or compiled C code (when Inline::C is installed) [rocky]
* Fix various Bio::Tools::Analysis remote server config problems [cjfields]
* Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
* Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
* For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
to be consistent with "$hit->bits" behaviour [fjossandon]
* Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
aminoacids made "next_seq" confused and broke the parser [fjossandon]
* Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
to "complement(join(A..B,C..D))" [fjossandon]
* For the many many many fixes that weren't mentioned - blame the release guy!
1. Compile C code with the C compiler, not the fortran compiler.
2. Use f2c, not g95, as the fortran compiler.
XXX This package builds only with f2c, not g95.
XXX There does not appear to be any way to specify this other
XXX than by abusively setting PKGSRC_FORTRAN. So do that for now.
Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden). Existing SHA1
digests retained for now as an audit trail.
Packaged in pkgsrc-wip by Jason Bacon.
BWA is a software package for mapping low-divergent sequences against a large
reference genome, such as the human genome.
Gabedit is a graphical user interface to computational chemistry
packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC,
OpenMopac, Orca, PCGamess and Q-Chem.
It can display a variety of calculation results including
support for most major molecular file formats.
The advanced "Molecule Builder" allows to rapidly sketch in
molecules and examine them in 3D. Graphics can be exported to
various formats, including animations.
Major features
* Gabedit can create input file for GAMESS(US), GAUSSIAN,
MOLCAS, MOLPRO , MPQC, OpenMopac, Orca, PCGamess and Q-Chem.
* Gabedit can graphically display a variety of Gamess-US,
Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess,
Q-Chem, (partially) ErgoSCF and (partially) ADF calculation
results, including the following:
+ Molecular orbitals.
+ Surfaces from the electron density, electrostatic
potential, NMR shielding density, and other properties.
+ Surfaces may be displayed in solid, translucent and wire
mesh modes. they are can be colorcoded by a separate property.
+ Contours (colorcoded), Planes colorcoded, Dipole. XYZ axes
and the principal axes of the molecule.
+ Animation of the normal modes corresponding to vibrational
frequencies.
+ Animation of the rotation of geometry, surfaces, contours,
planes colorcoded, xyz and the principal axes of the molecule.
+ Animation of contours, Animation of planes colorcoded.
* Gabedit can display UV-Vis, IR and Raman computed spectra.
* Gabedit can generate a povray file for geometry (including
hydrogen's bond),surfaces (including colorcoded surfaces),
contours, planes colorcoded.
* Gabedit can save picture in BMP, JPEG, PNG, PPM and PS format.
* Gabedit can generate automatically a series of pictures
for animation (vibration, geometry convergence, rotation, contours,
planes colorcoded).
* Simulated Annealing with Molecular Dynamics is implemented in Gabedit
(using Amber 99 molecular mechanics parameters).
{perl>=5.16.6,p5-ExtUtils-ParseXS>=3.15}:../../devel/p5-ExtUtils-ParseXS
since pkgsrc enforces the newest perl version anyway, so they
should always pick perl, but sometimes (pkg_add) don't due to the
design of the {,} syntax.
No effective change for the above reason.
Ok joerg
