[med-svn] [libtfbs-perl] branch master updated (423a8a0 -> a77924a)
Charles Plessy
plessy at moszumanska.debian.org
Sat Oct 21 02:48:16 UTC 2017
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository libtfbs-perl.
from 423a8a0 Upload to unstable
new 7ac36df Stop repacking upstream sources, that are cleaner.
new 16bdbb0 New upstream version 0.7.1
new 4eac69b Merge tag 'upstream/0.7.1'
new 26ca40e Add upstream's notice of deprecation to the package's description.
new fb6026d Refresh spelling error patch.
new fc8a912 Remove cruft Makefiles at build time.
new 392d4ec Conforms to Policy version 4.1.1.
new a77924a libtfbs-perl (0.7.1-1) unstable; urgency=medium
The 8 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
Changes | 1 +
License | 2 +
Ext/MYMETA.json => MYMETA.json | 4 +-
Ext/MYMETA.yml => MYMETA.yml | 4 +-
Ext/Makefile => Makefile | 704 +++++++++++++++------
Ext/Makefile.old => Makefile.old | 701 ++++++++++++++------
README | 154 -----
README.md | 117 ++++
TFBS/DB/JASPAR.pm | 8 +-
TFBS/DB/JASPAR2.pm | 2 +-
TFBS/DB/JASPAR4.pm | 4 +-
TFBS/DB/JASPAR5.pm | 2 +-
TFBS/DB/JASPAR6.pm | 2 +-
TFBS/DB/{JASPAR.pm => JASPAR7.pm} | 0
TFBS/DB/LocalTRANSFAC.pm | 2 +-
TFBS/DB/TRANSFAC.pm | 2 +-
TFBS/Matrix/Alignment.pm | 6 +-
TFBS/Matrix/ICM.pm | 2 +-
TFBS/Matrix/PWM.pm | 4 +-
TFBS/Matrix/_Alignment.pm | 2 +-
TFBS/MatrixSet.pm | 8 +-
TFBS/PatternGen.pm | 2 +-
TFBS/PatternGen/Elph.pm | 2 +-
TFBS/PatternGen/Gibbs.pm | 2 +-
TFBS/PatternGen/MEME.pm | 2 +-
TFBS/PatternGenI.pm | 2 +-
TFBS/Run/ConservationProfileGenerator.pm | 4 +-
TFBS/_Iterator/_MatrixSetIterator.pm | 54 +-
TFBS/_Iterator/_SiteSetIterator.pm | 14 +-
Ext/pm_to_blib => blib/arch/.exists | 0
Ext/pm_to_blib => blib/arch/auto/TFBS/.exists | 0
.../arch/auto/TFBS/Ext/pwmsearch/.exists | 0
.../arch/auto/TFBS/Ext/pwmsearch}/pwmsearch.bs | 0
blib/arch/auto/TFBS/Ext/pwmsearch/pwmsearch.bundle | Bin 0 -> 50652 bytes
Ext/pm_to_blib => blib/bin/.exists | 0
Ext/pm_to_blib => blib/lib/.exists | 0
{TFBS => blib/lib/TFBS}/DB.pm | 0
{TFBS => blib/lib/TFBS}/DB/FlatFileDir.pm | 9 +-
{TFBS => blib/lib/TFBS}/DB/JASPAR2.pm | 2 +-
{TFBS => blib/lib/TFBS}/DB/JASPAR4.pm | 10 +-
{TFBS => blib/lib/TFBS}/DB/LocalTRANSFAC.pm | 2 +-
{TFBS => blib/lib/TFBS}/DB/TRANSFAC.pm | 4 +-
Ext/pm_to_blib => blib/lib/TFBS/Ext/.exists | 0
{Ext => blib/lib/TFBS/Ext}/pwmsearch.pm | 0
{TFBS => blib/lib/TFBS}/Matrix.pm | 128 +---
{TFBS => blib/lib/TFBS}/Matrix/ICM.pm | 486 +++-----------
{TFBS => blib/lib/TFBS}/Matrix/PFM.pm | 0
{TFBS => blib/lib/TFBS}/Matrix/PWM.pm | 4 +-
{TFBS => blib/lib/TFBS}/Matrix/_Alignment.pm | 2 +-
{TFBS => blib/lib/TFBS}/MatrixSet.pm | 375 +----------
{TFBS => blib/lib/TFBS}/PatternGen.pm | 4 +-
{TFBS => blib/lib/TFBS}/PatternGen/AnnSpec.pm | 141 ++---
.../lib/TFBS}/PatternGen/AnnSpec/Motif.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/Elph.pm | 2 +-
{TFBS => blib/lib/TFBS}/PatternGen/Elph/Motif.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/Gibbs.pm | 2 +-
{TFBS => blib/lib/TFBS}/PatternGen/Gibbs/Motif.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/MEME.pm | 2 +-
{TFBS => blib/lib/TFBS}/PatternGen/MEME/Motif.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/Motif/Matrix.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/Motif/Word.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/SimplePFM.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/YMF.pm | 0
{TFBS => blib/lib/TFBS}/PatternGen/YMF/Motif.pm | 0
{TFBS => blib/lib/TFBS}/PatternGenI.pm | 2 +-
{TFBS => blib/lib/TFBS}/PatternI.pm | 0
{TFBS => blib/lib/TFBS}/Site.pm | 0
{TFBS => blib/lib/TFBS}/SitePair.pm | 13 +-
{TFBS => blib/lib/TFBS}/SitePairSet.pm | 0
{TFBS => blib/lib/TFBS}/SiteSet.pm | 0
{TFBS => blib/lib/TFBS}/Tools/SetOperations.pm | 0
{TFBS => blib/lib/TFBS}/Word.pm | 0
{TFBS => blib/lib/TFBS}/Word/Consensus.pm | 0
{TFBS => blib/lib/TFBS}/_Iterator.pm | 0
.../lib/TFBS}/_Iterator/_MatrixSetIterator.pm | 0
.../lib/TFBS}/_Iterator/_SiteSetIterator.pm | 0
Ext/pm_to_blib => blib/lib/auto/TFBS/.exists | 0
.../lib/auto/TFBS/Ext/pwmsearch/.exists | 0
{Ext => blib}/lib/pwm_search.h | 0
{Ext => blib}/lib/pwm_searchPFF.c | 0
Ext/pm_to_blib => blib/man1/.exists | 0
Ext/pm_to_blib => blib/man3/.exists | 0
blib/man3/TFBS::DB::FlatFileDir.3pm | 299 +++++++++
blib/man3/TFBS::DB::JASPAR2.3pm | 476 ++++++++++++++
blib/man3/TFBS::DB::JASPAR4.3pm | 392 ++++++++++++
blib/man3/TFBS::DB::LocalTRANSFAC.3pm | 221 +++++++
blib/man3/TFBS::DB::TRANSFAC.3pm | 232 +++++++
blib/man3/TFBS::Ext::pwmsearch.3pm | 155 +++++
blib/man3/TFBS::Matrix.3pm | 214 +++++++
blib/man3/TFBS::Matrix::ICM.3pm | 350 ++++++++++
blib/man3/TFBS::Matrix::PFM.3pm | 413 ++++++++++++
blib/man3/TFBS::Matrix::PWM.3pm | 370 +++++++++++
blib/man3/TFBS::MatrixSet.3pm | 298 +++++++++
blib/man3/TFBS::PatternGen.3pm | 175 +++++
blib/man3/TFBS::PatternGen::AnnSpec.3pm | 185 ++++++
blib/man3/TFBS::PatternGen::AnnSpec::Motif.3pm | 153 +++++
blib/man3/TFBS::PatternGen::Elph.3pm | 190 ++++++
blib/man3/TFBS::PatternGen::Elph::Motif.3pm | 152 +++++
blib/man3/TFBS::PatternGen::Gibbs.3pm | 191 ++++++
blib/man3/TFBS::PatternGen::Gibbs::Motif.3pm | 169 +++++
blib/man3/TFBS::PatternGen::MEME.3pm | 188 ++++++
blib/man3/TFBS::PatternGen::MEME::Motif.3pm | 152 +++++
blib/man3/TFBS::PatternGen::SimplePFM.3pm | 180 ++++++
blib/man3/TFBS::PatternGen::YMF.3pm | 188 ++++++
blib/man3/TFBS::PatternGen::YMF::Motif.3pm | 152 +++++
blib/man3/TFBS::PatternI.3pm | 206 ++++++
blib/man3/TFBS::Site.3pm | 284 +++++++++
blib/man3/TFBS::SitePair.3pm | 162 +++++
blib/man3/TFBS::SitePairSet.3pm | 241 +++++++
blib/man3/TFBS::SiteSet.3pm | 232 +++++++
blib/man3/TFBS::Word.3pm | 161 +++++
blib/man3/TFBS::Word::Consensus.3pm | 233 +++++++
Ext/pm_to_blib => blib/script/.exists | 0
debian/changelog | 11 +
debian/control | 6 +-
debian/copyright | 12 -
debian/patches/spelling-errors.patch | 141 +----
debian/rules | 3 +
debian/watch | 3 +-
Ext/pm_to_blib => pm_to_blib | 0
pod2htmd.tmp | 52 --
121 files changed, 8460 insertions(+), 1783 deletions(-)
create mode 100644 License
copy Ext/MYMETA.json => MYMETA.json (93%)
copy Ext/MYMETA.yml => MYMETA.yml (91%)
copy Ext/Makefile => Makefile (52%)
copy Ext/Makefile.old => Makefile.old (53%)
delete mode 100644 README
create mode 100644 README.md
copy TFBS/DB/{JASPAR.pm => JASPAR7.pm} (100%)
copy Ext/pm_to_blib => blib/arch/.exists (100%)
copy Ext/pm_to_blib => blib/arch/auto/TFBS/.exists (100%)
copy Ext/pm_to_blib => blib/arch/auto/TFBS/Ext/pwmsearch/.exists (100%)
copy {Ext => blib/arch/auto/TFBS/Ext/pwmsearch}/pwmsearch.bs (100%)
create mode 100755 blib/arch/auto/TFBS/Ext/pwmsearch/pwmsearch.bundle
copy Ext/pm_to_blib => blib/bin/.exists (100%)
copy Ext/pm_to_blib => blib/lib/.exists (100%)
copy {TFBS => blib/lib/TFBS}/DB.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/DB/FlatFileDir.pm (98%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/DB/JASPAR2.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/DB/JASPAR4.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/DB/LocalTRANSFAC.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/DB/TRANSFAC.pm (98%)
mode change 100755 => 100644
copy Ext/pm_to_blib => blib/lib/TFBS/Ext/.exists (100%)
copy {Ext => blib/lib/TFBS/Ext}/pwmsearch.pm (100%)
copy {TFBS => blib/lib/TFBS}/Matrix.pm (72%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Matrix/ICM.pm (59%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Matrix/PFM.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Matrix/PWM.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Matrix/_Alignment.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/MatrixSet.pm (59%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen.pm (97%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/AnnSpec.pm (63%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/AnnSpec/Motif.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/Elph.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/Elph/Motif.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/Gibbs.pm (99%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/Gibbs/Motif.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/MEME.pm (98%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/MEME/Motif.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/Motif/Matrix.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/Motif/Word.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/SimplePFM.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/YMF.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGen/YMF/Motif.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternGenI.pm (89%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/PatternI.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Site.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/SitePair.pm (85%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/SitePairSet.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/SiteSet.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Tools/SetOperations.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Word.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/Word/Consensus.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/_Iterator.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/_Iterator/_MatrixSetIterator.pm (100%)
mode change 100755 => 100644
copy {TFBS => blib/lib/TFBS}/_Iterator/_SiteSetIterator.pm (100%)
mode change 100755 => 100644
copy Ext/pm_to_blib => blib/lib/auto/TFBS/.exists (100%)
copy Ext/pm_to_blib => blib/lib/auto/TFBS/Ext/pwmsearch/.exists (100%)
copy {Ext => blib}/lib/pwm_search.h (100%)
copy {Ext => blib}/lib/pwm_searchPFF.c (100%)
copy Ext/pm_to_blib => blib/man1/.exists (100%)
copy Ext/pm_to_blib => blib/man3/.exists (100%)
create mode 100644 blib/man3/TFBS::DB::FlatFileDir.3pm
create mode 100644 blib/man3/TFBS::DB::JASPAR2.3pm
create mode 100644 blib/man3/TFBS::DB::JASPAR4.3pm
create mode 100644 blib/man3/TFBS::DB::LocalTRANSFAC.3pm
create mode 100644 blib/man3/TFBS::DB::TRANSFAC.3pm
create mode 100644 blib/man3/TFBS::Ext::pwmsearch.3pm
create mode 100644 blib/man3/TFBS::Matrix.3pm
create mode 100644 blib/man3/TFBS::Matrix::ICM.3pm
create mode 100644 blib/man3/TFBS::Matrix::PFM.3pm
create mode 100644 blib/man3/TFBS::Matrix::PWM.3pm
create mode 100644 blib/man3/TFBS::MatrixSet.3pm
create mode 100644 blib/man3/TFBS::PatternGen.3pm
create mode 100644 blib/man3/TFBS::PatternGen::AnnSpec.3pm
create mode 100644 blib/man3/TFBS::PatternGen::AnnSpec::Motif.3pm
create mode 100644 blib/man3/TFBS::PatternGen::Elph.3pm
create mode 100644 blib/man3/TFBS::PatternGen::Elph::Motif.3pm
create mode 100644 blib/man3/TFBS::PatternGen::Gibbs.3pm
create mode 100644 blib/man3/TFBS::PatternGen::Gibbs::Motif.3pm
create mode 100644 blib/man3/TFBS::PatternGen::MEME.3pm
create mode 100644 blib/man3/TFBS::PatternGen::MEME::Motif.3pm
create mode 100644 blib/man3/TFBS::PatternGen::SimplePFM.3pm
create mode 100644 blib/man3/TFBS::PatternGen::YMF.3pm
create mode 100644 blib/man3/TFBS::PatternGen::YMF::Motif.3pm
create mode 100644 blib/man3/TFBS::PatternI.3pm
create mode 100644 blib/man3/TFBS::Site.3pm
create mode 100644 blib/man3/TFBS::SitePair.3pm
create mode 100644 blib/man3/TFBS::SitePairSet.3pm
create mode 100644 blib/man3/TFBS::SiteSet.3pm
create mode 100644 blib/man3/TFBS::Word.3pm
create mode 100644 blib/man3/TFBS::Word::Consensus.3pm
copy Ext/pm_to_blib => blib/script/.exists (100%)
copy Ext/pm_to_blib => pm_to_blib (100%)
delete mode 100644 pod2htmd.tmp
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