[med-svn] [Git][med-team/libtfbs-perl][master] 10 commits: Import Debian changes 0.7.1-3.1
Bas Couwenberg (@sebastic)
gitlab at salsa.debian.org
Fri Sep 17 20:01:45 BST 2021
Bas Couwenberg pushed to branch master at Debian Med / libtfbs-perl
Commits:
19ac5557 by Bas Couwenberg at 2021-09-17T19:48:48+02:00
Import Debian changes 0.7.1-3.1
libtfbs-perl (0.7.1-3.1) unstable; urgency=medium
..
* Non-maintainer upload.
* No-change rebuild with PDL 2.0.57.
(closes: #993427)
- - - - -
2a77e931 by Steffen Moeller at 2021-09-17T19:49:26+02:00
d/u/metadata: yamllint
- - - - -
984a0c2d by Bas Couwenberg at 2021-09-17T19:51:48+02:00
Add gbp.conf to use pristine-tar & --source-only-changes by default.
- - - - -
b7e084a3 by Bas Couwenberg at 2021-09-17T19:55:09+02:00
Update changelog.
- - - - -
8909abb2 by Bas Couwenberg at 2021-09-17T19:55:27+02:00
Bump Standards-Version to 4.6.0, no changes.
- - - - -
597bbf88 by Bas Couwenberg at 2021-09-17T20:08:48+02:00
Use AUTOPKGTEST_TMP instead of deprecated ADTTMP variable.
- - - - -
05d0bcb4 by Bas Couwenberg at 2021-09-17T20:12:58+02:00
Update upstream metadata for GitHub repository.
- - - - -
c1a3b8b1 by Bas Couwenberg at 2021-09-17T20:59:11+02:00
Update spelling errors path.
- - - - -
7808efc4 by Bas Couwenberg at 2021-09-17T20:59:11+02:00
Enable PIE hardening flags too.
- - - - -
12f393b6 by Bas Couwenberg at 2021-09-17T20:59:11+02:00
Don't override dh_auto_configure.
- - - - -
9 changed files:
- debian/changelog
- debian/control
- + debian/gbp.conf
- + debian/patches/configure.patch
- debian/patches/series
- debian/patches/spelling-errors.patch
- debian/rules
- debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,29 @@
+libtfbs-perl (0.7.1-4) UNRELEASED; urgency=medium
+
+ * Team upload.
+
+ [ Steffen Moeller ]
+ * d/u/metadata: yamllint
+
+ [ Bas Couwenberg ]
+ * Add gbp.conf to use pristine-tar & --source-only-changes by default.
+ * Bump Standards-Version to 4.6.0, no changes.
+ * Use AUTOPKGTEST_TMP instead of deprecated ADTTMP variable.
+ * Update upstream metadata for GitHub repository.
+ * Update spelling errors path.
+ * Enable PIE hardening flags too.
+ * Don't override dh_auto_configure.
+
+ -- Bas Couwenberg <sebastic at debian.org> Fri, 17 Sep 2021 19:54:38 +0200
+
+libtfbs-perl (0.7.1-3.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * No-change rebuild with PDL 2.0.57.
+ (closes: #993427)
+
+ -- Bas Couwenberg <sebastic at debian.org> Sun, 05 Sep 2021 07:29:33 +0200
+
libtfbs-perl (0.7.1-3) unstable; urgency=medium
[ Xavier Guimard ]
=====================================
debian/control
=====================================
@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 12),
bioperl,
libwww-perl,
libdbi-perl
-Standards-Version: 4.4.0
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/libtfbs-perl
Vcs-Git: https://salsa.debian.org/med-team/libtfbs-perl.git
Homepage: http://tfbs.genereg.net
=====================================
debian/gbp.conf
=====================================
@@ -0,0 +1,19 @@
+[DEFAULT]
+
+# The default name for the upstream branch is "upstream".
+# Change it if the name is different (for instance, "master").
+upstream-branch = upstream
+
+# The default name for the Debian branch is "master".
+# Change it if the name is different (for instance, "debian/unstable").
+debian-branch = master
+
+# git-import-orig uses the following names for the upstream tags.
+# Change the value if you are not using git-import-orig
+upstream-tag = upstream/%(version)s
+
+# Always use pristine-tar.
+pristine-tar = True
+
+[buildpackage]
+pbuilder-options = --source-only-changes
=====================================
debian/patches/configure.patch
=====================================
@@ -0,0 +1,14 @@
+Description: Use environment variable to prevent interactive prompt.
+Author: Bas Couwenberg <sebastic at debian.org>
+Forwarded: not-needed
+
+--- a/Makefile.PL
++++ b/Makefile.PL
+@@ -21,6 +21,7 @@ WriteMakefile(
+
+ sub get_sql_data {
+ my $ans = "abc";
++ $ans = $ENV{HAVE_MYSQL} if($ENV{HAVE_MYSQL});
+ do {
+ print "Do you have write access to a MySQL database server? [n] ";
+ $ans=<STDIN>; chomp $ans;
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
hardening.patch
spelling-errors.patch
+configure.patch
=====================================
debian/patches/spelling-errors.patch
=====================================
@@ -1,11 +1,13 @@
Description: Fix spelling errors.
hierachical -> hierarchical
occurence -> occurrence
+ acces -> access
+ aaccession -> accession
Author: Bas Couwenberg <sebastic at debian.org>
--- a/TFBS/PatternGen/YMF.pm
+++ b/TFBS/PatternGen/YMF.pm
-@@ -177,7 +177,7 @@
+@@ -177,7 +177,7 @@ sub _parse_stats_output{
my $motif =TFBS::PatternGen::YMF::Motif->new
(-word=>$word,
-tags => {z_score=>$z_score,
@@ -14,7 +16,7 @@ Author: Bas Couwenberg <sebastic at debian.org>
'expectation value'=>$expect,
'variance'=>$var}
);
-@@ -190,4 +190,4 @@
+@@ -190,4 +190,4 @@ sub _parse_stats_output{
}
#
@@ -23,7 +25,7 @@ Author: Bas Couwenberg <sebastic at debian.org>
+1;
--- a/TFBS/MatrixSet.pm
+++ b/TFBS/MatrixSet.pm
-@@ -763,7 +763,7 @@
+@@ -763,7 +763,7 @@ sub _build_cluster {
Title : cluster
Usage : $matrixset->cluster(%args)
Function: Clusters the matrices in the set
@@ -34,7 +36,7 @@ Author: Bas Couwenberg <sebastic at debian.org>
Args : Many:
--- a/TFBS/Matrix/PFM.pm
+++ b/TFBS/Matrix/PFM.pm
-@@ -366,7 +366,7 @@
+@@ -366,7 +366,7 @@ sub to_ICM {
# "pseudocounts" - standard pseudocount
# correction, more suitable for
# PFMs with large r column sums
@@ -43,3 +45,206 @@ Author: Bas Couwenberg <sebastic at debian.org>
# sample correction is not applied
-draw_error_bars # if true, adds error bars to each position
+--- a/TFBS/DB/JASPAR.pm
++++ b/TFBS/DB/JASPAR.pm
+@@ -231,7 +231,7 @@ sub new {
+ ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
+ In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
+ use the actual values. PASSWORD and USERNAME might be
+- optional, depending on the user's acces permissions for
++ optional, depending on the user's access permissions for
+ the database server.
+
+ =cut
+--- a/TFBS/DB/JASPAR2.pm
++++ b/TFBS/DB/JASPAR2.pm
+@@ -237,7 +237,7 @@ sub new {
+ ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
+ In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
+ use the actual values. PASSWORD and USERNAME might be
+- optional, depending on the user acces permissions for
++ optional, depending on the user access permissions for
+ the database server.
+
+ =cut
+@@ -263,7 +263,7 @@ sub connect {
+ ("dbi:mysql:NEWDATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
+ In place of NEWDATABASENAME, HOSTNAME, USERNAME and
+ PASSWORD use the actual values. PASSWORD and USERNAME
+- might be optional, depending on the users acces permissions
++ might be optional, depending on the users access permissions
+ for the database server.
+
+ =cut
+--- a/TFBS/DB/JASPAR4.pm
++++ b/TFBS/DB/JASPAR4.pm
+@@ -188,7 +188,7 @@ sub new {
+ ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
+ In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
+ use the actual values. PASSWORD and USERNAME might be
+- optional, depending on the user's acces permissions for
++ optional, depending on the user's access permissions for
+ the database server.
+
+ =cut
+--- a/TFBS/DB/JASPAR5.pm
++++ b/TFBS/DB/JASPAR5.pm
+@@ -177,7 +177,7 @@ sub new {
+ ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
+ In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
+ use the actual values. PASSWORD and USERNAME might be
+- optional, depending on the user's acces permissions for
++ optional, depending on the user's access permissions for
+ the database server.
+
+ =cut
+--- a/TFBS/DB/JASPAR6.pm
++++ b/TFBS/DB/JASPAR6.pm
+@@ -178,7 +178,7 @@ sub new {
+ ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
+ In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
+ use the actual values. PASSWORD and USERNAME might be
+- optional, depending on the user's acces permissions for
++ optional, depending on the user's access permissions for
+ the database server.
+
+ =cut
+--- a/TFBS/DB/JASPAR7.pm
++++ b/TFBS/DB/JASPAR7.pm
+@@ -231,7 +231,7 @@ sub new {
+ ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
+ In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
+ use the actual values. PASSWORD and USERNAME might be
+- optional, depending on the user's acces permissions for
++ optional, depending on the user's access permissions for
+ the database server.
+
+ =cut
+--- a/blib/lib/TFBS/DB/JASPAR2.pm
++++ b/blib/lib/TFBS/DB/JASPAR2.pm
+@@ -237,7 +237,7 @@ sub new {
+ ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
+ In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
+ use the actual values. PASSWORD and USERNAME might be
+- optional, depending on the user acces permissions for
++ optional, depending on the user access permissions for
+ the database server.
+
+ =cut
+@@ -263,7 +263,7 @@ sub connect {
+ ("dbi:mysql:NEWDATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
+ In place of NEWDATABASENAME, HOSTNAME, USERNAME and
+ PASSWORD use the actual values. PASSWORD and USERNAME
+- might be optional, depending on the users acces permissions
++ might be optional, depending on the users access permissions
+ for the database server.
+
+ =cut
+--- a/blib/lib/TFBS/DB/JASPAR4.pm
++++ b/blib/lib/TFBS/DB/JASPAR4.pm
+@@ -188,7 +188,7 @@ sub new {
+ ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
+ In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
+ use the actual values. PASSWORD and USERNAME might be
+- optional, depending on the user's acces permissions for
++ optional, depending on the user's access permissions for
+ the database server.
+
+ =cut
+--- a/blib/man3/TFBS::DB::JASPAR2.3pm
++++ b/blib/man3/TFBS::DB::JASPAR2.3pm
+@@ -314,7 +314,7 @@ methods. Internal methods are preceded w
+ \& ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
+ \& In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
+ \& use the actual values. PASSWORD and USERNAME might be
+-\& optional, depending on the user acces permissions for
++\& optional, depending on the user access permissions for
+ \& the database server.
+ .Ve
+ .SS "create"
+@@ -332,7 +332,7 @@ methods. Internal methods are preceded w
+ \& ("dbi:mysql:NEWDATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
+ \& In place of NEWDATABASENAME, HOSTNAME, USERNAME and
+ \& PASSWORD use the actual values. PASSWORD and USERNAME
+-\& might be optional, depending on the users acces permissions
++\& might be optional, depending on the users access permissions
+ \& for the database server.
+ .Ve
+ .SS "dbh"
+--- a/TFBS/DB/LocalTRANSFAC.pm
++++ b/TFBS/DB/LocalTRANSFAC.pm
+@@ -105,7 +105,7 @@ ENDNOTICE
+
+ Title : get_Matrix_by_acc
+ Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM');
+- Function: fetches matrix data under the given TRANSFAC aaccession number
++ Function: fetches matrix data under the given TRANSFAC accession number
+ from database and returns a TFBS::Matrix::* object
+ Returns : a TFBS::Matrix::* object; the exact type of the
+ object depending on the second argument (allowed
+--- a/TFBS/DB/TRANSFAC.pm
++++ b/TFBS/DB/TRANSFAC.pm
+@@ -151,7 +151,7 @@ sub get_Matrix_by_ID {
+
+ Title : get_Matrix_by_acc
+ Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM');
+- Function: fetches matrix data under the given TRANSFAC aaccession number
++ Function: fetches matrix data under the given TRANSFAC accession number
+ from database and returns a TFBS::Matrix::* object
+ Returns : a TFBS::Matrix::* object; the exact type of the
+ object depending on the second argument (allowed
+--- a/blib/lib/TFBS/DB/LocalTRANSFAC.pm
++++ b/blib/lib/TFBS/DB/LocalTRANSFAC.pm
+@@ -105,7 +105,7 @@ ENDNOTICE
+
+ Title : get_Matrix_by_acc
+ Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM');
+- Function: fetches matrix data under the given TRANSFAC aaccession number
++ Function: fetches matrix data under the given TRANSFAC accession number
+ from database and returns a TFBS::Matrix::* object
+ Returns : a TFBS::Matrix::* object; the exact type of the
+ object depending on the second argument (allowed
+--- a/blib/lib/TFBS/DB/TRANSFAC.pm
++++ b/blib/lib/TFBS/DB/TRANSFAC.pm
+@@ -151,7 +151,7 @@ sub get_Matrix_by_ID {
+
+ Title : get_Matrix_by_acc
+ Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM');
+- Function: fetches matrix data under the given TRANSFAC aaccession number
++ Function: fetches matrix data under the given TRANSFAC accession number
+ from database and returns a TFBS::Matrix::* object
+ Returns : a TFBS::Matrix::* object; the exact type of the
+ object depending on the second argument (allowed
+--- a/blib/man3/TFBS::DB::LocalTRANSFAC.3pm
++++ b/blib/man3/TFBS::DB::LocalTRANSFAC.3pm
+@@ -188,7 +188,7 @@ TFBS::DB::LocalTRANSFAC is a read only d
+ .Vb 10
+ \& Title : get_Matrix_by_acc
+ \& Usage : my $pfm = $db\->get_Matrix_by_acc(\*(AqV$CREB_01\*(Aq, \*(AqPFM\*(Aq);
+-\& Function: fetches matrix data under the given TRANSFAC aaccession number
++\& Function: fetches matrix data under the given TRANSFAC accession number
+ \& from database and returns a TFBS::Matrix::* object
+ \& Returns : a TFBS::Matrix::* object; the exact type of the
+ \& object depending on the second argument (allowed
+--- a/blib/man3/TFBS::DB::TRANSFAC.3pm
++++ b/blib/man3/TFBS::DB::TRANSFAC.3pm
+@@ -217,7 +217,7 @@ retrieving a TFBS::Matrix::* object from
+ .Vb 10
+ \& Title : get_Matrix_by_acc
+ \& Usage : my $pfm = $db\->get_Matrix_by_acc(\*(AqV$CREB_01\*(Aq, \*(AqPFM\*(Aq);
+-\& Function: fetches matrix data under the given TRANSFAC aaccession number
++\& Function: fetches matrix data under the given TRANSFAC accession number
+ \& from database and returns a TFBS::Matrix::* object
+ \& Returns : a TFBS::Matrix::* object; the exact type of the
+ \& object depending on the second argument (allowed
+--- a/blib/man3/TFBS::DB::JASPAR4.3pm
++++ b/blib/man3/TFBS::DB::JASPAR4.3pm
+@@ -256,7 +256,7 @@ methods. Internal methods are preceded w
+ \& ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
+ \& In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
+ \& use the actual values. PASSWORD and USERNAME might be
+-\& optional, depending on the user\*(Aqs acces permissions for
++\& optional, depending on the user\*(Aqs access permissions for
+ \& the database server.
+ .Ve
+ .SS "dbh"
=====================================
debian/rules
=====================================
@@ -1,9 +1,9 @@
#!/usr/bin/make -f
# Enable hardening build flags
-export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
-CFLAGS += $(CPPFLAGS)
+export HAVE_MYSQL=n
include /usr/share/dpkg/default.mk
@@ -13,10 +13,6 @@ include /usr/share/dpkg/default.mk
override_dh_auto_clean:
rm --force Makefile Makefile.old
-override_dh_auto_configure:
- echo "n" | perl Makefile.PL INSTALLDIRS=vendor
- $(MAKE) OPTIMIZE="$(CFLAGS)" LD_RUN_PATH="" OTHERLDFLAGS="$(LDFLAGS)"
-
# Do not run network test unless in maintainer mode.
ifneq (1,$(DEB_MAINTAINER_MODE))
TEST_FILES := $(filter-out t/04_DB_TRANSFAC.t,$(shell echo t/*.t))
=====================================
debian/tests/run-unit-test
=====================================
@@ -2,11 +2,11 @@
pkg=libtfbs-perl
-if [ "$ADTTMP" = "" ] ; then
- ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
fi
-cd $ADTTMP
-cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP
+cd $AUTOPKGTEST_TMP
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
find . -name "*.gz" -exec gunzip \{\} \;
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/ComputationalRegulatoryGenomicsICL/TFBS/issues
+Bug-Submit: https://github.com/ComputationalRegulatoryGenomicsICL/TFBS/issues/new
Reference:
- Author: Lenhard, Boris and Wasserman, Wyeth W.
DOI: 10.1093/bioinformatics/18.8.1135
@@ -10,7 +12,8 @@ Reference:
Pages: 1135-1136
Year: 2002
URL: https://github.com/ComputationalRegulatoryGenomicsICL/TFBS.git
-Repository: http://www.ii.uib.no/svn/lenhard/TFBS/
+Repository: https://github.com/ComputationalRegulatoryGenomicsICL/TFBS.git
+Repository-Browse: https://github.com/ComputationalRegulatoryGenomicsICL/TFBS
Registry:
- Name: SciCrunch
Entry: SCR_015774
View it on GitLab: https://salsa.debian.org/med-team/libtfbs-perl/-/compare/c5c5d21c72098ee87568bc16b553148807022c61...12f393b6900037f9dee9a7b68bed374bab49b15d
--
View it on GitLab: https://salsa.debian.org/med-team/libtfbs-perl/-/compare/c5c5d21c72098ee87568bc16b553148807022c61...12f393b6900037f9dee9a7b68bed374bab49b15d
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