Source: libtfbs-perl
Version: 0.7.0+dfsg-1
Severity: normal
Tags: patch
Dear Maintainer,
As part of the PDL update to 2.016 [0], all its reverse dependencies have
been rebuilt in preparation of the transition (from pdlapi-10 to pdlapi-12).
While libtfbs-perl doesn't require changes for the upcoming pdl
transition, I couldn't resist updating the package to incorporate some
best practices.
Please condider applying the attached patches.
[0]
https://lists.alioth.debian.org/pipermail/pkg-perl-maintainers/2016-June/100093.html
Kind Regards,
Bas
>From f1f79db99d2f8d43874fbfa9d32f61e2cd8797ba Mon Sep 17 00:00:00 2001
From: Bas Couwenberg <sebas...@xs4all.nl>
Date: Fri, 17 Jun 2016 01:43:20 +0200
Subject: Use dh_pdl to set versioned pdl dependency via ${pdl:Depends}.
---
debian/changelog | 7 +++++++
debian/control | 2 +-
debian/rules | 4 ++++
3 files changed, 12 insertions(+), 1 deletion(-)
diff --git a/debian/changelog b/debian/changelog
index 5a4516d..3b62ecd 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+libtfbs-perl (0.7.0+dfsg-1.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * Use dh_pdl to set versioned pdl dependency via ${pdl:Depends}.
+
+ -- Bas Couwenberg <sebas...@debian.org> Fri, 17 Jun 2016 01:42:27 +0200
+
libtfbs-perl (0.7.0+dfsg-1) unstable; urgency=medium
* New upstream version
diff --git a/debian/control b/debian/control
index 278889f..ca1bbfc 100644
--- a/debian/control
+++ b/debian/control
@@ -20,9 +20,9 @@ Homepage: http://tfbs.genereg.net
Package: libtfbs-perl
Architecture: any
Depends: ${perl:Depends},
+ ${pdl:Depends},
${shlibs:Depends},
${misc:Depends},
- pdl,
bioperl,
libwww-perl,
libdbi-perl
diff --git a/debian/rules b/debian/rules
index c72dc9e..71ae0e6 100755
--- a/debian/rules
+++ b/debian/rules
@@ -26,5 +26,9 @@ override_dh_installexamples:
mkdir -p debian/$(DEBPKGNAME)/usr/share/doc/$(DEBPKGNAME)/examples/Ext
cp -a Ext/t debian/$(DEBPKGNAME)/usr/share/doc/$(DEBPKGNAME)/examples/Ext
+override_dh_perl:
+ dh_perl
+ dh_pdl
+
get-orig-source:
uscan --verbose --force-download --repack --compress xz
--
2.1.4
>From 89bafb6d4b789b548f5cc36171fdf2d501fc53c9 Mon Sep 17 00:00:00 2001
From: Bas Couwenberg <sebas...@xs4all.nl>
Date: Fri, 17 Jun 2016 01:44:31 +0200
Subject: Update Vcs-Browser URL to use HTTPS.
---
debian/changelog | 1 +
debian/control | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/debian/changelog b/debian/changelog
index 3b62ecd..207f5b2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,7 @@ libtfbs-perl (0.7.0+dfsg-1.1) UNRELEASED; urgency=medium
* Non-maintainer upload.
* Use dh_pdl to set versioned pdl dependency via ${pdl:Depends}.
+ * Update Vcs-Browser URL to use HTTPS.
-- Bas Couwenberg <sebas...@debian.org> Fri, 17 Jun 2016 01:42:27 +0200
diff --git a/debian/control b/debian/control
index ca1bbfc..fa3fd3c 100644
--- a/debian/control
+++ b/debian/control
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 9),
libwww-perl,
libdbi-perl
Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libtfbs-perl/trunk/
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/libtfbs-perl/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/libtfbs-perl/trunk/
Homepage: http://tfbs.genereg.net
--
2.1.4
>From 1135647aaa07194b3c47d37a6593cde9fa435608 Mon Sep 17 00:00:00 2001
From: Bas Couwenberg <sebas...@xs4all.nl>
Date: Fri, 17 Jun 2016 01:49:43 +0200
Subject: Update watch file to handle common issues.
---
debian/changelog | 1 +
debian/watch | 8 ++++++--
2 files changed, 7 insertions(+), 2 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 207f5b2..5c89f2f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,7 @@ libtfbs-perl (0.7.0+dfsg-1.1) UNRELEASED; urgency=medium
* Non-maintainer upload.
* Use dh_pdl to set versioned pdl dependency via ${pdl:Depends}.
* Update Vcs-Browser URL to use HTTPS.
+ * Update watch file to handle common issues.
-- Bas Couwenberg <sebas...@debian.org> Fri, 17 Jun 2016 01:42:27 +0200
diff --git a/debian/watch b/debian/watch
index 0b62cdf..b936233 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,3 +1,7 @@
version=3
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
- http://tfbs.genereg.net/TFBS-(.*)\.tar\.gz
+opts=\
+dversionmangle=s/\+(debian|dfsg|ds|deb)\d*$//,\
+uversionmangle=s/(\d)[_\.\-\+]?((RC|rc|pre|dev|beta|alpha)\d*)$/$1~$2/;s/RC/rc/,\
+repacksuffix=+dfsg \
+http://tfbs.genereg.net/ \
+(?:.*?/)?(?:TFBS|v)?[\-\_]?(\d\S*)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
--
2.1.4
>From 7e612931fa9b7214da446f5b446648a2577627a5 Mon Sep 17 00:00:00 2001
From: Bas Couwenberg <sebas...@xs4all.nl>
Date: Fri, 17 Jun 2016 01:51:28 +0200
Subject: Enable all hardening buildflags, except PIE (causes build failure).
---
debian/changelog | 1 +
debian/rules | 5 +++++
2 files changed, 6 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index 5c89f2f..4b72881 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,6 +4,7 @@ libtfbs-perl (0.7.0+dfsg-1.1) UNRELEASED; urgency=medium
* Use dh_pdl to set versioned pdl dependency via ${pdl:Depends}.
* Update Vcs-Browser URL to use HTTPS.
* Update watch file to handle common issues.
+ * Enable all hardening buildflags, except PIE (causes build failure).
-- Bas Couwenberg <sebas...@debian.org> Fri, 17 Jun 2016 01:42:27 +0200
diff --git a/debian/rules b/debian/rules
index 71ae0e6..8279c98 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,5 +1,10 @@
#!/usr/bin/make -f
+# Enable hardening build flags
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie
+
+CFLAGS += $(CPPFLAGS)
+
DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
%:
--
2.1.4
>From 9bf838f9dbea526b0d2decba5dad290510172ec1 Mon Sep 17 00:00:00 2001
From: Bas Couwenberg <sebas...@xs4all.nl>
Date: Fri, 17 Jun 2016 01:53:05 +0200
Subject: Bump Standards-Version to 3.9.8, no changes.
---
debian/changelog | 1 +
debian/control | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/debian/changelog b/debian/changelog
index 4b72881..115f7d1 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -5,6 +5,7 @@ libtfbs-perl (0.7.0+dfsg-1.1) UNRELEASED; urgency=medium
* Update Vcs-Browser URL to use HTTPS.
* Update watch file to handle common issues.
* Enable all hardening buildflags, except PIE (causes build failure).
+ * Bump Standards-Version to 3.9.8, no changes.
-- Bas Couwenberg <sebas...@debian.org> Fri, 17 Jun 2016 01:42:27 +0200
diff --git a/debian/control b/debian/control
index fa3fd3c..568eec0 100644
--- a/debian/control
+++ b/debian/control
@@ -12,7 +12,7 @@ Build-Depends: debhelper (>= 9),
bioperl,
libwww-perl,
libdbi-perl
-Standards-Version: 3.9.6
+Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/libtfbs-perl/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/libtfbs-perl/trunk/
Homepage: http://tfbs.genereg.net
--
2.1.4
>From ef00591d5e8890adc43c7d4e3d461ab7bab17a4e Mon Sep 17 00:00:00 2001
From: Bas Couwenberg <sebas...@xs4all.nl>
Date: Fri, 17 Jun 2016 02:22:40 +0200
Subject: Add patch to fix spelling errors.
---
debian/changelog | 1 +
debian/patches/series | 1 +
debian/patches/spelling-errors.patch | 146 +++++++++++++++++++++++++++++++++++
3 files changed, 148 insertions(+)
create mode 100644 debian/patches/spelling-errors.patch
diff --git a/debian/changelog b/debian/changelog
index 115f7d1..ef1b31a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -6,6 +6,7 @@ libtfbs-perl (0.7.0+dfsg-1.1) UNRELEASED; urgency=medium
* Update watch file to handle common issues.
* Enable all hardening buildflags, except PIE (causes build failure).
* Bump Standards-Version to 3.9.8, no changes.
+ * Add patch to fix spelling errors.
-- Bas Couwenberg <sebas...@debian.org> Fri, 17 Jun 2016 01:42:27 +0200
diff --git a/debian/patches/series b/debian/patches/series
index 814900f..ba2a7ef 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
hardening.patch
+spelling-errors.patch
diff --git a/debian/patches/spelling-errors.patch b/debian/patches/spelling-errors.patch
new file mode 100644
index 0000000..93a75a6
--- /dev/null
+++ b/debian/patches/spelling-errors.patch
@@ -0,0 +1,146 @@
+Description: Fix spelling errors.
+ classs -> class
+ infromation -> information
+ occurence -> occurrence
+ repective -> respective
+ supresses -> suppresses
+ taht -> that
+Author: Bas Couwenberg <sebas...@debian.org>
+
+--- a/TFBS/DB/JASPAR2.pm
++++ b/TFBS/DB/JASPAR2.pm
+@@ -458,7 +458,7 @@ gives a set of PWMs whose (structural cl
+ OR 'Mus musculus').
+
+ The -min_ic filter is applied after the query in the sense that the
+-matrices profiles with total infromation content less than specified
++matrices profiles with total information content less than specified
+ are not included in the set.
+
+ =cut
+--- a/TFBS/DB/JASPAR4.pm
++++ b/TFBS/DB/JASPAR4.pm
+@@ -409,7 +409,7 @@ sub get_Matrix_by_name {
+ database storage, any tag can be used for information retrieval.
+ Additionally, arguments as 'name' and 'class' can be used (even though
+ they are not tags.
+- As with get_Matrix methods, it is important to realize taht any matrix
++ As with get_Matrix methods, it is important to realize that any matrix
+ format can be stored in the database: the TFBS::MatrixSet might therefore
+ consist of PFMs, ICMs and PWMS, depending on how matrices are stored,
+
+@@ -445,7 +445,7 @@ gives a set of TFBS::Matrix::PFM objects
+ from is 'Homo sapiens'OR 'Mus musculus').
+
+ The -min_ic filter is applied after the query in the sense that the
+-matrices profiles with total infromation content less than specified
++matrices profiles with total information content less than specified
+ are not included in the set.
+
+ =cut
+--- a/TFBS/PatternGen.pm
++++ b/TFBS/PatternGen.pm
+@@ -14,7 +14,7 @@ TFBS::PatternGen - a base class for patt
+
+ =head1 DESCRIPTION
+
+-TFBS::PatternGen is a base classs providing methods common to all pattern generating
++TFBS::PatternGen is a base class providing methods common to all pattern generating
+ modules. It is meant to be inherited by a concrete pattern generator, which must have its own
+ constructor.
+
+--- a/TFBS/Matrix/ICM.pm
++++ b/TFBS/Matrix/ICM.pm
+@@ -98,7 +98,7 @@ following information content matrix:
+ G:[0.00 0.89 2.00 0.00 0.00 0.00]
+ T:[0.00 0.00 0.00 0.13 0.06 2.00]
+
+-which contains the "weights" associated with the occurence of each
++which contains the "weights" associated with the occurrence of each
+ nucleotide at the given position in a pattern.
+
+ A TFBS::Matrix::PWM object is equipped with methods to search nucleotide
+--- a/TFBS/Matrix/PWM.pm
++++ b/TFBS/Matrix/PWM.pm
+@@ -100,7 +100,7 @@ following position weight matrix:
+ G:[-1.57 1.85 -2.57 -1.34 -1.57 1.14]
+ T:[ 0.31 -3.16 -2.57 1.76 0.24 -0.83]
+
+-which contains the "weights" associated with the occurence of each
++which contains the "weights" associated with the occurrence of each
+ nucleotide at the given position in a pattern.
+
+ A TFBS::Matrix::PWM object is equipped with methods to search nucleotide
+--- a/TFBS/PatternGen/Elph.pm
++++ b/TFBS/PatternGen/Elph.pm
+@@ -66,7 +66,7 @@ use Bio::SeqIO;
+ Other arguments are:
+ -binary # a fully qualified path to Gibbs executable
+ # OPTIONAL: default 'Gibbs'
+- -nr_hits # a presumed number of pattern occurences in the
++ -nr_hits # a presumed number of pattern occurrences in the
+ # sequence set: it can be a single integer, e.g.
+ # -nr_hits => 24 , or a reference to an array of
+ # integers, e.g -nr_hits => [12, 24, 36]
+--- a/TFBS/PatternGen/Gibbs.pm
++++ b/TFBS/PatternGen/Gibbs.pm
+@@ -67,7 +67,7 @@ use Bio::SeqIO;
+ Other arguments are:
+ -binary # a fully qualified path to Gibbs executable
+ # OPTIONAL: default 'Gibbs'
+- -nr_hits # a presumed number of pattern occurences in the
++ -nr_hits # a presumed number of pattern occurrences in the
+ # sequence set: it can be a single integer, e.g.
+ # -nr_hits => 24 , or a reference to an array of
+ # integers, e.g -nr_hits => [12, 24, 36]
+--- a/TFBS/PatternGen/YMF.pm
++++ b/TFBS/PatternGen/YMF.pm
+@@ -177,7 +177,7 @@ sub _parse_stats_output{
+ my $motif =TFBS::PatternGen::YMF::Motif->new
+ (-word=>$word,
+ -tags => {z_score=>$z_score,
+- 'occurences'=>$occ,
++ 'occurrences'=>$occ,
+ 'expectation value'=>$expect,
+ 'variance'=>$var}
+ );
+@@ -190,4 +190,4 @@ sub _parse_stats_output{
+ }
+ #
+
+-1;
+\ No newline at end of file
++1;
+--- a/TFBS/Matrix/Alignment.pm
++++ b/TFBS/Matrix/Alignment.pm
+@@ -239,7 +239,7 @@ sub new {
+ Title : alignment
+ Usage : my $alignment_string = $alignmentobject->alignment();
+ Function: access a string describing the alignment
+- Returns : an string, where each number refers to a position in repective PFM.
++ Returns : an string, where each number refers to a position in respective PFM.
+ Position numbering is according to orientation: ie if the second profile is
+ reversed, position 1 corresponds to the last position in the input profile.
+ Gaps are denoted as - .
+--- a/TFBS/DB/LocalTRANSFAC.pm
++++ b/TFBS/DB/LocalTRANSFAC.pm
+@@ -70,7 +70,7 @@ use TFBS::Matrix::PFM;
+ # have read and accepted the terms
+ # of use of TRANSFAC at
+ # http://transfac.gbf.de/TRANSFAC/disclaimer.htm;
+- # this also supresses the annoying
++ # this also suppresses the annoying
+ # message that is printed to STDERR
+ # upon invoking the method
+
+--- a/TFBS/DB/TRANSFAC.pm
++++ b/TFBS/DB/TRANSFAC.pm
+@@ -69,7 +69,7 @@ use LWP::Simple qw($ua get);
+ # have read and accepted the terms
+ # of use of TRANSFAC at
+ # http://transfac.gbf.de/TRANSFAC/disclaimer.htm;
+- # this also supresses the annoying
++ # this also suppresses the annoying
+ # message that is printed to STDERR
+ # upon invoking the method
+
--
2.1.4
