[med-svn] [Git][med-team/profphd][master] 8 commits: Do not force users to install pp-popularity-contest
Andreas Tille
gitlab at salsa.debian.org
Thu Oct 10 21:29:00 BST 2019
Andreas Tille pushed to branch master at Debian Med / profphd
Commits:
2a76f35e by Andreas Tille at 2019-10-10T20:26:13Z
Do not force users to install pp-popularity-contest
- - - - -
583adc05 by Andreas Tille at 2019-10-10T20:26:28Z
debhelper-compat 12
- - - - -
69799b00 by Andreas Tille at 2019-10-10T20:26:32Z
Standards-Version: 4.4.1
- - - - -
4aae9502 by Andreas Tille at 2019-10-10T20:26:32Z
Drop useless get-orig-source target
- - - - -
44092495 by Andreas Tille at 2019-10-10T20:26:32Z
Remove trailing whitespace in debian/changelog
- - - - -
f53adc1d by Andreas Tille at 2019-10-10T20:26:33Z
Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
- - - - -
72e7121b by Andreas Tille at 2019-10-10T20:26:34Z
Use secure URI in Homepage field.
Fixes lintian: homepage-field-uses-insecure-uri
See https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html for more details.
- - - - -
76b18a1d by Andreas Tille at 2019-10-10T20:26:35Z
Remove obsolete fields Name from debian/upstream/metadata.
- - - - -
7 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/6_no_pp_popcon_cnt.patch
- debian/patches/series
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,17 @@
profphd (1.0.42-4) UNRELEASED; urgency=medium
* pp-popularity-contest only suggested
-
- -- Andreas Tille <tille at debian.org> Thu, 18 Oct 2018 13:06:42 +0200
+ * Do not force users to install pp-popularity-contest
+ Closes: #942064
+ * debhelper-compat 12
+ * Standards-Version: 4.4.1
+ * Drop useless get-orig-source target
+ * Remove trailing whitespace in debian/changelog
+ * Trim trailing whitespace.
+ * Use secure URI in Homepage field.
+ * Remove obsolete fields Name from debian/upstream/metadata.
+
+ -- Andreas Tille <tille at debian.org> Thu, 10 Oct 2019 22:23:45 +0200
profphd (1.0.42-3) unstable; urgency=medium
@@ -19,10 +28,10 @@ profphd (1.0.42-2) unstable; urgency=medium
* cme fix dpkg-control
* cme fix dpkg-copyright
* add hardening in d/rules
- * add patches 1-4 to use latest perl 5.22 (UNFINISHED! checking if this works)
+ * add patches 1-4 to use latest perl 5.22 (UNFINISHED! checking if this works)
* add debian/tests (unfinished too)
- * remove autopkgtest-perl commands - they actually do nothing - and replaced
- them with syntax check for all .pm files inside src dir (which is run with
+ * remove autopkgtest-perl commands - they actually do nothing - and replaced
+ them with syntax check for all .pm files inside src dir (which is run with
command 'perl -c <name>.pm')
* update comments in debian/tests/profphd-install-test
* add header to debian/patches/5_fix_regex_warning.patch
@@ -209,7 +218,7 @@ profphd (1.0.19)
profphd (1.0.18)
- * resolved bug #10 html formatting of ouput
+ * resolved bug #10 html formatting of ouput
-- Guy Yachdav <gyachdav at rostlab.org> Sun, 02 May 2010 13:28:27 +0200
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -4,13 +4,13 @@ Uploaders: Laszlo Kajan <lkajan at rostlab.org>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
perl,
rsync
-Standards-Version: 4.1.5
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/profphd
Vcs-Git: https://salsa.debian.org/med-team/profphd.git
-Homepage: http://predictprotein.org/
+Homepage: https://predictprotein.org/
Package: profphd
Architecture: all
=====================================
debian/patches/6_no_pp_popcon_cnt.patch
=====================================
@@ -0,0 +1,26 @@
+Description: Do not force users to install pp-popularity-contest
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 10 Oct 2019 22:23:45 +0200
+
+--- a/src/prof/prof.pl
++++ b/src/prof/prof.pl
+@@ -12,7 +12,7 @@
+ no warnings 'deprecated';
+
+ # popularity contest
+-if( system('pp_popcon_cnt', '-p', 'prof') == -1 ){ warn("The Rost Lab recommends you install the pp-popularity-contest package that provides pp_popcon_cnt:\n\nsudo apt-get install pp-popularity-contest\n"); }
++# if( system('pp_popcon_cnt', '-p', 'prof') == -1 ){ warn("The Rost Lab recommends you install the pp-popularity-contest package that provides pp_popcon_cnt:\n\nsudo apt-get install pp-popularity-contest\n"); }
+
+ # ---------------------------------------------------------------------------- #
+ # change to port (install) program: #
+--- a/src/prof/embl/phd.pl
++++ b/src/prof/embl/phd.pl
+@@ -13,7 +13,7 @@ no warnings 'deprecated';
+ #------------------------------------------------------------------------------#
+
+ # popularity contest
+-{ if( system('pp_popcon_cnt', '-p', 'phd.pl') == -1 ){ warn("The Rost Lab recommends you install the pp-popularity-contest package that provides pp_popcon_cnt:\n\nsudo apt-get install pp-popularity-contest\n"); } }
++# { if( system('pp_popcon_cnt', '-p', 'phd.pl') == -1 ){ warn("The Rost Lab recommends you install the pp-popularity-contest package that provides pp_popcon_cnt:\n\nsudo apt-get install pp-popularity-contest\n"); } }
+
+ # ---------------------------------------------------------------------------- #
+ # change to port (install) program: #
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@
3_fix_indexing.patch
4_fix_negative_repeat_count.patch
5_fix_regex_warning.patch
+6_no_pp_popcon_cnt.patch
=====================================
debian/rules
=====================================
@@ -9,7 +9,3 @@ include /usr/share/dpkg/default.mk
override_dh_auto_install:
make prefix=/usr DESTDIR=$(CURDIR)/debian/$(DEB_SOURCE)/ install
-
-get-orig-source:
- mkdir -p ../tarballs
- uscan --verbose --force-download --destdir=../tarballs
=====================================
debian/upstream/metadata
=====================================
@@ -1,34 +1,29 @@
-Name: profphd
Reference:
- - Author: Rost, B. and Sander, C.
- Title: >
- Combining evolutionary information and neural networks to predict
- protein secondary structure.
- Journal: Proteins
- Volume: 19
- Number: 1
- Pages: 55-72
- Year: 1994
- URL: http://www.ncbi.nlm.nih.gov/pubmed/8066087
- PMID: 8066087
- - Author: Rost, B. and Sander, C.
- Title: >
- Conservation and prediction of solvent accessibility in protein
- families.
- Journal: Proteins
- Volume: 20
- Number: 3
- Pages: 216-26
- Year: 1994
- URL: http://www.ncbi.nlm.nih.gov/pubmed/7892171
- PMID: 7892171
- - Author: Rost, B. and Casadio, R. and Fariselli, P. and Sander, C.
- Title: >
- Transmembrane helices predicted at 95% accuracy.
- Journal: Protein Sci
- Volume: 4
- Number: 3
- Pages: 521-33
- Year: 1995
- URL: http://www.ncbi.nlm.nih.gov/pubmed/7795533
- PMID: 7795533
+- Author: Rost, B. and Sander, C.
+ Title: "Combining evolutionary information and neural networks to predict protein\
+ \ secondary structure.\n"
+ Journal: Proteins
+ Volume: 19
+ Number: 1
+ Pages: 55-72
+ Year: 1994
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/8066087
+ PMID: 8066087
+- Author: Rost, B. and Sander, C.
+ Title: "Conservation and prediction of solvent accessibility in protein families.\n"
+ Journal: Proteins
+ Volume: 20
+ Number: 3
+ Pages: 216-26
+ Year: 1994
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/7892171
+ PMID: 7892171
+- Author: Rost, B. and Casadio, R. and Fariselli, P. and Sander, C.
+ Title: "Transmembrane helices predicted at 95% accuracy.\n"
+ Journal: Protein Sci
+ Volume: 4
+ Number: 3
+ Pages: 521-33
+ Year: 1995
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/7795533
+ PMID: 7795533
View it on GitLab: https://salsa.debian.org/med-team/profphd/compare/96681fc0c7f71ffba286f3f3e878fcca5203864c...76b18a1d930c33ec9b3141f0f32e6fb96caa046d
--
View it on GitLab: https://salsa.debian.org/med-team/profphd/compare/96681fc0c7f71ffba286f3f3e878fcca5203864c...76b18a1d930c33ec9b3141f0f32e6fb96caa046d
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