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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Sun, 02 May 2010 13:28:27 +0200 ===================================== debian/compat deleted ===================================== @@ -1 +0,0 @@ -11 ===================================== debian/control ===================================== @@ -4,13 +4,13 @@ Uploaders: Laszlo Kajan <[email protected]>, Andreas Tille <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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