diff -Nru profphd-1.0.39/ChangeLog profphd-1.0.40/ChangeLog --- profphd-1.0.39/ChangeLog 2012-08-14 17:43:28.000000000 +0000 +++ profphd-1.0.40/ChangeLog 2013-05-19 16:52:38.000000000 +0000 @@ -1,3 +1,10 @@ +profphd (1.0.40) unstable; urgency=low + + * More scripts with no warnings 'deprecated'. We silence the issue, not fix + it. + + -- Laszlo Kajan Sun, 19 May 2013 18:27:09 +0200 + profphd (1.0.39) unstable; urgency=low * improved man page with bug workaround diff -Nru profphd-1.0.39/Makefile profphd-1.0.40/Makefile --- profphd-1.0.39/Makefile 2012-08-14 17:44:24.000000000 +0000 +++ profphd-1.0.40/Makefile 2013-05-19 16:27:00.000000000 +0000 @@ -1,5 +1,5 @@ export PACKAGE := profphd -export VERSION := 1.0.39 +export VERSION := 1.0.40 export PACKAGE_VERSION := $(VERSION) export PACKAGE_STRING := $(PACKAGE) $(PACKAGE_VERSION) export DISTDIR := $(PACKAGE)-$(VERSION) @@ -64,7 +64,7 @@ dist: dist-profphd dist-profphd: $(DISTDIR) - tar -c -f - "$(DISTDIR)" | xz --best -c >$(DISTDIR).tar.xz + tar -c -f - "$(DISTDIR)" | xz -c >$(DISTDIR).tar.xz rm -rf $(DISTDIR) $(DISTDIR): distclean diff -Nru profphd-1.0.39/debian/changelog profphd-1.0.40/debian/changelog --- profphd-1.0.39/debian/changelog 2012-08-14 17:55:07.000000000 +0000 +++ profphd-1.0.40/debian/changelog 2013-08-29 07:11:11.000000000 +0000 @@ -1,3 +1,19 @@ +profphd (1.0.40-1) unstable; urgency=low + + [ Laszlo Kajan ] + * New upstream release. + + [ Gregor Herrmann ] + * Fix "FTBFS with perl 5.18: POD failure": + add patch to fix POD + (Closes: #720497) + + [ Andreas Tille ] + * cme fix dpkg-control + * anonscm in Vcs fields + + -- Andreas Tille Thu, 29 Aug 2013 08:52:49 +0200 + profphd (1.0.39-1) unstable; urgency=low [ Andreas Tille ] diff -Nru profphd-1.0.39/debian/control profphd-1.0.40/debian/control --- profphd-1.0.39/debian/control 2012-08-14 17:55:07.000000000 +0000 +++ profphd-1.0.40/debian/control 2013-08-29 06:56:06.000000000 +0000 @@ -1,22 +1,31 @@ Source: profphd -Section: science -Priority: extra Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan , - Andreas Tille -Build-Depends: cdbs, debhelper (>= 7.0.50~), perl, rsync -Standards-Version: 3.9.3 -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rostlab/profphd/trunk/ -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rostlab/profphd/trunk/ -DM-Upload-Allowed: yes + Andreas Tille +Section: science +Priority: extra +Build-Depends: cdbs, + debhelper (>= 7.0.50~), + perl, + rsync +Standards-Version: 3.9.4 +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/profphd/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/profphd/trunk/ Homepage: http://predictprotein.org/ Package: profphd Architecture: all -Depends: ${perl:Depends}, ${misc:Depends}, librg-utils-perl (>= 1.0.16), profnet-prof, profphd-utils, profphd-net -Replaces: profphd-data, profphd-perl -Conflicts: profphd-data, profphd-perl +Depends: ${perl:Depends}, + ${misc:Depends}, + librg-utils-perl (>= 1.0.16), + profnet-prof, + profphd-utils, + profphd-net Recommends: pp-popularity-contest +Conflicts: profphd-data, + profphd-perl +Replaces: profphd-data, + profphd-perl Description: secondary structure and solvent accessibility predictor This package provides prof(1), the protein secondary structure, accessibility and transmembrane helix predictor from Burkhard Rost. Prediction is either @@ -35,3 +44,4 @@ * Transmembrane helix prediction has an expected per-residue accuracy of about 95%. The number of false positives, i.e., transmembrane helices predicted in globular proteins, is about 2%. + diff -Nru profphd-1.0.39/debian/copyright profphd-1.0.40/debian/copyright --- profphd-1.0.39/debian/copyright 2011-09-27 15:29:37.000000000 +0000 +++ profphd-1.0.40/debian/copyright 2013-05-21 15:30:41.000000000 +0000 @@ -1,50 +1,58 @@ -This package was debianized by Laszlo Kajan on +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: profphd +Upstream-Contact: Laszlo Kajan +Source: ftp://rostlab.org/profphd/ + +Files: src/prof/embl/scr/ctime.pl src/prof/embl/scr/lib/ctime.pl +Copyright: 1988 Waldemar Kebsch + March 1990, Feb 1991 Marion Hakanson , Oregon Graduate Institute of Science and Technology +License: GPL-1+ or Artistic + +Files: debian/* +Copyright: 2009 Laszlo Kajan +License: GPL-2+ - Tue, 17 Nov 2009 10:50:19 +0100. - -It was downloaded from: - - ftp://rostlab.org/profphd-utils/ - -Upstream Authors: - - B. Rost +Files: * +Copyright: + 1998 B. Rost EMBL, CUBIC (Columbia University, NY, USA) and LION Biosciences (Heidelberg, DE) C. Sander P. Fariselli R. Casadio J. Liu - G. Yachdav - L. Kajan - -Copyright: - - Copyright 1998 by Burkhard Rost EMBL, CUBIC (Columbia University, NY, USA) and LION Biosciences (Heidelberg, DE) - - Copyright 2009-2011 by Laszlo Kajan Technical University Munich (Munich, DE) - - Copyright 2009-2011 by Guy Yachdav CUBIC (Columbia University, NY, USA) and Technical University Munich (Munich, DE) - -License: - - This package is free software; you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. - - This package is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this package; if not, write to the Free Software - Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA - -On Debian systems, the complete text of the GNU General -Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. - -The Debian packaging is: - - (C) 2009, Laszlo Kajan - -and is licensed under the GPL, see above. + 2009-2013 G. Yachdav CUBIC (Columbia University, NY, USA) and Technical University Munich (Munich, DE) + 2009-2013 L. Kajan Laszlo Kajan Technical University Munich (Munich, DE) +License: GPL-2+ + +License: GPL-2+ + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + . + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + . + On Debian systems, the complete text of the GNU General + Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. + +License: GPL-1+ + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 1, or (at your option) + any later version. + . + On Debian systems, the complete text of version 1 of the GNU General + Public License can be found in `/usr/share/common-licenses/GPL-1'. + +License: Artistic + This program is free software; you can redistribute it and/or modify + it under the terms of the Artistic License, which comes with Perl. + . + On Debian systems, the complete text of the Artistic License can be + found in `/usr/share/common-licenses/Artistic'. diff -Nru profphd-1.0.39/debian/patches/fix-pod.patch profphd-1.0.40/debian/patches/fix-pod.patch --- profphd-1.0.39/debian/patches/fix-pod.patch 1970-01-01 00:00:00.000000000 +0000 +++ profphd-1.0.40/debian/patches/fix-pod.patch 2013-08-29 06:50:09.000000000 +0000 @@ -0,0 +1,18 @@ +Description: perl 5.18 doesn't allow numbers after =item, so mask it +Origin: vendor +Bug-Debian: http://bugs.debian.org/720497 +Forwarded: no +Author: gregor herrmann +Last-Update: 2013-08-23 + +--- a/src/prof/prof ++++ b/src/prof/prof +@@ -238,7 +238,7 @@ See each keyword for more help. Most of + + alternative connectivity patterns (default=3) + +-=item 3 ++=item Z<>3 + + predict sec + acc + htm + diff -Nru profphd-1.0.39/debian/patches/series profphd-1.0.40/debian/patches/series --- profphd-1.0.39/debian/patches/series 1970-01-01 00:00:00.000000000 +0000 +++ profphd-1.0.40/debian/patches/series 2013-08-29 06:49:50.000000000 +0000 @@ -0,0 +1 @@ +fix-pod.patch diff -Nru profphd-1.0.39/debian/rules profphd-1.0.40/debian/rules --- profphd-1.0.39/debian/rules 2011-09-27 15:29:37.000000000 +0000 +++ profphd-1.0.40/debian/rules 2013-05-21 15:30:41.000000000 +0000 @@ -6,3 +6,7 @@ # Add here any variable or target overrides you need. DEB_MAKE_BUILD_TARGET = prefix=/usr all DEB_MAKE_INSTALL_TARGET = prefix=/usr DESTDIR=$(CURDIR)/debian/tmp/ install + +get-orig-source: + mkdir -p ../tarballs + uscan --verbose --force-download --destdir=../tarballs diff -Nru profphd-1.0.39/debian/watch profphd-1.0.40/debian/watch --- profphd-1.0.39/debian/watch 2012-08-14 17:55:07.000000000 +0000 +++ profphd-1.0.40/debian/watch 2012-10-06 07:51:18.000000000 +0000 @@ -1,2 +1,2 @@ version=3 -ftp://rostlab.org/profphd/profphd-([0-9.]+)\.tar\.[a-z]z debian uupdate +opts=pasv ftp://rostlab.org/profphd/profphd-([0-9.]+)\.tar\.[a-z]z debian uupdate diff -Nru profphd-1.0.39/src/prof/embl/scr/conv_phd2ascii.pl profphd-1.0.40/src/prof/embl/scr/conv_phd2ascii.pl --- profphd-1.0.39/src/prof/embl/scr/conv_phd2ascii.pl 2011-09-28 12:37:19.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/conv_phd2ascii.pl 2013-05-19 16:43:41.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; # $scrName=$0;$scrName=~s/^.*\/|\.pl//g; $scrGoal="converts a PHD.rdb file to PHD.phd ASCII human readable format.\n". diff -Nru profphd-1.0.39/src/prof/embl/scr/conv_phd2casp2.pl profphd-1.0.40/src/prof/embl/scr/conv_phd2casp2.pl --- profphd-1.0.39/src/prof/embl/scr/conv_phd2casp2.pl 2011-06-21 17:36:54.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/conv_phd2casp2.pl 2013-05-19 16:44:07.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; # # convert PHD .rdb_phd into CASP2 format # diff -Nru profphd-1.0.39/src/prof/embl/scr/conv_phd2casp4.pl profphd-1.0.40/src/prof/embl/scr/conv_phd2casp4.pl --- profphd-1.0.39/src/prof/embl/scr/conv_phd2casp4.pl 2011-06-21 17:37:10.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/conv_phd2casp4.pl 2013-05-19 16:44:11.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; # # convert PHD .rdb_phd into CASP4 format # diff -Nru profphd-1.0.39/src/prof/embl/scr/conv_phd2dssp.pl profphd-1.0.40/src/prof/embl/scr/conv_phd2dssp.pl --- profphd-1.0.39/src/prof/embl/scr/conv_phd2dssp.pl 2011-06-21 17:37:01.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/conv_phd2dssp.pl 2013-05-19 16:44:09.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # phd2dssp # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff -Nru profphd-1.0.39/src/prof/embl/scr/conv_phd2hssp.pl profphd-1.0.40/src/prof/embl/scr/conv_phd2hssp.pl --- profphd-1.0.39/src/prof/embl/scr/conv_phd2hssp.pl 2011-09-27 16:58:45.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/conv_phd2hssp.pl 2013-05-19 16:43:29.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ $scriptName= "phd2hssp"; diff -Nru profphd-1.0.39/src/prof/embl/scr/conv_phd2html.pl profphd-1.0.40/src/prof/embl/scr/conv_phd2html.pl --- profphd-1.0.39/src/prof/embl/scr/conv_phd2html.pl 2011-09-28 12:37:02.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/conv_phd2html.pl 2013-05-19 16:43:59.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; # $scrName=$0;$scrName=~s/^.*\/|\.pl//g; $scrGoal="convert PHDrdb to HTML"; diff -Nru profphd-1.0.39/src/prof/embl/scr/conv_phd2html2000.pl profphd-1.0.40/src/prof/embl/scr/conv_phd2html2000.pl --- profphd-1.0.39/src/prof/embl/scr/conv_phd2html2000.pl 2011-09-28 12:42:34.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/conv_phd2html2000.pl 2013-05-19 16:44:02.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; # $scrName=$0;$scrName=~s/^.*\/|\.pl//g; $scrGoal="convert PHDrdb to HTML"; diff -Nru profphd-1.0.39/src/prof/embl/scr/conv_phd2msf.pl profphd-1.0.40/src/prof/embl/scr/conv_phd2msf.pl --- profphd-1.0.39/src/prof/embl/scr/conv_phd2msf.pl 2011-06-21 17:36:03.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/conv_phd2msf.pl 2013-05-19 16:43:35.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # phd2msf # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff -Nru profphd-1.0.39/src/prof/embl/scr/conv_rdb2pred.pl profphd-1.0.40/src/prof/embl/scr/conv_rdb2pred.pl --- profphd-1.0.39/src/prof/embl/scr/conv_rdb2pred.pl 2011-06-21 17:37:05.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/conv_rdb2pred.pl 2013-05-19 16:43:37.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #---------------------------------------------------------------------- # phdrdb_to_pred # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff -Nru profphd-1.0.39/src/prof/embl/scr/ctime.pl profphd-1.0.40/src/prof/embl/scr/ctime.pl --- profphd-1.0.39/src/prof/embl/scr/ctime.pl 2009-08-18 09:05:57.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/ctime.pl 2013-05-19 16:43:45.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #;# ctime.pl is a simple Perl emulation for the well known ctime(3C) function. ;# ;# Waldemar Kebsch, Federal Republic of Germany, November 1988 diff -Nru profphd-1.0.39/src/prof/embl/scr/lib/all5.pl profphd-1.0.40/src/prof/embl/scr/lib/all5.pl --- profphd-1.0.39/src/prof/embl/scr/lib/all5.pl 2011-06-21 17:41:03.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/lib/all5.pl 2013-05-19 16:42:47.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # Copyright June, 1998 # # Burkhard Rost rost@LION-ag.de,rost@EMBL-heidelberg.de # diff -Nru profphd-1.0.39/src/prof/embl/scr/lib/br.pl profphd-1.0.40/src/prof/embl/scr/lib/br.pl --- profphd-1.0.39/src/prof/embl/scr/lib/br.pl 2011-06-21 17:35:12.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/lib/br.pl 2013-05-19 16:43:09.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # Copyright Sep, 1998 # # Burkhard Rost rost@LION-ag.de,rost@EMBL-heidelberg.de # diff -Nru profphd-1.0.39/src/prof/embl/scr/lib/comp.pl profphd-1.0.40/src/prof/embl/scr/lib/comp.pl --- profphd-1.0.39/src/prof/embl/scr/lib/comp.pl 2011-06-21 17:41:11.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/lib/comp.pl 2013-05-19 16:42:56.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # Copyright Sep, 1998 # # Burkhard Rost rost@LION-ag.de,rost@EMBL-heidelberg.de # diff -Nru profphd-1.0.39/src/prof/embl/scr/lib/ctime.pl profphd-1.0.40/src/prof/embl/scr/lib/ctime.pl --- profphd-1.0.39/src/prof/embl/scr/lib/ctime.pl 2009-08-18 09:05:56.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/lib/ctime.pl 2013-05-19 16:43:04.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #;# ctime.pl is a simple Perl emulation for the well known ctime(3C) function. ;# ;# Waldemar Kebsch, Federal Republic of Germany, November 1988 diff -Nru profphd-1.0.39/src/prof/embl/scr/lib/file.pl profphd-1.0.40/src/prof/embl/scr/lib/file.pl --- profphd-1.0.39/src/prof/embl/scr/lib/file.pl 2011-06-21 17:35:17.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/lib/file.pl 2013-05-19 16:43:02.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # Copyright Sep, 1998 # # Burkhard Rost rost@LION-ag.de,rost@EMBL-heidelberg.de # diff -Nru profphd-1.0.39/src/prof/embl/scr/lib/formats.pl profphd-1.0.40/src/prof/embl/scr/lib/formats.pl --- profphd-1.0.39/src/prof/embl/scr/lib/formats.pl 2011-09-28 12:31:44.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/lib/formats.pl 2013-05-19 16:42:45.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # Copyright Sep, 1998 # # Burkhard Rost rost@LION-ag.de,rost@EMBL-heidelberg.de # diff -Nru profphd-1.0.39/src/prof/embl/scr/lib/hssp.pl profphd-1.0.40/src/prof/embl/scr/lib/hssp.pl --- profphd-1.0.39/src/prof/embl/scr/lib/hssp.pl 2011-09-28 12:31:53.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/lib/hssp.pl 2013-05-19 16:42:50.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # Copyright Sep, 1998 # # Burkhard Rost rost@LION-ag.de,rost@EMBL-heidelberg.de # diff -Nru profphd-1.0.39/src/prof/embl/scr/lib/hssp_new.pl profphd-1.0.40/src/prof/embl/scr/lib/hssp_new.pl --- profphd-1.0.39/src/prof/embl/scr/lib/hssp_new.pl 2011-09-28 12:31:58.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/lib/hssp_new.pl 2013-05-19 16:42:39.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; foreach $arg (@ARGV){ $kwd=""; diff -Nru profphd-1.0.39/src/prof/embl/scr/lib/molbio.pl profphd-1.0.40/src/prof/embl/scr/lib/molbio.pl --- profphd-1.0.39/src/prof/embl/scr/lib/molbio.pl 2011-06-21 17:35:14.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/lib/molbio.pl 2013-05-19 16:43:07.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # Copyright Sep, 1998 # # Burkhard Rost rost@LION-ag.de,rost@EMBL-heidelberg.de # diff -Nru profphd-1.0.39/src/prof/embl/scr/lib/prot.pl profphd-1.0.40/src/prof/embl/scr/lib/prot.pl --- profphd-1.0.39/src/prof/embl/scr/lib/prot.pl 2011-09-28 12:32:07.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/lib/prot.pl 2013-05-19 16:43:12.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # Copyright Sep, 1998 # # Burkhard Rost rost@LION-ag.de,rost@EMBL-heidelberg.de # diff -Nru profphd-1.0.39/src/prof/embl/scr/lib/scr.pl profphd-1.0.40/src/prof/embl/scr/lib/scr.pl --- profphd-1.0.39/src/prof/embl/scr/lib/scr.pl 2011-09-28 12:34:36.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/lib/scr.pl 2013-05-19 16:42:42.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # Copyright Sep, 1998 # # Burkhard Rost rost@LION-ag.de,rost@EMBL-heidelberg.de # diff -Nru profphd-1.0.39/src/prof/embl/scr/lib/sys.pl profphd-1.0.40/src/prof/embl/scr/lib/sys.pl --- profphd-1.0.39/src/prof/embl/scr/lib/sys.pl 2010-08-27 07:40:31.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/lib/sys.pl 2013-05-19 16:42:59.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; use Carp; #------------------------------------------------------------------------------# # Copyright June, 1998 # diff -Nru profphd-1.0.39/src/prof/embl/scr/lib-phdhtml.pm profphd-1.0.40/src/prof/embl/scr/lib-phdhtml.pm --- profphd-1.0.39/src/prof/embl/scr/lib-phdhtml.pm 2010-05-14 22:15:07.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/lib-phdhtml.pm 2013-05-19 16:43:53.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; ##------------------------------------------------------------------------------# # Copyright Sep, 1998 # # Burkhard Rost rost@LION-ag.de,rost@columbia.edu # diff -Nru profphd-1.0.39/src/prof/embl/scr/pack/copf.pm profphd-1.0.40/src/prof/embl/scr/pack/copf.pm --- profphd-1.0.39/src/prof/embl/scr/pack/copf.pm 2011-09-28 12:36:25.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/pack/copf.pm 2013-05-19 16:43:16.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; ##------------------------------------------------------------------------------# # Copyright 1998 # # Burkhard Rost rost@EMBL-Heidelberg.DE # diff -Nru profphd-1.0.39/src/prof/embl/scr/pack/hssp_filter.pm profphd-1.0.40/src/prof/embl/scr/pack/hssp_filter.pm --- profphd-1.0.39/src/prof/embl/scr/pack/hssp_filter.pm 2011-09-28 12:35:35.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/pack/hssp_filter.pm 2013-05-19 16:43:24.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; ##------------------------------------------------------------------------------# # Copyright 1998 # # Burkhard Rost rost@EMBL-Heidelberg.DE # diff -Nru profphd-1.0.39/src/prof/embl/scr/pack/phd_htmfil.pm profphd-1.0.40/src/prof/embl/scr/pack/phd_htmfil.pm --- profphd-1.0.39/src/prof/embl/scr/pack/phd_htmfil.pm 2010-05-14 14:34:23.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/pack/phd_htmfil.pm 2013-05-19 16:43:18.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; ##------------------------------------------------------------------------------# # Copyright 1998 # # Burkhard Rost rost@EMBL-Heidelberg.DE # diff -Nru profphd-1.0.39/src/prof/embl/scr/pack/phd_htmref.pm profphd-1.0.40/src/prof/embl/scr/pack/phd_htmref.pm --- profphd-1.0.39/src/prof/embl/scr/pack/phd_htmref.pm 2011-09-28 12:34:49.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/pack/phd_htmref.pm 2013-05-19 16:43:21.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; ##------------------------------------------------------------------------------# # Copyright 1998 # # Burkhard Rost rost@EMBL-Heidelberg.DE # diff -Nru profphd-1.0.39/src/prof/embl/scr/pack/phd_htmtop.pm profphd-1.0.40/src/prof/embl/scr/pack/phd_htmtop.pm --- profphd-1.0.39/src/prof/embl/scr/pack/phd_htmtop.pm 2011-09-28 12:34:59.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/pack/phd_htmtop.pm 2013-05-19 16:43:14.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; ##------------------------------------------------------------------------------# # Copyright 1998 # # Burkhard Rost rost@EMBL-Heidelberg.DE # diff -Nru profphd-1.0.39/src/prof/embl/scr/pdbid_sort.pl profphd-1.0.40/src/prof/embl/scr/pdbid_sort.pl --- profphd-1.0.39/src/prof/embl/scr/pdbid_sort.pl 2011-06-21 17:37:14.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/pdbid_sort.pl 2013-05-19 16:43:39.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #---------------------------------------------------------------------- # pdbid_sort # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff -Nru profphd-1.0.39/src/prof/embl/scr/phd-mergeRdbSecAcc.pl profphd-1.0.40/src/prof/embl/scr/phd-mergeRdbSecAcc.pl --- profphd-1.0.39/src/prof/embl/scr/phd-mergeRdbSecAcc.pl 2011-06-21 17:37:23.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/phd-mergeRdbSecAcc.pl 2013-05-19 16:43:48.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; # # merges PHD.rdb files (Sec,Acc,Htm) # diff -Nru profphd-1.0.39/src/prof/embl/scr/phd_htmfil.pl profphd-1.0.40/src/prof/embl/scr/phd_htmfil.pl --- profphd-1.0.39/src/prof/embl/scr/phd_htmfil.pl 2011-06-21 17:36:11.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/phd_htmfil.pl 2013-05-19 16:44:14.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #---------------------------------------------------------------------- # htmfil_phd # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff -Nru profphd-1.0.39/src/prof/embl/scr/phd_htmref.pl profphd-1.0.40/src/prof/embl/scr/phd_htmref.pl --- profphd-1.0.39/src/prof/embl/scr/phd_htmref.pl 2011-06-21 17:36:15.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/phd_htmref.pl 2013-05-19 16:43:26.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # htmref_phd # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff -Nru profphd-1.0.39/src/prof/embl/scr/phd_htmtop.pl profphd-1.0.40/src/prof/embl/scr/phd_htmtop.pl --- profphd-1.0.39/src/prof/embl/scr/phd_htmtop.pl 2011-06-21 17:36:19.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/phd_htmtop.pl 2013-05-19 16:43:57.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # htmtop_phd # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff -Nru profphd-1.0.39/src/prof/embl/scr/rdb_tokg.pl profphd-1.0.40/src/prof/embl/scr/rdb_tokg.pl --- profphd-1.0.39/src/prof/embl/scr/rdb_tokg.pl 2011-06-21 17:37:17.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/rdb_tokg.pl 2013-05-19 16:43:42.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #---------------------------------------------------------------------- # rdb_tokg # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff -Nru profphd-1.0.39/src/prof/embl/scr/test-install.pl profphd-1.0.40/src/prof/embl/scr/test-install.pl --- profphd-1.0.39/src/prof/embl/scr/test-install.pl 2011-09-28 12:37:11.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/test-install.pl 2013-05-19 16:43:32.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; # $scrName=$0;$scrName=~s/^.*\/|\.pl//g; $scrGoal="testing PHD installation"; diff -Nru profphd-1.0.39/src/prof/embl/scr/tlphd-add-nali2rdb.pl profphd-1.0.40/src/prof/embl/scr/tlphd-add-nali2rdb.pl --- profphd-1.0.39/src/prof/embl/scr/tlphd-add-nali2rdb.pl 2011-09-28 12:36:34.000000000 +0000 +++ profphd-1.0.40/src/prof/embl/scr/tlphd-add-nali2rdb.pl 2013-05-19 16:43:44.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; # $scrName=$0;$scrName=~s/^.*\/|\.pl//g; $scrGoal="add line with number of alignments to PHD.rdb file\n". diff -Nru profphd-1.0.39/src/prof/profconv profphd-1.0.40/src/prof/profconv --- profphd-1.0.39/src/prof/profconv 2011-09-28 12:40:20.000000000 +0000 +++ profphd-1.0.40/src/prof/profconv 2013-05-19 16:46:32.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl -w +no warnings 'deprecated'; # $scrName=$0;$scrName=~s/^.*\/|\.pl//g; $scrGoal="converts a PROF.rdb file to PROF.prof ASCII human readable format.\n". diff -Nru profphd-1.0.39/src/prof/scr/conv_prof.pl profphd-1.0.40/src/prof/scr/conv_prof.pl --- profphd-1.0.39/src/prof/scr/conv_prof.pl 2011-09-28 12:40:05.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/conv_prof.pl 2013-05-19 16:45:44.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; # $scrName=$0;$scrName=~s/^.*\/|\.pl//g; $scrGoal="converts a PROF.rdb file to PROF.prof ASCII human readable format.\n". diff -Nru profphd-1.0.39/src/prof/scr/conv_prof2hssp.pl profphd-1.0.40/src/prof/scr/conv_prof2hssp.pl --- profphd-1.0.39/src/prof/scr/conv_prof2hssp.pl 2011-09-27 16:59:17.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/conv_prof2hssp.pl 2013-05-19 16:44:48.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ $scriptName= "phd2hssp"; diff -Nru profphd-1.0.39/src/prof/scr/lib/dead_code.pl profphd-1.0.40/src/prof/scr/lib/dead_code.pl --- profphd-1.0.39/src/prof/scr/lib/dead_code.pl 2009-08-18 09:05:57.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/lib/dead_code.pl 2013-05-19 16:44:17.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; ##=============================================================================== sub nnJurySigma { local(@fileOutNetLoc) = @_; diff -Nru profphd-1.0.39/src/prof/scr/lib/lib-proferr.pl profphd-1.0.40/src/prof/scr/lib/lib-proferr.pl --- profphd-1.0.39/src/prof/scr/lib/lib-proferr.pl 2011-09-28 12:37:55.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/lib/lib-proferr.pl 2013-05-19 16:44:28.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # Copyright Sep, 1998 # # Burkhard Rost rost@LION-ag.de,rost@EMBL-heidelberg.de # diff -Nru profphd-1.0.39/src/prof/scr/lib/lib-profhtml.pl profphd-1.0.40/src/prof/scr/lib/lib-profhtml.pl --- profphd-1.0.39/src/prof/scr/lib/lib-profhtml.pl 2011-09-28 12:37:32.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/lib/lib-profhtml.pl 2013-05-19 16:44:33.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; ##------------------------------------------------------------------------------# # Copyright Sep, 1998 # # Burkhard Rost rost@LION-ag.de,rost@columbia.edu # diff -Nru profphd-1.0.39/src/prof/scr/lib/lib-profwrt.pl profphd-1.0.40/src/prof/scr/lib/lib-profwrt.pl --- profphd-1.0.39/src/prof/scr/lib/lib-profwrt.pl 2011-09-28 12:37:37.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/lib/lib-profwrt.pl 2013-05-19 16:44:31.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; ##------------------------------------------------------------------------------# # Copyright Sep, 1998 # # Burkhard Rost rost@LION-ag.de,rost@columbia.edu # diff -Nru profphd-1.0.39/src/prof/scr/pack/tlprof_htmfil.pm profphd-1.0.40/src/prof/scr/pack/tlprof_htmfil.pm --- profphd-1.0.39/src/prof/scr/pack/tlprof_htmfil.pm 2010-05-14 14:49:55.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/pack/tlprof_htmfil.pm 2013-05-19 16:44:35.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; ##------------------------------------------------------------------------------# # Copyright 1998 # # Burkhard Rost rost@EMBL-Heidelberg.DE # diff -Nru profphd-1.0.39/src/prof/scr/pack/tlprof_htmref.pm profphd-1.0.40/src/prof/scr/pack/tlprof_htmref.pm --- profphd-1.0.39/src/prof/scr/pack/tlprof_htmref.pm 2011-09-28 12:39:19.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/pack/tlprof_htmref.pm 2013-05-19 16:44:37.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; ##------------------------------------------------------------------------------# # Copyright 1998 # # Burkhard Rost rost@EMBL-Heidelberg.DE # diff -Nru profphd-1.0.39/src/prof/scr/pack/tlprof_htmtop.pm profphd-1.0.40/src/prof/scr/pack/tlprof_htmtop.pm --- profphd-1.0.39/src/prof/scr/pack/tlprof_htmtop.pm 2011-09-28 12:39:27.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/pack/tlprof_htmtop.pm 2013-05-19 16:44:39.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; ##------------------------------------------------------------------------------# # Copyright 1998 # # Burkhard Rost rost@EMBL-Heidelberg.DE # diff -Nru profphd-1.0.39/src/prof/scr/prof.pl profphd-1.0.40/src/prof/scr/prof.pl --- profphd-1.0.39/src/prof/scr/prof.pl 2011-06-21 17:38:06.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/prof.pl 2013-05-19 16:44:41.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # Copyright 1998 # # Burkhard Rost rost@LION-ag.de,rost@columbia.edu # diff -Nru profphd-1.0.39/src/prof/scr/test-install.pl profphd-1.0.40/src/prof/scr/test-install.pl --- profphd-1.0.39/src/prof/scr/test-install.pl 2011-09-28 12:39:43.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/test-install.pl 2013-05-19 16:45:38.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; # $scrName=$0;$scrName=~s/^.*\/|\.pl//g; $scrGoal="testing PROF installation"; diff -Nru profphd-1.0.39/src/prof/scr/tlprof_blastmat2hssp.pl profphd-1.0.40/src/prof/scr/tlprof_blastmat2hssp.pl --- profphd-1.0.39/src/prof/scr/tlprof_blastmat2hssp.pl 2011-09-28 12:39:33.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/tlprof_blastmat2hssp.pl 2013-05-19 16:45:28.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; # $scrName=$0;$scrName=~s/^.*\/|\.pl//g; $scrGoal="substitutes HSSP profiles by PSI-BLAST profiles\n". diff -Nru profphd-1.0.39/src/prof/scr/tlprof_htmfil.pl profphd-1.0.40/src/prof/scr/tlprof_htmfil.pl --- profphd-1.0.39/src/prof/scr/tlprof_htmfil.pl 2011-06-21 17:38:25.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/tlprof_htmfil.pl 2013-05-19 16:44:45.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #---------------------------------------------------------------------- # htmfil_phd # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff -Nru profphd-1.0.39/src/prof/scr/tlprof_htmref.pl profphd-1.0.40/src/prof/scr/tlprof_htmref.pl --- profphd-1.0.39/src/prof/scr/tlprof_htmref.pl 2011-06-21 17:38:29.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/tlprof_htmref.pl 2013-05-19 16:45:17.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # htmref_phd # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff -Nru profphd-1.0.39/src/prof/scr/tlprof_htmtop.pl profphd-1.0.40/src/prof/scr/tlprof_htmtop.pl --- profphd-1.0.39/src/prof/scr/tlprof_htmtop.pl 2011-06-21 17:38:33.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/tlprof_htmtop.pl 2013-05-19 16:45:35.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; #------------------------------------------------------------------------------# # htmtop_phd # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff -Nru profphd-1.0.39/src/prof/scr/tlprof_jury.pl profphd-1.0.40/src/prof/scr/tlprof_jury.pl --- profphd-1.0.39/src/prof/scr/tlprof_jury.pl 2011-09-28 12:39:52.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/tlprof_jury.pl 2013-05-19 16:45:33.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; # $scrName=$0;$scrName=~s/^.*\/|\.pl//g; $scrGoal="compiles jury for PHD.rdb files.\n". diff -Nru profphd-1.0.39/src/prof/scr/tlprof_ri-sigma.pl profphd-1.0.40/src/prof/scr/tlprof_ri-sigma.pl --- profphd-1.0.39/src/prof/scr/tlprof_ri-sigma.pl 2011-09-28 12:39:38.000000000 +0000 +++ profphd-1.0.40/src/prof/scr/tlprof_ri-sigma.pl 2013-05-19 16:45:31.000000000 +0000 @@ -1,4 +1,5 @@ #!/usr/bin/perl +no warnings 'deprecated'; # $scrName=$0;$scrName=~s/^.*\/|\.pl//g; $scrGoal="\n".