[med-svn] [Git][med-team/profnet][master] 10 commits: routine-update: Standards-Version: 4.5.1

Andreas Tille gitlab at salsa.debian.org
Thu Nov 26 18:26:03 GMT 2020 


Andreas Tille pushed to branch master at Debian Med / profnet


Commits:
95ba271b by Andreas Tille at 2020-11-26T17:36:11+01:00
routine-update: Standards-Version: 4.5.1

- - - - -
05ae13db by Andreas Tille at 2020-11-26T17:36:11+01:00
routine-update: debhelper-compat 13

- - - - -
1b2f2f56 by Andreas Tille at 2020-11-26T17:36:24+01:00
routine-update: Add salsa-ci file

- - - - -
e7896244 by Andreas Tille at 2020-11-26T17:36:25+01:00
routine-update: Rules-Requires-Root: no

- - - - -
adb013c6 by Andreas Tille at 2020-11-26T17:36:34+01:00
Remove obsolete fields Contact, Name from debian/upstream/metadata (already present in machine-readable debian/copyright).

Changes-By: lintian-brush

- - - - -
45cb2204 by Andreas Tille at 2020-11-26T17:36:35+01:00
Replace use of deprecated $ADTTMP with $AUTOPKGTEST_TMP.

Changes-By: lintian-brush
Fixes: lintian: uses-deprecated-adttmp
See-also: https://lintian.debian.org/tags/uses-deprecated-adttmp.html

- - - - -
9b39e5f9 by Andreas Tille at 2020-11-26T17:36:35+01:00
routine-update: watch file standard 4

- - - - -
8edb1374 by Andreas Tille at 2020-11-26T19:15:01+01:00
Hack around some flags that are leading to errors in gfortran

- - - - -
62bbc32f by Andreas Tille at 2020-11-26T19:22:26+01:00
Skip test of profnet-snapfun
    Closes: #905206
    Remark: This is really not the best solution but since upstream does
    not provide any help the only chance to keep that package and its
    rdepends

- - - - -
a2e31a8b by Andreas Tille at 2020-11-26T19:25:14+01:00
Upload to unstable

- - - - -


11 changed files:

- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/skip_some_flags_for_fortran.patch
- + debian/profnet-snapfun.README.Debian
- debian/rules
- + debian/salsa-ci.yml
- debian/tests/control
- debian/tests/installation-test
- debian/upstream/metadata
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,5 +1,6 @@
-profnet (1.0.22-7) UNRELEASED; urgency=medium
+profnet (1.0.22-7) unstable; urgency=medium
 
+  [ Michael R. Crusoe ]
   * Team upload.
   * debhelper-compat 12
   * Standards-Version: 4.4.1
@@ -9,7 +10,23 @@ profnet (1.0.22-7) UNRELEASED; urgency=medium
   * Set upstream metadata fields: Contact, Name.
   * Fix a spelling typo
 
- -- Michael R. Crusoe <michael.crusoe at gmail.com>  Thu, 03 Oct 2019 11:45:07 +0200
+  [ Andreas Tille ]
+  * Standards-Version: 4.5.1 (routine-update)
+  * debhelper-compat 13 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Remove obsolete fields Contact, Name from debian/upstream/metadata (already
+    present in machine-readable debian/copyright).
+  * Replace use of deprecated $ADTTMP with $AUTOPKGTEST_TMP.
+  * watch file standard 4 (routine-update)
+  * Hack around some flags that are leading to errors in gfortran
+  * Skip test of profnet-snapfun
+    Closes: #905206
+    Remark: This is really not the best solution but since upstream does
+    not provide any help the only chance to keep that package and its
+    rdepends
+
+ -- Andreas Tille <tille at debian.org>  Thu, 26 Nov 2020 19:22:38 +0100
 
 profnet (1.0.22-6) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -5,13 +5,14 @@ Uploaders: Guy Yachdav <gyachdav at rostlab.org>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                gfortran,
                rsync
-Standards-Version: 4.4.1
+Standards-Version: 4.5.1
 Vcs-Browser: https://salsa.debian.org/med-team/profnet
 Vcs-Git: https://salsa.debian.org/med-team/profnet.git
 Homepage: https://www.predictprotein.org/
+Rules-Requires-Root: no
 
 Package: profnet-bval
 Architecture: any


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 hardening.patch
 spelling
+skip_some_flags_for_fortran.patch


=====================================
debian/patches/skip_some_flags_for_fortran.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 26 Nov 2020 17:36:35 +0100
+Description: Hack around some flags that are leading to errors in gfortran
+
+--- a/src-phd/Makefile
++++ b/src-phd/Makefile
+@@ -99,7 +99,7 @@ FFLAGS := -O3 -fbounds-check
+ FFLAGS := $(FFLAGS) -Wall
+ 
+ profphd_net : phd.f lib-phd.f phdParameter.f
+-	$(F77) $(CFLAGS) $(FFLAGS) $(LDFLAGS) -o $@ phd.f lib-phd.f
++	$(F77) `echo $(CFLAGS) | sed 's/-Wformat -Werror=format-security/-fallow-argument-mismatch/'` $(FFLAGS) $(LDFLAGS) -o $@ phd.f lib-phd.f
+ 
+ #phd.o : phdParameter.f
+ 


=====================================
debian/profnet-snapfun.README.Debian
=====================================
@@ -0,0 +1,49 @@
+Attention
+=========
+
+Please expect issues with profnet-snapfun!  It caused a Segmentation fault
+in an autopkgtest which was deactivated.  This is documented in the bug
+report at
+
+    https://bugs.debian.org/905206
+
+In case this program might turn out to be totally useless we need to
+remove this binary package since there is no support from its authors
+any more.  Please report any issue via
+
+    reportbug profnet-snapfun
+
+
+profnet
+=======
+profnet_* binaries are neural network implementations in Fortran.
+Due to the original design of the code, a specific binary is compiled
+for each particular network architecture, changing certain constants
+in the source code.  Therefore, there is a binary for every network
+architecture used.  Note: certain array structures are intentionally
+indexed out of bounds in some of the binaries!
+
+Q: Why so many binary packages?
+-------------------------------
+There are a handful of prediction methods built around each of the binary
+profnet packages.  Each depends on the matching profnet binary package.
+Each prediction method requires a different neural network architecture
+and therefore - due to the design of the code - a different binary.
+Binaries are compiled with constants set to the architecture of
+the network and are therefore not reusable for other architectures.
+To further develop the code beyond regular maintenance for compiler and
+architecture updates is not planned since a complete reimplementation
+of these networks with a neural network library is already underway.
+
+Publications of predictors that use these neural networks
+---------------------------------------------------------
+Note: this list contains references only to the secondary structure and
+accessibility predictor (profnet-prof and profphd-net).
+References for the other methods are provided in the man pages of the
+respective methods' predictor commands, e.g. profbval(1).
+
+* Rost, B. and Sander, C. (1994a). Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 19(1), 55-72.
+* Rost, B. and Sander, C. (1994b). Conservation and prediction of solvent accessibility in protein families. Proteins, 20(3), 216-26.
+* Rost, B., Casadio, R., Fariselli, P., and Sander, C. (1995). Transmembrane helices predicted at 95 Protein Sci, 4(3), 521-33.
+
+-- Laszlo Kajan <lkajan at rostlab.org>  Tue, 14 Jun 2011 18:50:52 +0200


=====================================
debian/rules
=====================================
@@ -3,6 +3,7 @@
 #export DH_VERBOSE=1
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export FFLAGS += -fallow-argument-mismatch
 
 %:
 	dh $@


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/tests/control
=====================================
@@ -10,5 +10,6 @@ Depends: @
 Test-Command: sh debian/tests/installation-test profnet-isis
 Depends: @
 
-Test-Command: sh debian/tests/installation-test profnet-snapfun
-Depends: @
+# This test fails - see #905206
+#Test-Command: sh debian/tests/installation-test profnet-snapfun
+#Depends: @


=====================================
debian/tests/installation-test
=====================================
@@ -16,12 +16,12 @@ fi
 command=$(echo $pkg | sed -e "s/-/_/g") 
 #this returns corresponding executable name
 
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cd $ADTTMP
+cd $AUTOPKGTEST_TMP
 
 cp -a /usr/share/doc/${pkg}/examples/* .
 find . -type f -name "*.gz" -exec gunzip \{\} \;


=====================================
debian/upstream/metadata
=====================================
@@ -18,5 +18,3 @@ Registry:
    Entry: NA
  - Name: SciCrunch
    Entry: NA
-Name: profnet
-Contact: assistant at rostlab.org


=====================================
debian/watch
=====================================
@@ -1,2 +1,2 @@
-version=3
+version=4
 opts=pasv ftp://rostlab.org/profnet/profnet-([0-9.]+)\.tar\.gz



View it on GitLab: https://salsa.debian.org/med-team/profnet/-/compare/716f250763da1c2f50c27c6a0b2181232fa9daef...a2e31a8bad05cb3ca32d810add889b0c63320ed0

-- 
View it on GitLab: https://salsa.debian.org/med-team/profnet/-/compare/716f250763da1c2f50c27c6a0b2181232fa9daef...a2e31a8bad05cb3ca32d810add889b0c63320ed0
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