[med-svn] [logol] 01/01: fix drmaa removal, remove unexpected symlink
Olivier Sallou
osallou at debian.org
Tue Oct 10 09:17:20 UTC 2017
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository logol.
commit b3741acfd9860177e1ba6f9b057eb89711c9c54c
Author: Olivier Sallou <osallou at debian.org>
Date: Tue Oct 10 06:50:21 2017 +0000
fix drmaa removal, remove unexpected symlink
---
debian/changelog | 7 ++++---
debian/control | 2 --
debian/logol.links | 6 +++---
debian/patches/fix_swipl_declarations | 16 ++++++++++++++++
debian/patches/patch_java8 | 16 ++++++++++++++++
debian/patches/series | 2 ++
debian/rules | 11 +++++++++--
7 files changed, 50 insertions(+), 10 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index da58838..4fdce64 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,12 @@
-logol (1.7.5-2) UNRELEASED; urgency=medium
+logol (1.7.5-2) unstable; urgency=medium
* Team upload.
* Moved packaging from SVN to Git
* cme fix dpkg-control
* Standards-Version: 4.1.1
- * (Build-)Depends: libdrmaa1.0-java
- Closes: #877461
+ * remove drmaa sym link as patches remove drmaa support
+ while drmaa is back in Debian, new release is not compatible
+ with current upstream code, Closes: #877461
* debhelper 10
-- Andreas Tille <tille at debian.org> Sat, 07 Oct 2017 21:23:51 +0200
diff --git a/debian/control b/debian/control
index 9860c7a..166ced8 100644
--- a/debian/control
+++ b/debian/control
@@ -16,7 +16,6 @@ Build-Depends: debhelper (>= 10),
libcommons-configuration-java,
libcommons-lang-java,
libcommons-logging-java,
- libdrmaa1.0-java,
libxalan2-java,
libxerces2-java,
junit4,
@@ -48,7 +47,6 @@ Depends: ${shlibs:Depends},
libcommons-configuration-java,
libcommons-lang-java,
libcommons-logging-java,
- libdrmaa1.0-java,
libxalan2-java,
libxerces2-java,
libmail-java,
diff --git a/debian/logol.links b/debian/logol.links
index 5f9e135..8280b5a 100644
--- a/debian/logol.links
+++ b/debian/logol.links
@@ -2,9 +2,9 @@ usr/share/logol/LogolMultiExec.sh usr/bin/LogolMultiExec
usr/share/logol/LogolExec.sh usr/bin/LogolExec
etc/logol/logol.properties usr/share/logol/prolog/logol.properties
usr/share/java/biojava.jar usr/share/logol/lib/biojava.jar
-usr/share/java/activation.jar usr/share/logol/lib/activation.jar
-usr/share/java/bytecode.jar usr/share/logol/lib/bytecode.jar
-usr/share/java/drmaa.jar usr/share/logol/lib/drmaa.jar
+#usr/share/java/activation.jar usr/share/logol/lib/activation.jar
+#usr/share/java/bytecode.jar usr/share/logol/lib/bytecode.jar
+#usr/share/java/drmaa.jar usr/share/logol/lib/drmaa.jar
usr/share/java/antlr3-runtime.jar usr/share/logol/lib/antlr.jar
usr/share/java/commons-cli.jar usr/share/logol/lib/commons-cli.jar
usr/share/java/commons-lang.jar usr/share/logol/lib/commons-lang.jar
diff --git a/debian/patches/fix_swipl_declarations b/debian/patches/fix_swipl_declarations
new file mode 100644
index 0000000..b6eb84e
--- /dev/null
+++ b/debian/patches/fix_swipl_declarations
@@ -0,0 +1,16 @@
+Author: Olivier Sallou <osallou at debian.org>
+Subject: swi-prolog raise error instead of warnings for undefined modules
+Description: swi-prolog raise an error for exported procedure not matching
+ declared procedure.
+ It also raises error on modules declared for sicstus prolog. Patch need to
+ remove them (not needed for swi-prolog)
+Forwarded: yes
+Bug: https://github.com/genouest/logol/issues/1
+--- a/prolog/logol.pl
++++ b/prolog/logol.pl
+@@ -1,4 +1,4 @@
+-:- module(logol,[writeFinalMatches/0,isMin/5,replaceMatch/4,appendMatch/3,getCounter/1,config/1,optimalmatch/5,matchstore/2,isMax/3,parseResults/2,checkAlphabetPercentage/3,mapListExact/2,mapListGlobal/2,mapListLocal/2,mapListLocal0/2,matchExist/2,mapModels/3,externalinterfacewithspacer/2,externalinterface/2,notpred_pos/6,between/3,notexact_pos/6,notexact/3,matchExist/1,mapModels/2,mapList/2,mydb/1,matchlist/2,isexactwithgaponly/5,isexactwithgaponly_pos/5,setParent/2,getParent/2,logData [...]
++:- module(logol,[writeFinalMatches/0,isMin/5,replaceMatch/4,appendMatch/3,getCounter/1,config/1,optimalmatch/5,matchstore/2,isMax/3,parseResults/2,checkAlphabetPercentage/3,mapListExact/2,mapListGlobal/2,mapListLocal/2,mapListLocal0/2,matchExist/2,mapModels/3,notpred_pos/6,between/3,notexact_pos/6,notexact/3,matchExist/1,mapModels/2,mapList/2,mydb/1,matchlist/2,isexactwithgaponly/5,isexactwithgaponly_pos/5,setParent/2,getParent/2,logData/2,logolMain/5,cut_sequence/3,isequal/2,isexact_po [...]
+ %:- module(logol,[writeFinalMatches/0,isMin/5,replaceMatch/4,appendMatch/3,getCounter/1,config/1,optimalmatch/5,matchstore/2,isMax/3,parseResults/2,checkAlphabetPercentage/3,mapListExact/2,mapListGlobal/2,mapListLocal/2,mapListLocal0/2,matchExist/2,mapModels/3,externalinterfacewithspacer/2,externalinterface/2,notpred_pos/6,between/3,notexact_pos/6,notexact/3,matchExist/1,mapModels/2,mapList/2,mydb/1,matchlist/2,isexactwithgaponly/5,isexactwithgaponly_pos/5,setParent/2,getParent/2,logDat [...]
+
+
diff --git a/debian/patches/patch_java8 b/debian/patches/patch_java8
new file mode 100644
index 0000000..c1b2738
--- /dev/null
+++ b/debian/patches/patch_java8
@@ -0,0 +1,16 @@
+--- a/src/org/irisa/genouest/logol/dispatcher/SGEJobManager.java
++++ b/src/org/irisa/genouest/logol/dispatcher/SGEJobManager.java
+@@ -80,11 +80,11 @@
+ jt.setOutputPath(":" + out+".out");
+ jt.setErrorPath(":" + out + ".err");
+ if(OS.startsWith("win")) {
+- jt.setArgs(new String[] {installPath + System.getProperty(Constants.FILESEPARATORPROPERTY)+ "LogolExec.rb", arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)});
++ jt.setArgs(new ArrayList<String> {installPath + System.getProperty(Constants.FILESEPARATORPROPERTY)+ "LogolExec.rb", arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)});
+ jt.setRemoteCommand("ruby");
+ }
+ else {
+- jt.setArgs(new String[] {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)});
++ jt.setArgs(new ArrayList<String> {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)});
+ jt.setRemoteCommand(installPath + System.getProperty(Constants.FILESEPARATORPROPERTY)+ "LogolExec.sh");
+ }
+ jobId = session.runJob(jt);
diff --git a/debian/patches/series b/debian/patches/series
index 7d7b238..34476a7 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,5 @@
remove_drmaa_support
+#patch_java8
fixLibPath
#fixDrmmato6.2
setDebianDirs
@@ -6,3 +7,4 @@ fix_doc_generation
remove_rubygems_usage
#fix_swipl72
fix_antlr35
+fix_swipl_declarations
diff --git a/debian/rules b/debian/rules
index 7fc6614..0fbc32a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,8 +11,10 @@ DEB_ANT_ARGS=-Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5
dh $@
override_dh_auto_build:
+ if [ ! -e lib ]; then mkdir -p lib; fi
mv tools/pldoc.sty tools/pldoc.sty.upstream
dh_auto_build -- $(DEB_ANT_ARGS)
+ mkdir -p test/tmp test/results
ant -f build.xml doc
override_dh_install:
@@ -26,10 +28,15 @@ override_dh_install:
if [ -e debian/logol ]; then chmod -f 755 debian/logol/usr/share/logol/tools/*.rb; fi
if [ -e debian/logol ]; then chmod -f 755 debian/logol/usr/share/logol/tools/mycostfunction; fi
+override_dh_auto_clean:
+ if [ ! -e test/tmp ]; then mkdir -p test/tmp; fi
+ if [ ! -e test/results ]; then mkdir -p test/results; fi
+ dh_auto_clean
+
override_dh_clean:
if [ -e tools/pldoc.sty.upstream ]; then mv tools/pldoc.sty.upstream tools/pldoc.sty; fi
- mkdir -p test/tmp
- mkdir -p test/results
+ if [ ! -e test/tmp ]; then mkdir -p test/tmp; fi
+ if [ ! -e test/results ]; then mkdir -p test/results; fi
dh_clean
rm -f Swi*.xml
rm -f prolog/*.exe
--
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