Bug#776131: Bug#778665: unblock: logol/1.7.0-2
Hi, On Thu, Feb 19, 2015 at 11:39:20AM +, olivier sallou wrote: > I can well undestand that you are the upstream author and are confident > with the introduced changes. This doesn't mean that any change you may > introduce is bug-free. Any change requires some amount of time for > testing, > even if appears trivial. > > It only removes one of the execution options. I unblocked logol and added a removal hint for gridengine. If it turns out there are issues with the new version of logol, it can still be removed from jessie. Cheers, Ivo -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#778665: unblock: logol/1.7.0-2
Le Thu Feb 19 2015 at 11:08:46 AM, Mehdi Dogguy a écrit : > Le 2015-02-19 07:50, olivier sallou a écrit : > > > >> b) It was not part of past stable releases. > > > > As it did not exist before, it could not be in previous stable > > releases > > Please understand that this is an important bit of information for us > since > it means that there are no stable users that will keep an old and no > secure > version of the software... because it has been removed from the new > stable > release. > Well this matters to keeping gridengine or not. Logol has no security issue by itself, it only depends on a gridengine library. > > > c) I am not comfortable with the introduced changes to remove DRMAA > > support. > > I am the author of the software, so I can tell you changes are fine. > > We > > just remove the drmaa support option. > > I can well undestand that you are the upstream author and are confident > with the introduced changes. This doesn't mean that any change you may > introduce is bug-free. Any change requires some amount of time for > testing, > even if appears trivial. > It only removes one of the execution options. > > Regards, > > -- > Mehdi >
Bug#778665: unblock: logol/1.7.0-2
Le 2015-02-19 07:50, olivier sallou a écrit : b) It was not part of past stable releases. As it did not exist before, it could not be in previous stable releases Please understand that this is an important bit of information for us since it means that there are no stable users that will keep an old and no secure version of the software... because it has been removed from the new stable release. c) I am not comfortable with the introduced changes to remove DRMAA support. I am the author of the software, so I can tell you changes are fine. We just remove the drmaa support option. I can well undestand that you are the upstream author and are confident with the introduced changes. This doesn't mean that any change you may introduce is bug-free. Any change requires some amount of time for testing, even if appears trivial. Regards, -- Mehdi -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#778665: unblock: logol/1.7.0-2
Le Wed Feb 18 2015 at 9:25:56 PM, Mehdi Dogguy a écrit : > On Wed, Feb 18, 2015 at 06:21:05AM +, olivier sallou < > olivier.sal...@gmail.com> wrote: > > Package: release.debian.org > > Severity: normal > > User: release.debian@packages.debian.org > > Usertags: unblock > > X-CC: debian-...@lists.debian.org > > > > Please unblock package logol > > > > I have to admit that I have troubles to take a decision for this case. > If we are going to remove gridengine, then I'd remove logol as well > because: > a) I don't know if releasing w/o DRMAA support in logol makes much sense. >Does it? > Yes it does. Logol works in local mode or drmaa mode. Here we just remove the drmaa mode. b) It was not part of past stable releases. > As it did not exist before, it could not be in previous stable releases c) I am not comfortable with the introduced changes to remove DRMAA support. > I am the author of the software, so I can tell you changes are fine. We just remove the drmaa support option. > > Also, I wonder if it is a good time to remove gridengine at all. It is > not like it needed many updates in stable or oldstable to worry about it. > My preference would be to keep gridengine and not bother ourselves. > Keeping gridengine would be fine for me ;-) But the bug causing the gridengine removal (and consequently logol) contains quite a lot of discussions already. It seems that current release contains security issues and maintenance issues. Olivier > > Any other opinions from the team? > > Regards, > > -- > Mehdi Dogguy >
Bug#778665: unblock: logol/1.7.0-2
On Wed, 2015-02-18 at 21:25 +0100, Mehdi Dogguy wrote: > On Wed, Feb 18, 2015 at 06:21:05AM +, olivier sallou > wrote: > > Package: release.debian.org > > Severity: normal > > User: release.debian@packages.debian.org > > Usertags: unblock > > X-CC: debian-...@lists.debian.org > > > > Please unblock package logol > > > > I have to admit that I have troubles to take a decision for this case. > If we are going to remove gridengine, then I'd remove logol as well > because: I'm confused. My understanding from the thread ending at https://lists.debian.org/950673988.3780910.1423380824041.javamail.zim...@irisa.fr was that we were keeping the drmaa package. [...] > Also, I wonder if it is a good time to remove gridengine at all. It is > not like it needed many updates in stable or oldstable to worry about it. > My preference would be to keep gridengine and not bother ourselves. http://lists.alioth.debian.org/pipermail/pkg-gridengine-devel/2014-October/000737.html says "It should be removed in its current state, particularly as the configuration is totally insecure and doesn't ship the components to secure it" and the package has been RFH for nearly two years. Given that and the discussion in #776131, I'm not sure keeping the package in its current state is the best idea. Regards, Adam -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#778665: unblock: logol/1.7.0-2
On Wed, Feb 18, 2015 at 06:21:05AM +, olivier sallou wrote: > Package: release.debian.org > Severity: normal > User: release.debian@packages.debian.org > Usertags: unblock > X-CC: debian-...@lists.debian.org > > Please unblock package logol > I have to admit that I have troubles to take a decision for this case. If we are going to remove gridengine, then I'd remove logol as well because: a) I don't know if releasing w/o DRMAA support in logol makes much sense. Does it? b) It was not part of past stable releases. c) I am not comfortable with the introduced changes to remove DRMAA support. Also, I wonder if it is a good time to remove gridengine at all. It is not like it needed many updates in stable or oldstable to worry about it. My preference would be to keep gridengine and not bother ourselves. Any other opinions from the team? Regards, -- Mehdi Dogguy -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#778665: unblock: logol/1.7.0-2
Package: release.debian.org
Severity: normal
User: release.debian@packages.debian.org
Usertags: unblock
X-CC: debian-...@lists.debian.org
Please unblock package logol
Logol package is affected by gridengine RC bug and removal request from
Jessie (gridengine is RC buggy and effectively unmaintained , see the
discussion
in #776131).
This patch release removes the dependency on libdrmaa-java waiting for
reintroduction in backports of gridengine. At this time, logol will put
back support and will "follow" in backports.
There is no other modification.
Debidiff is attached to mail.
diff -Nru logol-1.7.0/debian/changelog logol-1.7.0/debian/changelog
--- logol-1.7.0/debian/changelog2014-05-21 21:26:35.0 +0200
+++ logol-1.7.0/debian/changelog2015-02-05 15:24:35.0 +0100
@@ -1,3 +1,12 @@
+logol (1.7.0-2) unstable; urgency=medium
+
+ * d/control,d/patches/remove_drmaa_support: Remove libdrmaa-java dependency
+due to gridengine removal from Jessie (#776131).
+d/series: remove drmaa patch
+d/README.Debian: explain non drmaa support of this release
+
+ -- Olivier Sallou Sun, 01 Feb 2015 08:56:52 +0100
+
logol (1.7.0-1.1) unstable; urgency=high
* Non-maintainer upload.
diff -Nru logol-1.7.0/debian/control logol-1.7.0/debian/control
--- logol-1.7.0/debian/control 2014-04-18 13:38:41.0 +0200
+++ logol-1.7.0/debian/control 2015-02-01 09:00:22.0 +0100
@@ -7,13 +7,14 @@
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/logol/
Build-Depends: debhelper (>= 8.0.0),default-jdk (>= 1:1.6),ant,ruby,
gawk, swi-prolog (>=6.4.1-3),
- libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java,
+ libbiojava-java, antlr3, libcommons-cli-java,
libcommons-collections3-java, libcommons-configuration-java,
libcommons-lang-java, libcommons-logging-java, libxalan2-java,
libxerces2-java, junit4, libgnumail-java,
liblog4j1.2-java,texlive, texlive-latex-extra, tex4ht,
libncursesw5-dev, ant-optional,
cassiopee, ruby-cassiopee
+#libdrmaa-java removed from Jessie, to be reintroduced.
Standards-Version: 3.9.5
Homepage: http://logol.genouest.org
@@ -21,11 +22,12 @@
Architecture: all
Depends: ${shlibs:Depends}, ${misc:Depends}, default-jre | java7-runtime,
ruby, gawk,
- libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java,
+ libbiojava-java, antlr3, libcommons-cli-java,
libcommons-collections3-java, libcommons-configuration-java,
libcommons-lang-java, libcommons-logging-java, libxalan2-java,
libxerces2-java, libgnumail-java, liblog4j1.2-java,
cassiopee, logol-bin
+#libdrmaa-java removed from Jessie, to be reintroduced.
Suggests: ruby-cassiopee (>=0.1.12)
Description: Pattern matching tool using Logol language
Logol is a pattern matching tool using the Logol language.
diff -Nru logol-1.7.0/debian/patches/remove_drmaa_support
logol-1.7.0/debian/patches/remove_drmaa_support
--- logol-1.7.0/debian/patches/remove_drmaa_support 1970-01-01
01:00:00.0 +0100
+++ logol-1.7.0/debian/patches/remove_drmaa_support 2015-02-01
09:10:24.0 +0100
@@ -0,0 +1,166 @@
+Subject: libdrmaa-java removed from Debian (gridengine)
+Description: DRMAA job submission needs a Java drmaa library.
+ libdrmaa-java has been removed from Debian, bug: 776131.
+ This patch removes DRMAA related code waiting for library
+ reintroduction.
+ Logol will work on local mode only.
+Author: Olivier Sallou
+Last-Updated: 2015-02-01
+--- a/src/org/irisa/genouest/logol/dispatcher/Dispatch.java
b/src/org/irisa/genouest/logol/dispatcher/Dispatch.java
+@@ -230,7 +230,6 @@
+options.addOption("h",false,"get usage");
+
+options.addOption("s", true, "sequence database");
+- options.addOption("sge", false, "use SGE");
+options.addOption("local", false, "use local system");
+options.addOption("dna", false, "analyse dna, is default");
+options.addOption("rna", false, "analyse rna");
+@@ -290,7 +289,6 @@
+ usageOptions.addOption("s", true, "sequence
database");
+ usageOptions.addOption("g", true, "grammar file
to analyse");
+ usageOptions.addOption("m", true, "model file
to analyse");
+- usageOptions.addOption("sge", false, "use SGE");
+ usageOptions.addOption("local", false, "use
local system");
+ usageOptions.addOption("dna", false, "analyse
dna, is default");
+ usageOptions.addOption("rna", false, "analyse
rna");
+@@ -355,11 +353,6 @@
+ type=LOCAL;
+ jobmngr = (JobManager) new LocalJobManager();
+}
+- if( cmd.hasOption( "sge" ) ) {
+- logger.info("Using sge system");
+- type=SGE;
