Bug#925902: unblock: cnvkit/0.9.5-3
Package: release.debian.org
Severity: normal
User: release.debian@packages.debian.org
Usertags: unblock
X-Debbugs-CC: debian-...@lists.debian.org
This upload fixes bug #925568 about build reproducibility (failing). It
simply add a small patch to fix the issue adds a metadata entry.
Waiting for a *go* to upload package to unstable.
Thanks
Olivier
debdiff result =>
debian@ccf6b68dd723:/opt/debian/build-area$ debdiff cnvkit_0.9.5-2.dsc
cnvkit_0.9.5-3.dsc
dpkg-source: warning: extracting unsigned source package
(/opt/debian/build-area/cnvkit_0.9.5-3.dsc)
diff -Nru cnvkit-0.9.5/debian/changelog cnvkit-0.9.5/debian/changelog
--- cnvkit-0.9.5/debian/changelog 2019-01-06 12:12:46.0 +
+++ cnvkit-0.9.5/debian/changelog 2019-03-27 08:00:39.0 +
@@ -1,3 +1,10 @@
+cnvkit (0.9.5-3) unstable; urgency=medium
+
+ * Fix buster rebuilds (Closes: #925568)
+d/patches/controldir.patch
+
+ -- Olivier Sallou Wed, 27 Mar 2019 08:00:39 +
+
cnvkit (0.9.5-2) unstable; urgency=medium
[ Jelmer Vernooij ]
diff -Nru cnvkit-0.9.5/debian/patches/controldir
cnvkit-0.9.5/debian/patches/controldir
--- cnvkit-0.9.5/debian/patches/controldir 1970-01-01 00:00:00.0
+
+++ cnvkit-0.9.5/debian/patches/controldir 2019-03-27 08:00:39.0
+
@@ -0,0 +1,21 @@
+Subject: do not create dir if it exists
+Description: command tries to create an output dir during tests, even if it
+ already exists, raising an error. Skip creation if already present
+Author: Olivier Sallou
+Bug: 925568
+Forwaded: no
+Last-Updated: 2019-03-27
+--- a/cnvlib/commands.py
b/cnvlib/commands.py
+@@ -1365,8 +1365,9 @@
+ 'anti' if 'antitarget' in fname else ''))
+ if args.output_dir:
+ if not os.path.isdir(args.output_dir):
+-os.mkdir(args.output_dir)
+-logging.info("Created directory %s", args.output_dir)
++if not os.path.exists(args.output_dir):
++os.mkdir(args.output_dir)
++logging.info("Created directory %s", args.output_dir)
+ outfname = os.path.join(args.output_dir, outfname)
+ tabio.write(garr, outfname)
+
diff -Nru cnvkit-0.9.5/debian/patches/series
cnvkit-0.9.5/debian/patches/series
--- cnvkit-0.9.5/debian/patches/series 2019-01-06 09:41:24.0 +
+++ cnvkit-0.9.5/debian/patches/series 2019-03-27 08:00:39.0 +
@@ -1,3 +1,4 @@
no-py-ext
python3compat.patch
spelling
+controldir
diff -Nru cnvkit-0.9.5/debian/upstream/metadata
cnvkit-0.9.5/debian/upstream/metadata
--- cnvkit-0.9.5/debian/upstream/metadata 2018-06-19 21:48:37.0
+
+++ cnvkit-0.9.5/debian/upstream/metadata 2019-03-27 08:00:39.0
+
@@ -19,6 +19,6 @@
- Name: OMICtools
Entry: OMICS_11538
- Name: bio.tools
- Entry: NA
- - Name: bio.tools
+ Entry: cnvkit
+ - Name: SciCrunch
Entry: NA
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Bug#778665: unblock: logol/1.7.0-2
Le Thu Feb 19 2015 at 11:08:46 AM, Mehdi Dogguy me...@dogguy.org 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 Wed Feb 18 2015 at 9:25:56 PM, Mehdi Dogguy me...@dogguy.org 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
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 osal...@debian.org 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 osal...@debian.org
+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
Bug#777114: Re : Re: [Debian-med-packaging] Bug#777114: RM: gridengine/6.2u5-7.3
- Ondřej Surý ond...@debian.org a écrit : I don't see src:gridengine in DELAYED: Tha s fine, i found it in deferred... It is removed. I need to fight to make a clean build. Indeed gridengine doesnt build anymore in jessie because libtiff2 dev is not in jessie. This impacts the build for qmon. I know how to make it pass but needs multiple modifications in d/rules , not simpky skipping all bins generation (but drmaa). I will continue my work next week and expect an upload to unstable before end of next week. Olivier https://ftp-master.debian.org/deferred.html However if you make a correct upload to unstable with same or higher Debian revision in 12 days, it will be discarded from DELAYED anyway. JFTR I always fight with removing from DELAYED as well, there's something specific you need to do and I never remember what it is :). Cheers, Ondrej On Fri, Feb 6, 2015, at 14:45, Olivier Sallou wrote: On 02/06/2015 12:55 PM, Ondřej Surý wrote: Please upload directly to unstable. DELAYED/X is meant as a safety to allow maintainer to react and this package is unmaintained for a long time. No need to wait 12 days to have this fixed. ok I will . I have made however a dcut removal of what I have uploaded. I 've just seen there was an issue with what I uploaded (a mix of builds that I cannot reproduce, and build stuff in debian dir...) Strangely, however, dcut rm returned me mails with: Log of processing your commands file /dcut.Olivier_Sallou__osallou_debian_org_.1423229957.10032.commands: rm --searchdirs libdrmaa-java_6.2u5-7.4_amd64.deb libdrmaa-java_6.2u5-7.4_amd64.deb did not match anything No files to delete I would not like to get what I uploaded in unstable. As I won't be available next few days, would you mind checking for removal ? I will try to fix build and reupload directly in unstable when I am back. Olivier Cheers, Ondrej On Fri, Feb 6, 2015, at 12:15, Olivier Sallou wrote: On 02/05/2015 04:58 PM, Ondřej Surý wrote: Control: retitle -1 (pre-approval) unblock: gridengine/6.2u5-7.4 Control: user release.debian@packages.debian.org Control: usertags -1 unblock The autoremoval is ticking till March, so I think next week is ok. Just close the RC bug on src:gridengine with the upload. Hi, I have upload to delayed/12 the grindengine package. I generate only the libdrmaa-java binary. I have sent to delayed so that one have time to react (as I won't be reachable for the next few days). After this, once accepted in unstable, we can ask for the unblock of the package. Olivier O. On Thu, Feb 5, 2015, at 16:53, Olivier Sallou wrote: On 02/05/2015 04:10 PM, Ondřej Surý wrote: Olivier, could you do NMU to src:gridengine where you remove all binary packages except the DRMAA parts? I am on holiday tonigh, so I won't have time to do it before one week. Do you mean modifying control by commenting out all binaries but the drmma lib binary , and regenerating/uploading the package ? what about the RC bug, we would lower its severity to ?? so that it is not removed ? Thanks Olivier I have no ties to src:gridengine apart to NMUing it once to finish some transition, so it would be better if somebody who actually works with the package would take care of it. Cheers, Ondrej On Thu, Feb 5, 2015, at 16:01, Olivier Sallou wrote: On 02/05/2015 03:56 PM, Salvatore Bonaccorso wrote: Hi, On Thu, Feb 05, 2015 at 09:44:46AM +0100, Ondřej Surý wrote: Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: rm -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 gridengine is RC buggy and effectively unmaintained (see the discussion in #776131). There's an offer to upgrade the package to new upstream and we have a new healthy upstream available, but it's not going to happen for jessie. Ccing logol maintainer who would be affected by the removal, so he can act and prepare logol build without drmaa support in timely manner. For completeness: Another option would be to keep the gridengine sourcepackage and just only built libdrmaa-java. That's what I proposed in bug. I have already made a patch for logol to work without libdrmaa-java but this is definitly a major feature removal :-( Please tell me what is decided so that I ask for patch unblock of logol if everything is removed. Olivier Regards, Salvatore ___ Debian-med-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB
Bug#777114: [Debian-med-packaging] Bug#777114: RM: gridengine/6.2u5-7.3
On 02/05/2015 04:58 PM, Ondřej Surý wrote: Control: retitle -1 (pre-approval) unblock: gridengine/6.2u5-7.4 Control: user release.debian@packages.debian.org Control: usertags -1 unblock The autoremoval is ticking till March, so I think next week is ok. Just close the RC bug on src:gridengine with the upload. Hi, I have upload to delayed/12 the grindengine package. I generate only the libdrmaa-java binary. I have sent to delayed so that one have time to react (as I won't be reachable for the next few days). After this, once accepted in unstable, we can ask for the unblock of the package. Olivier O. On Thu, Feb 5, 2015, at 16:53, Olivier Sallou wrote: On 02/05/2015 04:10 PM, Ondřej Surý wrote: Olivier, could you do NMU to src:gridengine where you remove all binary packages except the DRMAA parts? I am on holiday tonigh, so I won't have time to do it before one week. Do you mean modifying control by commenting out all binaries but the drmma lib binary , and regenerating/uploading the package ? what about the RC bug, we would lower its severity to ?? so that it is not removed ? Thanks Olivier I have no ties to src:gridengine apart to NMUing it once to finish some transition, so it would be better if somebody who actually works with the package would take care of it. Cheers, Ondrej On Thu, Feb 5, 2015, at 16:01, Olivier Sallou wrote: On 02/05/2015 03:56 PM, Salvatore Bonaccorso wrote: Hi, On Thu, Feb 05, 2015 at 09:44:46AM +0100, Ondřej Surý wrote: Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: rm -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 gridengine is RC buggy and effectively unmaintained (see the discussion in #776131). There's an offer to upgrade the package to new upstream and we have a new healthy upstream available, but it's not going to happen for jessie. Ccing logol maintainer who would be affected by the removal, so he can act and prepare logol build without drmaa support in timely manner. For completeness: Another option would be to keep the gridengine sourcepackage and just only built libdrmaa-java. That's what I proposed in bug. I have already made a patch for logol to work without libdrmaa-java but this is definitly a major feature removal :-( Please tell me what is decided so that I ask for patch unblock of logol if everything is removed. Olivier Regards, Salvatore ___ Debian-med-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-release-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/54d4a242.5050...@irisa.fr
Bug#777114: [Debian-med-packaging] Bug#777114: RM: gridengine/6.2u5-7.3
On 02/06/2015 12:55 PM, Ondřej Surý wrote: Please upload directly to unstable. DELAYED/X is meant as a safety to allow maintainer to react and this package is unmaintained for a long time. No need to wait 12 days to have this fixed. ok I will . I have made however a dcut removal of what I have uploaded. I 've just seen there was an issue with what I uploaded (a mix of builds that I cannot reproduce, and build stuff in debian dir...) Strangely, however, dcut rm returned me mails with: Log of processing your commands file /dcut.Olivier_Sallou__osallou_debian_org_.1423229957.10032.commands: rm --searchdirs libdrmaa-java_6.2u5-7.4_amd64.deb libdrmaa-java_6.2u5-7.4_amd64.deb did not match anything No files to delete I would not like to get what I uploaded in unstable. As I won't be available next few days, would you mind checking for removal ? I will try to fix build and reupload directly in unstable when I am back. Olivier Cheers, Ondrej On Fri, Feb 6, 2015, at 12:15, Olivier Sallou wrote: On 02/05/2015 04:58 PM, Ondřej Surý wrote: Control: retitle -1 (pre-approval) unblock: gridengine/6.2u5-7.4 Control: user release.debian@packages.debian.org Control: usertags -1 unblock The autoremoval is ticking till March, so I think next week is ok. Just close the RC bug on src:gridengine with the upload. Hi, I have upload to delayed/12 the grindengine package. I generate only the libdrmaa-java binary. I have sent to delayed so that one have time to react (as I won't be reachable for the next few days). After this, once accepted in unstable, we can ask for the unblock of the package. Olivier O. On Thu, Feb 5, 2015, at 16:53, Olivier Sallou wrote: On 02/05/2015 04:10 PM, Ondřej Surý wrote: Olivier, could you do NMU to src:gridengine where you remove all binary packages except the DRMAA parts? I am on holiday tonigh, so I won't have time to do it before one week. Do you mean modifying control by commenting out all binaries but the drmma lib binary , and regenerating/uploading the package ? what about the RC bug, we would lower its severity to ?? so that it is not removed ? Thanks Olivier I have no ties to src:gridengine apart to NMUing it once to finish some transition, so it would be better if somebody who actually works with the package would take care of it. Cheers, Ondrej On Thu, Feb 5, 2015, at 16:01, Olivier Sallou wrote: On 02/05/2015 03:56 PM, Salvatore Bonaccorso wrote: Hi, On Thu, Feb 05, 2015 at 09:44:46AM +0100, Ondřej Surý wrote: Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: rm -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 gridengine is RC buggy and effectively unmaintained (see the discussion in #776131). There's an offer to upgrade the package to new upstream and we have a new healthy upstream available, but it's not going to happen for jessie. Ccing logol maintainer who would be affected by the removal, so he can act and prepare logol build without drmaa support in timely manner. For completeness: Another option would be to keep the gridengine sourcepackage and just only built libdrmaa-java. That's what I proposed in bug. I have already made a patch for logol to work without libdrmaa-java but this is definitly a major feature removal :-( Please tell me what is decided so that I ask for patch unblock of logol if everything is removed. Olivier Regards, Salvatore ___ Debian-med-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Bug#777114: [Debian-med-packaging] Bug#777114: RM: gridengine/6.2u5-7.3
On 02/05/2015 03:56 PM, Salvatore Bonaccorso wrote: Hi, On Thu, Feb 05, 2015 at 09:44:46AM +0100, Ondřej Surý wrote: Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: rm -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 gridengine is RC buggy and effectively unmaintained (see the discussion in #776131). There's an offer to upgrade the package to new upstream and we have a new healthy upstream available, but it's not going to happen for jessie. Ccing logol maintainer who would be affected by the removal, so he can act and prepare logol build without drmaa support in timely manner. For completeness: Another option would be to keep the gridengine sourcepackage and just only built libdrmaa-java. That's what I proposed in bug. I have already made a patch for logol to work without libdrmaa-java but this is definitly a major feature removal :-( Please tell me what is decided so that I ask for patch unblock of logol if everything is removed. Olivier Regards, Salvatore ___ Debian-med-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-release-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/54d385cf.7070...@irisa.fr
Bug#777114: [Debian-med-packaging] Bug#777114: RM: gridengine/6.2u5-7.3
On 02/05/2015 04:58 PM, Ondřej Surý wrote: Control: retitle -1 (pre-approval) unblock: gridengine/6.2u5-7.4 Control: user release.debian@packages.debian.org Control: usertags -1 unblock The autoremoval is ticking till March, so I think next week is ok. Just close the RC bug on src:gridengine with the upload. I tried a quick build to see gridengine, but it fails to compile from source. compilation fails on 3rdparty/jemalloc/jemalloc.c (error: conflicting type qualifiers for '__malloc_initialize_hook' ...) Is there anything special to set? I am on amd64 arch. O. On Thu, Feb 5, 2015, at 16:53, Olivier Sallou wrote: On 02/05/2015 04:10 PM, Ondřej Surý wrote: Olivier, could you do NMU to src:gridengine where you remove all binary packages except the DRMAA parts? I am on holiday tonigh, so I won't have time to do it before one week. Do you mean modifying control by commenting out all binaries but the drmma lib binary , and regenerating/uploading the package ? what about the RC bug, we would lower its severity to ?? so that it is not removed ? Thanks Olivier I have no ties to src:gridengine apart to NMUing it once to finish some transition, so it would be better if somebody who actually works with the package would take care of it. Cheers, Ondrej On Thu, Feb 5, 2015, at 16:01, Olivier Sallou wrote: On 02/05/2015 03:56 PM, Salvatore Bonaccorso wrote: Hi, On Thu, Feb 05, 2015 at 09:44:46AM +0100, Ondřej Surý wrote: Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: rm -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 gridengine is RC buggy and effectively unmaintained (see the discussion in #776131). There's an offer to upgrade the package to new upstream and we have a new healthy upstream available, but it's not going to happen for jessie. Ccing logol maintainer who would be affected by the removal, so he can act and prepare logol build without drmaa support in timely manner. For completeness: Another option would be to keep the gridengine sourcepackage and just only built libdrmaa-java. That's what I proposed in bug. I have already made a patch for logol to work without libdrmaa-java but this is definitly a major feature removal :-( Please tell me what is decided so that I ask for patch unblock of logol if everything is removed. Olivier Regards, Salvatore ___ Debian-med-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-release-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/54d39c6a.6050...@irisa.fr
Bug#777114: [Debian-med-packaging] Bug#777114: RM: gridengine/6.2u5-7.3
Forget my previous message, I could go on on built (not yet over, but building). I had downloaded from git repo I have taken orig+diff from Debian packages and it's fine now. Would be nice however to have git repo synced. Olivier On 02/05/2015 04:58 PM, Ondřej Surý wrote: Control: retitle -1 (pre-approval) unblock: gridengine/6.2u5-7.4 Control: user release.debian@packages.debian.org Control: usertags -1 unblock The autoremoval is ticking till March, so I think next week is ok. Just close the RC bug on src:gridengine with the upload. O. On Thu, Feb 5, 2015, at 16:53, Olivier Sallou wrote: On 02/05/2015 04:10 PM, Ondřej Surý wrote: Olivier, could you do NMU to src:gridengine where you remove all binary packages except the DRMAA parts? I am on holiday tonigh, so I won't have time to do it before one week. Do you mean modifying control by commenting out all binaries but the drmma lib binary , and regenerating/uploading the package ? what about the RC bug, we would lower its severity to ?? so that it is not removed ? Thanks Olivier I have no ties to src:gridengine apart to NMUing it once to finish some transition, so it would be better if somebody who actually works with the package would take care of it. Cheers, Ondrej On Thu, Feb 5, 2015, at 16:01, Olivier Sallou wrote: On 02/05/2015 03:56 PM, Salvatore Bonaccorso wrote: Hi, On Thu, Feb 05, 2015 at 09:44:46AM +0100, Ondřej Surý wrote: Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: rm -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 gridengine is RC buggy and effectively unmaintained (see the discussion in #776131). There's an offer to upgrade the package to new upstream and we have a new healthy upstream available, but it's not going to happen for jessie. Ccing logol maintainer who would be affected by the removal, so he can act and prepare logol build without drmaa support in timely manner. For completeness: Another option would be to keep the gridengine sourcepackage and just only built libdrmaa-java. That's what I proposed in bug. I have already made a patch for logol to work without libdrmaa-java but this is definitly a major feature removal :-( Please tell me what is decided so that I ask for patch unblock of logol if everything is removed. Olivier Regards, Salvatore ___ Debian-med-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-release-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/54d3a098.20...@irisa.fr
Bug#773178: unblock: biomaj-watcher/1.2.2-2
Yep, remove/purge cleans files. New tomcat8 modifications mainly changes configuration context file and modifies directories. Le mar. 16 déc. 2014 19:56, Jonathan Wiltshire j...@debian.org a écrit : Control: tag -1 moreinfo On Mon, Dec 15, 2014 at 10:57:55AM +, olivier sallou wrote: biomaj-watcher depended on tomcat6. Jessie uses Tomcat8 a,d biomaj-watcher does not work anymore. This fix release changes the package to use tomcat8 and fixes bug 769348 Do the files for Tomcat 6 get properly cleaned up on upgrade? -- Jonathan Wiltshire j...@debian.org Debian Developer http://people.debian.org/~jmw 4096R: 0xD3524C51 / 0A55 B7C5 1223 3942 86EC 74C3 5394 479D D352 4C51
Bug#773178: unblock: biomaj-watcher/1.2.2-2
Package: release.debian.org
Severity: normal
User: release.debian@packages.debian.org
Usertags: unblock
X-CC: debian-...@lists.debian.org
Please unblock package biomaj-watcher
biomaj-watcher depended on tomcat6. Jessie uses Tomcat8 a,d biomaj-watcher
does not work anymore. This fix release changes the package to use tomcat8
and fixes bug 769348
Here is debdiff:
diff -Nru biomaj-watcher-1.2.2/debian/changelog
biomaj-watcher-1.2.2/debian/changelog
--- biomaj-watcher-1.2.2/debian/changelog 2014-06-23 09:13:13.0
+0200
+++ biomaj-watcher-1.2.2/debian/changelog 2014-12-15 11:26:27.0
+0100
@@ -1,3 +1,9 @@
+biomaj-watcher (1.2.2-2) unstable; urgency=medium
+
+ * Switch to Tomcat 8 (Closes: #769348).
+
+ -- Olivier Sallou osal...@debian.org Mon, 15 Dec 2014 08:03:09 +0100
+
biomaj-watcher (1.2.2-1) unstable; urgency=medium
* New usptream release:
diff -Nru biomaj-watcher-1.2.2/debian/control
biomaj-watcher-1.2.2/debian/control
--- biomaj-watcher-1.2.2/debian/control 2014-06-23 09:13:56.0 +0200
+++ biomaj-watcher-1.2.2/debian/control 2014-12-15 08:04:53.0 +0100
@@ -21,7 +21,7 @@
Package: biomaj-watcher
Architecture: all
-Depends: ${misc:Depends}, default-jdk, tomcat6 (=6.0.32-3), biomaj (=
1.2.1), debconf,
+Depends: ${misc:Depends}, default-jdk, tomcat8 , biomaj (= 1.2.1),
debconf,
liblog4j1.2-java, libjsch-java (= 0.1.42),libjdom1-java (= 1.1),
libcommons-lang-java (=2.4),
libcommons-logging-java (=1.1),libquartz-java(=1.6),libxerces2-java,
unzip, zip, libgnumail-java
Description: biological data-bank updater - web interface
diff -Nru biomaj-watcher-1.2.2/debian/patches/series
biomaj-watcher-1.2.2/debian/patches/series
--- biomaj-watcher-1.2.2/debian/patches/series 2014-01-09
16:25:31.0 +0100
+++ biomaj-watcher-1.2.2/debian/patches/series 2014-12-15
10:37:02.0 +0100
@@ -1 +1,2 @@
prevent_jobs_file_move
+use_tomcat8
diff -Nru biomaj-watcher-1.2.2/debian/patches/use_tomcat8
biomaj-watcher-1.2.2/debian/patches/use_tomcat8
--- biomaj-watcher-1.2.2/debian/patches/use_tomcat8 1970-01-01
01:00:00.0 +0100
+++ biomaj-watcher-1.2.2/debian/patches/use_tomcat8 2014-12-15
10:40:03.0 +0100
@@ -0,0 +1,17 @@
+Subject: adapt xml for Tomcat8
+Description: use tomcat8, this impact the context descriptor
+Author: Olivier Sallou osal...@debian.org
+Last-Updated: 2014-12-15
+Forwarded: No
+--- a/usr/share/biomaj-watcher/bin/WatcherConfigurator.java
b/usr/share/biomaj-watcher/bin/WatcherConfigurator.java
+@@ -45,7 +45,8 @@
+ PrintWriter pw = new PrintWriter(biomajConf + /BmajWatcher.xml);
+
+ pw.println(?xml version=\1.0\ encoding=\UTF-8\?);
+- pw.println(Context path=\/BmajWatcher\
docBase=\/usr/share/java/webapps/biomaj-watcher\ reloadable=\false\
allowLinking=\true\);
++ pw.println(Context path=\/BmajWatcher\
docBase=\/usr/share/java/webapps/biomaj-watcher\ reloadable=\false\
);
++ pw.println(Resources allowLinking=\true\/);
+
+ pw.println(Parameter name=\ADMIN_LOGIN\ value=\ +
params.get(app_login) + \ override=\false\/);
+
diff -Nru biomaj-watcher-1.2.2/debian/postinst
biomaj-watcher-1.2.2/debian/postinst
--- biomaj-watcher-1.2.2/debian/postinst 2014-01-09 16:25:31.0 +0100
+++ biomaj-watcher-1.2.2/debian/postinst 2014-12-15 11:05:48.0 +0100
@@ -49,8 +49,8 @@
ln -s /usr/share/java/gnumail.jar
/usr/share/java/webapps/biomaj-watcher/WEB-INF/lib/gnumail.jar
#cp /usr/share/biomaj/lib/biomaj.jar /var/lib/tomcat6/shared/
- rm -f /var/lib/tomcat6/shared/biomaj.jar
- cp /usr/share/biomaj/lib/biomaj.jar
/var/lib/tomcat6/shared/biomaj.jar
+ rm -f /usr/share/java/webapps/biomaj-watcher/WEB-INF/lib/biomaj.jar
+ cp /usr/share/biomaj/lib/biomaj.jar
/usr/share/java/webapps/biomaj-watcher/WEB-INF/lib/biomaj.jar
# Install latest definition
cp /usr/share/java/webapps/biomaj-watcher/jobs.xsd
/etc/biomaj-watcher/jobs.xsd
@@ -62,24 +62,17 @@
# Update logs
set_perms /var/log/biomaj
- #chown -R tomcat6 /etc/biomaj/db_properties
- chown -R tomcat6 /usr/share/java/webapps/biomaj-watcher
- #chmod -R 775 /etc/biomaj/db_properties
- #chown -R tomcat6 /var/log/biomaj
- #chmod -R 775 /var/log/biomaj
- #chown -R tomcat6 /var/lib/biomaj
- #chmod -R 775 /var/lib/biomaj
- chown -R tomcat6 /etc/biomaj-watcher
+ chown -R tomcat8 /usr/share/java/webapps/biomaj-watcher
+ chown -R tomcat8 /etc/biomaj-watcher
# Update context
java -cp $biomajwatcher_root/bin UpdateToBiomaj1_2
/usr/share/java/webapps/biomaj-watcher admin
- chown -R tomcat6 /etc/biomaj-watcher
- #cp /etc/biomaj-watcher/BmajWatcher*.xml
/var/lib/tomcat6/conf/Catalina/localhost/
- rm -f /etc/tomcat6/Catalina/localhost/BmajWatcher.xml
- rm -f /etc/tomcat6/Catalina/localhost/BmajWatcher#logs.xml
- ln -s /etc/biomaj-watcher/BmajWatcher.xml
/etc/tomcat6/Catalina/localhost/BmajWatcher.xml
- ln -s /etc/biomaj-watcher/BmajWatcher#logs.xml
/etc
Bug#771517: unblock: mobyle/1.5.3+dfsg-2
Package: release.debian.org
Severity: normal
User: release.debian@packages.debian.org
Usertags: unblock
X-CC: debian-...@lists.debian.org
Please unblock package mobyle
mobyle related packages are marked for auto-removal due to a bug in a
dependency:
Version 1.5.3+dfsg-1 of mobyle is marked for autoremoval from testing on
2015-01-05. It depends (transitively) on and maven, affected by RC bug(s)
and 770608
This dependency is not a required one, only a recommended one (though was
set as a Depends). I have updated the package to put this dependency in
Recommends to prevent autoremoval. This is the only change on the package.
Here is debdiff:
diff -Nru mobyle-1.5.3+dfsg/debian/changelog
mobyle-1.5.3+dfsg/debian/changelog
--- mobyle-1.5.3+dfsg/debian/changelog2014-04-29 08:35:14.0
+0200
+++ mobyle-1.5.3+dfsg/debian/changelog2014-11-30 12:53:54.0
+0100
@@ -1,3 +1,10 @@
+mobyle (1.5.3+dfsg-2) unstable; urgency=medium
+
+ * d/control: set jing as Recommends, jing is not mandatory but only
+useful for XML schema validation
+
+ -- Olivier Sallou osal...@debian.org Sun, 30 Nov 2014 12:51:07 +0100
+
mobyle (1.5.3+dfsg-1) unstable; urgency=medium
* New upstream release
diff -Nru mobyle-1.5.3+dfsg/debian/control mobyle-1.5.3+dfsg/debian/control
--- mobyle-1.5.3+dfsg/debian/control2014-04-29 08:32:53.0 +0200
+++ mobyle-1.5.3+dfsg/debian/control2014-11-30 12:53:47.0 +0100
@@ -19,7 +19,6 @@
Depends: ${misc:Depends}, python (= 2.5), apache2 (= 2.4) | httpd-cgi,
libjs-scriptaculous, libjs-jquery, libjs-prototype,
mobyle-utils,
- jing,
python-biopython,
python-imaging (= 1.1.5),
python-lxml (= 2.2.4),
@@ -31,7 +30,7 @@
squizz (=0.99b+dfsg),
ttf-bitstream-vera
Suggests: python-openid (= 2.2.4), python-dnspython (= 1.5.0)
-Recommends: mobyle-programs (= 3.1), mobyle-tutorials, ${misc:Recommends}
+Recommends: mobyle-programs (= 3.1), mobyle-tutorials,
${misc:Recommends}, jing
Description: Web portal that provides web forms for command-line software
Mobyle is a framework and web portal specifically aimed at the
integration of
bioinformatics software and databanks. It generates a web interface from
an xml
unblock mobyle/1.5.3+dfsg-2
-- System Information:
Debian Release: jessie/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Kernel: Linux 3.14-2-amd64 (SMP w/1 CPU core)
Locale: LANG=fr_FR.utf8, LC_CTYPE=fr_FR.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Bug#770096: unblock: biojava3-live/3.1.0+dfsg-2
Package: release.debian.org
Severity: normal
User: release.debian@packages.debian.org
Usertags: unblock
Please unblock package biojava3-live
Current release in Jessie has a serious FTBS bug (#768710) related to
character
encoding causing a build failure.
The new uploaded release in unstable fixes this bug (and only this bug).
Changelog can be found in following debgdiff.
Here is debdiff:
diff -Nru biojava3-live-3.1.0+dfsg/debian/build.xml
biojava3-live-3.1.0+dfsg/deb
ian/build.xml
--- biojava3-live-3.1.0+dfsg/debian/build.xml 2014-05-15 12:02:56.0
+0
200
+++ biojava3-live-3.1.0+dfsg/debian/build.xml 2014-11-18 19:56:35.0
+0
100
@@ -61,7 +61,7 @@
target name=javadocs
mkdir dir=${docs.dir}/
mkdir dir=${docs.lib.dir}/
- javadoc destdir=${docs.lib.dir} sourcepath=${src.dir} packa
genames=org.*
+ javadoc destdir=${docs.lib.dir} sourcepath=${src.dir} packa
genames=org.* encoding=UTF-8
link href=http://java.sun.com/j2se/1.6.0/docs/api//
/javadoc
/target
diff -Nru biojava3-live-3.1.0+dfsg/debian/changelog
biojava3-live-3.1.0+dfsg/deb
ian/changelog
--- biojava3-live-3.1.0+dfsg/debian/changelog 2014-09-03 08:11:23.0
+0
200
+++ biojava3-live-3.1.0+dfsg/debian/changelog 2014-11-18 20:26:43.0
+0
100
@@ -1,3 +1,13 @@
+biojava3-live (3.1.0+dfsg-2) unstable; urgency=medium
+
+ * Fix FTBFS in jessie: dh_install: libbiojava3-java-doc missing files
+(doc/biojava/*), aborting:
+debian/build.xml: tell javadoc that source files are encoded as UTF-8;
+otherwise it bails out, and dh_install finds nothing to install.
+(Closes: #768710), thanks to gregor herrmann gre...@debian.org
+
+ -- Olivier Sallou osal...@debian.org Tue, 18 Nov 2014 14:06:30 +0100
+
biojava3-live (3.1.0+dfsg-1) unstable; urgency=medium
* New upstream release
unblock biojava3-live/3.1.0+dfsg-2
-- System Information:
Debian Release: jessie/sid
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'testing')
Architecture: amd64 (x86_64)
Kernel: Linux 3.10-2-amd64 (SMP w/1 CPU core)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Bug#685900: unblock: circos/0.61-3
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: unblock Please unblock package circos I would like to ask to take into account circos 0.61-3 in stable release. The fix included in 0.61-3 fixes a bug preventing usage of the package (missing dependency in Depends). unblock circos/0.61-3 -- System Information: Debian Release: wheezy/sid APT prefers unstable APT policy: (500, 'unstable'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 2.6.32-5-amd64 (SMP w/1 CPU core) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash -- To UNSUBSCRIBE, email to debian-release-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120826084908.12747.87332.report...@debiansid.genouest.org
please include circos 0.61-3 in stable release
Hi, I would like to ask to take into account circos 0.61-3 in stable release (if package is considered). The fix in 0.61-3 fixes a bug preventing correct usage of the package (missing dependency in Depends). Thanks Olivier -- osal...@debian.org -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
