[Bug 1878617] Re: Apple pages file type should be added to MIME types

2020-05-15 Thread Charles Plessy
Hello,

You can add `application/vnd.apple.pages pages` in `/etc/mime.types` on
your system, and I will do it in a future update of the `mime-support`
package, but it will not effect the output of the `file` command, which
uses a different database.

You can open a bug on the `file` package to request it, but please have
a look if you can at <https://github.com/file/file/tree/master/magic>
before: as you will see, unless you can provide a “magic number” for
that format (a proprietary format from a proprietary software, if I may
comment), it may not be possible to detect it.

You can also have a look at the `shared-mime-info` package for another
way to associate the `.pages` file suffix to the
`application/vnd.apple.pages` media type.

Have a nice day,

Charles Plessy

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  Apple pages file type should be added to MIME types

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[Bug 1575074] Re: perlprimer crashes on start: Can't use 'defined(@array)'

2017-01-22 Thread Charles Plessy
Fixed in version 1.1.21-3

** Changed in: perlprimer (Ubuntu)
   Status: Confirmed => Fix Released

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[Bug 1357036] Re: please update apt-get install to latest version of FastQC available at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.2.zip

2015-01-20 Thread Charles Plessy
Hello,

fastqc is now at the latest version in Utopic and Vivid, so I close this
report.

Have a nice day,

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** Changed in: fastqc (Ubuntu)
   Status: New = Fix Released

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  please update apt-get install to latest version of FastQC available at
  http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.2.zip

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[Bug 1022824] Re: Incorrect mime type for deb extension

2014-07-13 Thread Charles Plessy
Closing this bug as the media type application/vnd.debian.binary-package
is being deployed.

** Changed in: mime-support (Ubuntu)
   Status: New = Fix Released

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[Bug 1316597] Re: test_smartos fails in a chroot

2014-06-02 Thread Charles Plessy
Thanks Scott !  This is very timely as Debian's cloud-init package just
got http://bugs.debian.org/750314 filed because the package could not be
rebuilt in a chroot.

Do you by chance plan an upstream release of cloud-init in the near
future ?  If not, I will apply revision 976 as a patch to the Debian
package.

Have a nice day,

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** Bug watch added: Debian Bug tracker #750314
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=750314

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[Bug 1316597] Re: test_smartos fails in a chroot

2014-06-02 Thread Charles Plessy
Thanks Scott !  This is very timely as Debian's cloud-init package just
got http://bugs.debian.org/750314 filed because the package could not be
rebuilt in a chroot.

Do you by chance plan an upstream release of cloud-init in the near
future ?  If not, I will apply revision 976 as a patch to the Debian
package.

Have a nice day,

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** Bug watch added: Debian Bug tracker #750314
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=750314

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  test_smartos fails in a chroot

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[Bug 1075913] Re: run-mailcap does not work on jpeg files

2013-11-27 Thread Charles Plessy
** Changed in: mime-support (Ubuntu)
   Status: Incomplete = Fix Released

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  run-mailcap does not work on jpeg files

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[Bug 1246939] Re: package mime-support 3.54ubuntu1 failed to install/upgrade: subprocess installed post-installation script returned error exit status 137

2013-11-23 Thread Charles Plessy
Thanks for the update.  Closing accordingly.

** Changed in: mime-support (Ubuntu)
   Status: Confirmed = Fix Released

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Title:
  package mime-support 3.54ubuntu1 failed to install/upgrade: subprocess
  installed post-installation script returned error exit status 137

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[Bug 1090657] Re: package okular 4:4.9.2-0ubuntu1 failed to install/upgrade: subprocess new post-removal script returned error exit status 2

2013-11-23 Thread Charles Plessy
** Changed in: mime-support (Ubuntu)
   Status: New = Fix Released

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  package okular 4:4.9.2-0ubuntu1 failed to install/upgrade: subprocess
  new post-removal script returned error exit status 2

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[Bug 552323] Re: Permission checking dialog leaves users confused about what to do next

2013-11-22 Thread Charles Plessy
Closing as this bug was solved in
https://bugs.launchpad.net/ubuntu/+bug/506702

** Changed in: mime-support (Ubuntu)
   Status: Triaged = Fix Released

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  Permission checking dialog leaves users confused about what to do next

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[Bug 561479] Re: Windows executable on unwritable removable media cannot execute with Wine due to lack of executable bit

2013-11-22 Thread Charles Plessy
Closing as it was fixed in https://bugs.launchpad.net/ubuntu/+bug/506702

** Changed in: mime-support (Ubuntu)
   Status: Confirmed = Fix Released

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  Windows executable on unwritable removable media cannot execute with
  Wine due to lack of executable bit

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[Bug 222470] Re: MIME-Type is not set properly

2013-11-22 Thread Charles Plessy
Closing as it is shared-mime-info, not mime-support, that provides the
media type ‘application-x-desktop’.  Please feel free to re-open,
preferably on mime-support.

** Changed in: mime-support (Ubuntu)
   Status: Confirmed = Fix Released

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  MIME-Type is not set properly

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[Bug 221748] Re: package mime-support 3.39-1ubuntu1 failed to install/upgrade:

2013-11-22 Thread Charles Plessy
Closing for lack of activity. Please feel free to reopen.

** Changed in: mime-support (Ubuntu)
   Status: Confirmed = Fix Released

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Title:
  package mime-support 3.39-1ubuntu1 failed to install/upgrade:

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[Bug 229040] Re: debdiff shown as html

2013-11-22 Thread Charles Plessy
Closing in mime-support as the bug was about Launchpad serving the wrong
media type.

** Changed in: mime-support (Ubuntu)
   Status: Confirmed = Fix Released

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Title:
  debdiff shown as html

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[Bug 456243] Re: package mime-support 3.44-1 failed to install/upgrade: unable to stat `./usr/lib/mime/mailcap' (which I was about to install): Input/output error

2013-11-22 Thread Charles Plessy
Closing for lack of activity.  Please feel free to reopen if you are
still affected by this bug.

** Changed in: mime-support (Ubuntu)
   Status: New = Fix Released

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Title:
  package mime-support 3.44-1 failed to install/upgrade: unable to stat
  `./usr/lib/mime/mailcap' (which I was about to install): Input/output
  error

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[Bug 392771] Re: package mime-support 3.46-1 failed to install/upgrade:

2013-11-22 Thread Charles Plessy
Closing as the attached file seems corrupted (impossible to decompress)
and for lack of activity.

** Changed in: mime-support (Ubuntu)
   Status: Confirmed = Fix Released

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  package mime-support 3.46-1 failed to install/upgrade:

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[Bug 460904] Re: Wrong flag causing 'terminate called after throwing an instance of 'com::sun::star::uno::RuntimeException'

2013-11-22 Thread Charles Plessy
Closing as it was solved in the libreoffice packages (which are where
the bug should have been reported).

** Changed in: mime-support (Ubuntu)
   Status: New = Fix Released

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  Wrong flag causing 'terminate called after throwing an instance of
  'com::sun::star::uno::RuntimeException'

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[Bug 926940] Re: Visio files not associated with LibreOffice Draw

2013-11-22 Thread Charles Plessy
Closing in mime-support as /etc/mime.types contains application/visio
since 3.51-1.

** Changed in: mime-support (Ubuntu)
   Status: Confirmed = Fix Released

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  Visio files not associated with LibreOffice Draw

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[Bug 1075913] Re: run-mailcap does not work on jpeg files

2013-11-22 Thread Charles Plessy
Dear  wdesmet,

thank you for your report.  I suspect that the problem may rather be
that the JPEG file is corrupted.  Have you tested with another JPEG
file, and have you confirmed that the p1000459.jpg file can be opened
with other programs ?

Have a nice day,

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** Changed in: mime-support (Ubuntu)
   Status: Confirmed = Incomplete

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  run-mailcap does not work on jpeg files

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[Bug 1090657] Re: package okular 4:4.9.2-0ubuntu1 failed to install/upgrade: subprocess new post-removal script returned error exit status 2

2013-11-22 Thread Charles Plessy
Dear Fehrat,

are you still affected by this bug ?  If not, I will close it.

Have a nice week-end,

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Title:
  package okular 4:4.9.2-0ubuntu1 failed to install/upgrade: subprocess
  new post-removal script returned error exit status 2

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[Bug 1246939] Re: package mime-support 3.54ubuntu1 failed to install/upgrade: subprocess installed post-installation script returned error exit status 137

2013-11-22 Thread Charles Plessy
Dear Simon,

in the ‘Df.txt’ file that you submitted, I note that your root
filesystem is almost entirely full (97 %), could that be the problem ?
I also note some strange errors in the ‘Dmseg.txt’ file. Do you
experience other problems with your computer, that are not related to
mime-support ?

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  package mime-support 3.54ubuntu1 failed to install/upgrade: subprocess
  installed post-installation script returned error exit status 137

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[Bug 606316] Re: treeviewx crashes when opening a file

2013-10-19 Thread Charles Plessy
** Changed in: treeviewx (Ubuntu)
   Status: New = Fix Released

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  treeviewx crashes when opening a file

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[Bug 562320] Re: paths in the nucmer script point to a path used during the build process

2013-10-19 Thread Charles Plessy
The problem is not there anymore in version 3.23~dfsg-2.

** Changed in: mummer (Ubuntu)
   Status: New = Fix Released

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[Bug 1083426] Re: Emboss-explorer broken in 12.10

2013-10-08 Thread Charles Plessy
** Changed in: emboss-explorer (Ubuntu)
   Status: New = Fix Released

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  Emboss-explorer broken in 12.10

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[Bug 788283] Re: srf2fastq produces invalid fastq quality scores.

2013-08-09 Thread Charles Plessy
Hi Diane,

I am closing this bug as it looks like the support for 10.04 LTS has
expired except for server issues.

Have a nice weeke-end,

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** Changed in: staden-io-lib (Ubuntu)
   Status: New = Fix Released

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Re: [Bug 1189646] Re: unowned files after purge (policy 6.8, 10.8): /etc/apt/apt.conf.d/90cloud-init-pipelining

2013-07-14 Thread Charles Plessy
Le Thu, Jun 20, 2013 at 08:56:13PM -, Scott Moser a écrit :
 
   I looked today at separating grub-legacy-ec2 out of cloud-init and saw
 your repo at
 http://anonscm.debian.org/gitweb/?p=collab-maint/pv-grub-menu.lst.git and
 the ITP at #6721024.  I've done a bit of work here to get it to build and
 to fix some lintian errors.  I wonder what your plans are for that (if any).
 
   Mainly, I'd like to get that code out of cloud-init's packaging tree and
 somewhere else, and it seems like you were possibly doing some of that also.
 
   I'm willing to do some of the grunt work, but will need the result to
 work as desired on ubuntu.
   Thoughts?

Hi Scott,

sorry for taking so much time to anwer.

I think that it would be great to have a grub-legacy-ec2 in a separate
package, be it pv-grub-menu.lst or anything else.  While drafting
pv-grub-menu.lst, I wondered if most of the code is only there because it
is carried over from the original update-grub scripts.

Do you think that there is room or need for simplification ?  One of the
reasons I did not go further with pv-grub-menu.lst was that I was
uncomfortable running a package where I barely understand much of
what its main script seems to be capable of doing.

Apart from this, unless Ubuntu has diverged on the kernel hooks, it seems to me
that the package should be working fine on both Debian and Ubuntu.

Have a nice Sunday,

Charles

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Title:
  unowned files after purge (policy 6.8, 10.8): /etc/apt/apt.conf.d
  /90cloud-init-pipelining

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Re: [Bug 1189646] Re: unowned files after purge (policy 6.8, 10.8): /etc/apt/apt.conf.d/90cloud-init-pipelining

2013-07-14 Thread Charles Plessy
Le Thu, Jun 20, 2013 at 08:56:13PM -, Scott Moser a écrit :
 
   I looked today at separating grub-legacy-ec2 out of cloud-init and saw
 your repo at
 http://anonscm.debian.org/gitweb/?p=collab-maint/pv-grub-menu.lst.git and
 the ITP at #6721024.  I've done a bit of work here to get it to build and
 to fix some lintian errors.  I wonder what your plans are for that (if any).
 
   Mainly, I'd like to get that code out of cloud-init's packaging tree and
 somewhere else, and it seems like you were possibly doing some of that also.
 
   I'm willing to do some of the grunt work, but will need the result to
 work as desired on ubuntu.
   Thoughts?

Hi Scott,

sorry for taking so much time to anwer.

I think that it would be great to have a grub-legacy-ec2 in a separate
package, be it pv-grub-menu.lst or anything else.  While drafting
pv-grub-menu.lst, I wondered if most of the code is only there because it
is carried over from the original update-grub scripts.

Do you think that there is room or need for simplification ?  One of the
reasons I did not go further with pv-grub-menu.lst was that I was
uncomfortable running a package where I barely understand much of
what its main script seems to be capable of doing.

Apart from this, unless Ubuntu has diverged on the kernel hooks, it seems to me
that the package should be working fine on both Debian and Ubuntu.

Have a nice Sunday,

Charles

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Title:
  unowned files after purge (policy 6.8, 10.8): /etc/apt/apt.conf.d
  /90cloud-init-pipelining

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[Bug 1084606] Re: wise depends on files in -doc to run

2013-07-14 Thread Charles Plessy
Fixed in 2.4.1-13.

** Changed in: wise (Ubuntu)
   Status: New = Fix Released

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  wise depends on files in -doc to run

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[Bug 1189646] [NEW] unowned files after purge (policy 6.8, 10.8): /etc/apt/apt.conf.d/90cloud-init-pipelining

2013-06-10 Thread Charles Plessy
Public bug reported:

Hi Scott,

this is http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=674237.  Can
you add the following line in debian/cloud-init.postrm for the purge ?

rm -f /etc/apt/apt.conf.d/90cloud-init-pipelining

Have a nice day,

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** Affects: cloud-init (Ubuntu)
 Importance: Undecided
 Status: New

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Title:
  unowned files after purge (policy 6.8, 10.8): /etc/apt/apt.conf.d
  /90cloud-init-pipelining

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[Bug 1189646] [NEW] unowned files after purge (policy 6.8, 10.8): /etc/apt/apt.conf.d/90cloud-init-pipelining

2013-06-10 Thread Charles Plessy
Public bug reported:

Hi Scott,

this is http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=674237.  Can
you add the following line in debian/cloud-init.postrm for the purge ?

rm -f /etc/apt/apt.conf.d/90cloud-init-pipelining

Have a nice day,

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** Affects: cloud-init (Ubuntu)
 Importance: Undecided
 Status: New

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[Bug 760644] Re: Default handler lookup by extension fails

2013-05-11 Thread Charles Plessy
Conversely, what can be corrected is the absence of programs that
declare that they handle application/x-debian-package.  I see that for
instance MimeType=application/x-deb;application/x-debian-package; in
/usr/share/applications/gdebi.desktop.

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[Bug 1022824] Re: Incorrect mime type for deb extension

2013-05-11 Thread Charles Plessy
Hello,

Maybe Wikipedia should be corrected instead of mime-support ?  Some
packages like gdebi support both media types.

In the long-term, I think that we should migrate to something like
application/vnd.debian.binary-package.

Cheers,

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[Bug 695888] Re: add application/json to /etc/mime.types

2013-05-11 Thread Charles Plessy
Closing as it is fixed since 3.51-1.

** Changed in: mime-support (Ubuntu)
   Status: New = Fix Released

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[Bug 667595] Re: A few additional types

2013-05-11 Thread Charles Plessy
Hello,

I am adding application/xhtml+xml to /etc/mime.types in the next version
of mime-support.  For the other requests, please consider registering
MIME media types to the Internet Assigned Numbers Authority (IANA)
before requiring their inclusion in /etc/mime.types. Simplified
registration procedures for vendor and personal trees are being
implemented with the update of RFC 4288[1], that states: it should
rarely, if ever, be necessary to use unregistered types.  Therefore, use
of types in the 'x.' tree is strongly discouraged.

Have a nice week-end,

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[Bug 611764] Re: text files ending in .md get marked as 'application/x-genesis-rom'

2013-05-11 Thread Charles Plessy
Hello,

this must be coming from another package, because /etc/mime.types does
not mention this extension nor this media type. Also it may have been
solved sicne. (I do not see the problem in shared-mime-info, for
example). I am therefore closing this bug.

Have a nice week-end,

-- Charles Plessy, Tsurumi, Kanagawa, Japan.

** Changed in: mime-support (Ubuntu)
   Status: New = Fix Released

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[Bug 309619] Re: /etc/mailcap quotes violate RFC 1524

2013-05-11 Thread Charles Plessy
This was a bug in the antiword package, which seems to have been fixed
already.  I am therefore closing this bug.

** Changed in: mime-support (Ubuntu)
   Status: New = Fix Released

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[Bug 1093948] Re: Add audio/opus mimetype for .opus extension to mime.types

2012-12-27 Thread Charles Plessy
Precision: the change has been committed, but it will only be uploaded
to Debian unstable after the next stable release.

Cheers,

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** Bug watch added: Debian Bug tracker #688383
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=688383

** Also affects: mime-support (Debian) via
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=688383
   Importance: Unknown
   Status: Unknown

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[Bug 1083426] Re: Emboss-explorer broken in 12.10

2012-12-01 Thread Charles Plessy
Thanks Wolfgang for the report !

I just tried on my Debian Sid, and emboss-explorer hangs because the
EMBOSS command 'wossname' hangs.  Can you confirm it on Ubuntu, and
reassign the bug to emboss if it is the case ?

Have a nice Sunday,

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[Bug 725717] Re: Garbled/pseudo-HTML characters in package description

2012-09-19 Thread Charles Plessy
Closing as next update will change the description in a way that removes
the non-breaking space (SeaView now works with Clustal Omega instead of
Custal W).

** Changed in: seaview (Ubuntu)
   Status: New = Fix Released

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[Bug 1026608] Re: Package doesn't install correctly. See upstream debian install bug for details.

2012-08-07 Thread Charles Plessy
*** This bug is a duplicate of bug 1009027 ***
https://bugs.launchpad.net/bugs/1009027

Dear Folmer,

I just marked the bug as duplicate of #1009027.

As I wrote in the other report, it does not look like mafft will be
fixed in Precise (but I may be wrong). To workaround the problem, I made
a backport on Debian Med's PPA:

https://launchpad.net/~debian-med/+archive/ppa/+sourcepub/2512983
/+listing-archive-extra

Have a nice day,

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** This bug has been marked a duplicate of bug 1009027
   incorrectly installed

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[Bug 712004] Re: samtools version is outdated in Lucid

2012-07-26 Thread Charles Plessy
Marking invalid as I do not think that samtools will ever be updated in
Lucid.

** Changed in: samtools (Ubuntu)
   Status: New = Invalid

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[Bug 1019778] Re: Obsoleted by r-bioc-qvalue.

2012-07-03 Thread Charles Plessy
This is already fixed in our Subversion repository and will take effect
at the upload of debian-med 1.12.

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** Changed in: debian-med (Ubuntu)
   Status: New = Fix Committed

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[Bug 1019778] [NEW] Obsoleted by r-bioc-qvalue.

2012-07-01 Thread Charles Plessy
Public bug reported:

Dear MOTUs,

r-cran-qvalue is replaced by r-bioc-qvalue (as the upstream source moved
from CRAN to Bioconductor).  You can delete r-cran-qvalue from Ubuntu.

Have a nice day,

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** Affects: r-cran-qvalue (Ubuntu)
 Importance: Undecided
 Status: New

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[Bug 1009027] Re: incorrectly installed

2012-06-16 Thread Charles Plessy
** Bug watch added: Debian Bug tracker #636634
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=636634

** Also affects: mafft (Debian) via
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=636634
   Importance: Unknown
   Status: Unknown

** Changed in: mafft (Ubuntu)
   Status: New = Confirmed

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[Bug 1009027] Re: incorrectly installed

2012-06-16 Thread Charles Plessy
Hello,

mafft 6.850-1 is indeed broken.  This is the bug #636634 in Debian.

I have just uploaded in Debian Med's PPA a backport of the current
version in Debian Wheezy.

https://launchpad.net/~debian-med/+archive/ppa/+sourcepub/2512983
/+listing-archive-extra

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[Bug 1009027] Re: incorrectly installed

2012-06-16 Thread Charles Plessy
I am not a Ubuntu user (I track the bugs in this package because I
maintain it in Debian, where it comes from), so I only have guesses...

For Lucid (LTS as well), I have not seen bugs in scientific packages
from the multiverse component being corrected, so I am not sure if
mafft will be updated in this LTS. Perhaps you can ask to the MOTU
Science, or to a generic Ubuntu mailing list.

However the next releases of Ubuntu track the Debian packages, and
6.864-1 is already in Quantal.

Cheers,

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[Bug 615858] Re: Build bouncycastle for Java 1.5 or later

2012-05-30 Thread Charles Plessy
Hello,

1.46+dfsg-5 was built using jdk16.xml.  Can you confirm that it solved
your problem ?

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[Bug 997838] [NEW] Support for cloud-init.

2012-05-10 Thread Charles Plessy
Public bug reported:

Dear ureadahead maintainers,

the cloud-init package's postinst script disables ureadahead using
dpkg diversions.  In Debian, this would be a policy violation, and I
am now packaging cloud-init for Debian.

I have discussed with cloud-init's maintainer in Ubuntu and we agreed
that ideally, ureadahead should detect cloud-init's presence and not
start in that case, instead of being diverted by cloud init.

  http://lists.debian.org/debian-python/2012/05/msg00047.html

Given that ureadahead is not packaged in Debian, the dpkg diversion in
cloud-init is not causing trouble, so I will keep it to minimise the
delta with Ubuntu.

I am opening this bug in Launchpad to track the issue, in order to
remove the diversion if eventually ureadahead supports detecting
the presence of cloud-init.

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Tsurumi, Kanagawa, Japan

** Affects: ureadahead (Ubuntu)
 Importance: Undecided
 Status: New

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[Bug 779999] Re: seaview crash after alignment or some window resizing

2012-02-23 Thread Charles Plessy
Dear Tristan,

I am marking this bug incomplete as long as there is not test data
available to reproduce it.

Do you think you can provide ?

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** Changed in: seaview (Ubuntu)
   Status: New = Incomplete

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[Bug 862903] Re: Partman looks confused by the virtual disk name on the EC2 (/dev/xvda1)

2012-02-12 Thread Charles Plessy
Dear Ubuntu developers,

I have tried again with the netboot images 20101020ubuntu108 for
precise, and confirm that the problem is still there.  Partman makes a
new partition table, but /dev only contains an entry for xvda1 and not
xvda1p1, 2, 5 and 6, and therefore the formatting fails.

Is it a bug in Partman, or do you think it should be reassigned
somewhere else ?

Have a nice day,

-- Charles Plessy, Tsurumi, Kanagawa, Japan.

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  Partman looks confused by the virtual disk name on the EC2
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[Bug 862903] Re: Partman looks confused by the virtual disk name on the EC2 (/dev/xvda1)

2012-02-12 Thread Charles Plessy
Just for the record, here is the preseed file I use.

** Attachment added: Preseed to start the network console.
   
https://bugs.launchpad.net/ubuntu/+source/partman-base/+bug/862903/+attachment/2734690/+files/ubuntu-small-preseed.txt

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[Bug 624545] Re: package seaview (not installed) failed to install/upgrade: trying to overwrite '/usr/share/applications/seaview.desktop', which is also in package bio-linux-seaview 0:4.2-0

2011-12-02 Thread Charles Plessy
** Changed in: seaview (Ubuntu)
   Status: New = Fix Released

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  package bio-linux-seaview 0:4.2-0

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[Bug 889889] Re: Use PNG or SVG instead of GIF

2011-11-16 Thread Charles Plessy
Please remove njplot from the list of the packages affected by
LP#889889.

** Changed in: njplot (Ubuntu)
   Status: New = Invalid

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[Bug 889889] Re: Use PNG or SVG instead of GIF

2011-11-16 Thread Charles Plessy
 But njplot is affected.
 /usr/share/app-install/icons/njplot.gif

This file belongs to the app-install-data package:
http://packages.ubuntu.com/precise/all/app-install-data/filelist

And yes, I agree that a screenshot does not make a nice icon :)

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[Bug 862903] [NEW] Partman looks confused by the virtual disk name on the EC2 (/dev/xvda1)

2011-09-29 Thread Charles Plessy
Public bug reported:

Hello,

I am trying to install Ubuntu on the EC2 from scratch by booting on a
preseeded debian-installer (see
http://charles.plessy.org/Debian/debi%C3%A2neries/nuage/) that starts
the SSH network-console.

Using the Oneiric installer, this strategy works well until disk
partitioning.  The EBS volume of the instance is detected as /dev/xvda1
(not /dev/xvda).  Partman then partitions this as the following:

Disk /dev/xvda1: 1073 MB, 1073741824 bytes
255 heads, 63 sectors/track, 130 cylinders, total 2097152 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x000e9d61

  Device Boot  Start End  Blocks   Id  System
/dev/xvda1p12048 1161215  579584   83  Linux
/dev/xvda1p2 1163262 2095103  4659215  Extended
/dev/xvda1p5 1163264 1370111  103424   82  Linux swap / Solaris
/dev/xvda1p6 1372160 2095103  361472   83  Linux

Unfortunately, the formatting can not be started because of the
following error:

Error informing the kernel about modifications to partition /dev/xvda1p1
-- Invalid argument.  This means Linux won't know about any changes you
made to /dev/xvda1p1 until you reboot -- so you shouldn't mount it or
use it in any way before rebooting.

During its preparation, the EBS volume from which the installer was
booted was not partitioned and was formatted as a ext2 filesystem on the
whole disk (/dev/sdb). It was booted accordingly with the aki-ec5df7ed
kernel and ‘root  (hd0)’ in GRUB (see above blog post).

The Debian bug http://bugs.debian.org/637784 is probably related to
this.

Have a nice day,

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Tsurumi, Kanagawa, Japan

** Affects: partman-base (Ubuntu)
 Importance: Undecided
 Status: New

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[Bug 853686] Re: No network interfaces detected in the Amazon EC2.

2011-09-28 Thread Charles Plessy
*** This bug is a duplicate of bug 857662 ***
https://bugs.launchpad.net/bugs/857662

Thanks a lot.  I confirm that the problem is solved in the 28-Sep-2011
build of the oneiric installer.

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[Bug 853686] Re: No network interfaces detected in the Amazon EC2.

2011-09-24 Thread Charles Plessy
Console output for Oneirics d-i on EC2.

** Attachment added: Console output for Oneirics d-i on EC2.
   
https://bugs.launchpad.net/ubuntu/+source/netcfg/+bug/853686/+attachment/2451502/+files/853686_oneiric.txt.gz

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  No network interfaces detected in the Amazon EC2.

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[Bug 853686] Re: No network interfaces detected in the Amazon EC2.

2011-09-24 Thread Charles Plessy
Console output diff between Squeezes and Oneirics d-i on EC2.

** Patch added: Console output diff between Squeezes and Oneirics d-i on EC2.
   
https://bugs.launchpad.net/ubuntu/+source/netcfg/+bug/853686/+attachment/2451504/+files/853686_squeeze-oneiric.diff

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[Bug 853686] Re: No network interfaces detected in the Amazon EC2.

2011-09-24 Thread Charles Plessy
Thanks a lot for the fast response, and sorry for the delay in my answer
(holidays).  I attached a console output from Debian's and Ubuntu's
installers, that shows that indeed xen-netfront is needed and loaded
(“Initialising Xen virtual ethernet driver”) in Debian but not in
Ubuntu.  I also attached a diff made after removing the kernel's
timestamp and the lines containing too much control characters.

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  No network interfaces detected in the Amazon EC2.

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[Bug 853686] Re: No network interfaces detected in the Amazon EC2.

2011-09-24 Thread Charles Plessy
Console output for Squeezes d-i on EC2.

** Attachment added: Console output for Squeezes d-i on EC2.
   
https://bugs.launchpad.net/ubuntu/+source/netcfg/+bug/853686/+attachment/2451503/+files/853686_squeeze.txt.gz

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  No network interfaces detected in the Amazon EC2.

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[Bug 853686] [NEW] No network interfaces detected in the Amazon EC2.

2011-09-19 Thread Charles Plessy
Public bug reported:

Hello,

I am trying to boot the debian-installer in the Amazon EC2, as described
at the following URL:

http://charles.plessy.org/Debian/debi%C3%A2neries/nuage/

I prepared an AMI that contains the initrd.gz and vmlinuz files
downloaded at the following URL (September 11 build).

http://archive.ubuntu.com/ubuntu/dists/oneiric/main/installer-i386/current/images/netboot/xen/

It boots PV-Grub with the aki-ec5df7ed kernel, and then starts Debian-
Installer via a /boot/grub/menu.lst file.  Unfortunately the
configuration of the network fails with the following error.

   ┌─┤ [!] Configure the network ├─┐
   │   │
   │No network interfaces detected │
   │ No network interfaces were found. The installation system was unable  │
   │ to find a network device. │
   │   │
   │ You may need to load a specific module for your network card, if you  │
   │ have one. For this, go back to the network hardware detection step.   │
   │   │
   │ Go Back  Continue │
   │   │
   └───┘

Using the same approach with Debian Squeeze's installer, the network can
be autoconfigured successfully (via preseeding).

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** Affects: netcfg (Ubuntu)
 Importance: Undecided
 Status: New

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[Bug 779999] Re: seaview crash after alignment or some window resizing

2011-09-04 Thread Charles Plessy
Dear Tristan,

SeaView was upgraded to version 4.3 in Oneiric.  Do you think you could
try to reproduce the bug with that version ?

Have a nice day,

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[Bug 809756] Re: t-coffee version 8.99-1 failed to build on armel

2011-08-03 Thread Charles Plessy
** Bug watch added: Debian Bug tracker #631249
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=631249

** Also affects: t-coffee (Debian) via
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=631249
   Importance: Unknown
   Status: Unknown

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  t-coffee version 8.99-1 failed to build on armel

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[Bug 558403] Re: R CRAN packages built against old version of R

2011-06-28 Thread Charles Plessy
I am closing the bug, since it is fixed since Maverick.  Before this, I
tagged it ‘lucid’ as a reminder that it is not fixed in the LTS.  But I
do not know if it is the proper way to do…

** Tags added: lucid

** Changed in: r-cran-vcd (Ubuntu)
   Status: New = Fix Released

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[Bug 770926] Re: phyml version 2:20100123-1 failed to build on amd64 with GCC-4.6/oneiric

2011-06-24 Thread Charles Plessy
It looks like 2:20100720-1 built fine, so I will close this bug.

https://launchpad.net/ubuntu/+source/phyml/2:20100720-1

** Changed in: phyml (Ubuntu Oneiric)
   Status: New = Fix Released

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  phyml version 2:20100123-1 failed to build on amd64 with
  GCC-4.6/oneiric

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[Bug 766023] Re: amap-align version 2.2-1 failed to build on i386

2011-06-23 Thread Charles Plessy
Fixed in  2.2-3.

** Changed in: amap-align (Ubuntu Oneiric)
   Status: New = Fix Released

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[Bug 755927] Re: r-cran-surveillance version 1.2-1-1 failed to build on i386

2011-06-20 Thread Charles Plessy
Corrected by Andreas in 1.2-1-2.  Thak you for the patch.

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[Bug 732281] Re: libnucleus error in fdnapars and others after updates

2011-06-14 Thread Charles Plessy
Hi Wolfgang,

here in Yokohama things have settled down and life has returned to
normal.

In Ubuntu 11.04 (Natty Narwhal), you will find the latest EMBOSS
packages, properly tied with the EMBASSY packages.  I have installed
Natty on a friend's computer recently, and on the EMBOSS side, thinks
looked to work well.  GNOME 3 was a bit surprising, but the fallback
mode seems to emulate well the look and feel of GNOME 2.

Have a nice day,

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[Bug 732281] Re: libnucleus error in fdnapars and others after updates

2011-06-07 Thread Charles Plessy
Hello Wolfgang,

the 6.2.0-2 packages and the accompanying EMBASSY packages were not well
tied to each other.  Sorry for this.

embassy-phylip 3.68-1 is to be used with emboss 6.1.0.
embassy-phylip 3.69-1 is to be used with emboss 6.2.0.
embassy-phylip 3.69+20100721 is to be used with emboss 6.3.1 (and is properly 
tied to it).

Maverick does not have the right combination, so you need to stay with
EMBOSS 6.1.0, or upgrade to later versions.  I would have liked to
provide you a backport of embassy-phylip in Debian Med's PPA, but non-
free software is not allowed in PPAs.  How about the following:

 - Tell me which suite you are interested in, and I will upload a backport of 
emboss 6.3.1 there (https://launchpad.net/~debian-med/+archive/ppa)
 - Rebuild embassy-phylip by yourself if you do not mind installing extra 
packages. Something along these lines (not tested)

apt-get install build-essential devscripts
dget -x 
http://archive.ubuntu.com/ubuntu/pool/multiverse/e/embassy-phylip/embassy-phylip_3.69+20100721-3.dsc
cd embassy-phylip-3.69+20100721-3
sudo mk-build-deps -r -i
debuild -us -uc
cd ..
sudo dpkg -i  embassy-phylip*deb

Cheers,

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[Bug 749171] Re: epcr version 2.3.12-1 failed to build on i386

2011-06-07 Thread Charles Plessy
** Changed in: epcr (Ubuntu Oneiric)
   Status: Fix Committed = Fix Released

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[Bug 770831] Re: njplot version 2.3-2 failed to build on amd64 with GCC-4.6/oneiric

2011-06-07 Thread Charles Plessy
Fixed in 2.3-3

** Bug watch added: Debian Bug tracker #614432
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=614432

** Also affects: njplot (Debian) via
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=614432
   Importance: Unknown
   Status: Unknown

** Changed in: njplot (Ubuntu)
   Status: New = Fix Released

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[Bug 749107] Re: dialign version 2.2.1-3 failed to build on i386

2011-05-24 Thread Charles Plessy
** Changed in: dialign (Ubuntu)
   Status: New = Fix Released

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[Bug 771068] Re: probcons version 1.12-7 failed to build on amd64 with GCC-4.6/oneiric

2011-05-24 Thread Charles Plessy
Fixed, see http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=625036

** Changed in: probcons (Ubuntu)
   Status: New = Fix Released

** Bug watch added: Debian Bug tracker #625036
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=625036

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[Bug 712004] Re: samtools version is outdated in Lucid

2011-05-20 Thread Charles Plessy
Dear Bernard,

I have prepared a backport of Debian's samtools package 0.1.16-1 for
Lucid in the PPA of Debian Med:

https://launchpad.net/~debian-med/+archive/ppa

In the 0.1.16-1 package, the headers for libbam were moved in
/usr/lib/samtools, but I reverted this in the backport 0.1.16-1~lucid1,
as other packages like libbio-samtools-perl would not be buildable.  I
may revert again if we start to backport libbio-samtools-perl 1.28-2 or
superior, or new packages like cufflinks.

Have a nice week-end,

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[Bug 770770] Re: last-align version 146-1 failed to build on amd64 with GCC-4.6/oneiric

2011-05-15 Thread Charles Plessy
** Changed in: last-align (Ubuntu)
   Status: New = Fix Committed

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[Bug 749171] Re: epcr version 2.3.12-1 failed to build on i386

2011-05-15 Thread Charles Plessy
Fixed in 2.3.12-2

http://packages.qa.debian.org/e/epcr/news/20110222T111720Z.html

** Bug watch added: Debian Bug tracker #614482
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=614482

** Also affects: epcr (Debian) via
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=614482
   Importance: Unknown
   Status: Unknown

** Changed in: epcr (Ubuntu)
   Status: New = Fix Committed

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[Bug 766023] Re: amap-align version 2.2-1 failed to build on i386

2011-05-13 Thread Charles Plessy
** Bug watch added: Debian Bug tracker #624990
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=624990

** Also affects: amap-align (Debian) via
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=624990
   Importance: Unknown
   Status: Unknown

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[Bug 690997] Re: Would like package to include additional header files

2011-05-08 Thread Charles Plessy
Dear Harold,

we will soon upload samtools 0.1.16-1 to Debian, which will transiently
distribute sam.h in /usr/include.  We will later move it and all the
other headers to /usr/include/samtools.  (It is not possible to go
directly for /usr/include/samtools as we need to take care of not
touching libbio-samtools-perl during the transition to Perl 5.12 that
currently takes place in Debian.)

In addition, we are preparing a package for Cufflinks.  You can see its
development at the following URL.

http://git.debian.org/?p=debian-med/cufflinks.git

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[Bug 770770] Re: last-align version 146-1 failed to build on amd64 with GCC-4.6/oneiric

2011-05-07 Thread Charles Plessy
Fixed in Debian (162-1)

** Bug watch added: Debian Bug tracker #625084
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=625084

** Also affects: last-align (Debian) via
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=625084
   Importance: Unknown
   Status: Unknown

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[Bug 749107] Re: dialign version 2.2.1-3 failed to build on i386

2011-04-10 Thread Charles Plessy
** Bug watch added: Debian Bug tracker #618057
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=618057

** Also affects: dialign (Debian) via
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=618057
   Importance: Unknown
   Status: Unknown

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[Bug 658240] Re: package blast2 (not installed) failed to install/upgrade: trying to overwrite '/usr/bin/rpsblast', which is also in package ncbi-blast 0:2.2.22 -1

2011-02-21 Thread Charles Plessy
Dear Anke,

I think that the ncbi-blast package that blocks the installation of
blast2 is a third-party package. Ubuntu (nor Debian, from which most
Ubuntu packages come from) does not distribute a ncbi-blast package.

The simplest solution is therefore to remove the ncbi-blast package, if
you are fine with the version of the blast2 package.

Have a nice day,

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[Bug 690997] Re: Would like package to include additional header files

2010-12-28 Thread Charles Plessy
Dear Harold,

developments of the libbam-dev package take place in Debian. I monitor
Launchpad nevertheless. I can move the header files to /usr/include/bam,
but then another software, Bio::Samtools, will need manual configuration
as it expects the headers in /usr/include. I will ask to the SAMtools
developers for their recommendation.

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Debian Med packaging team
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Illkirch, France

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[Bug 668798] Re: jemboss package does not depend on emboss package

2010-10-31 Thread Charles Plessy
Dear Kris,

thank you very much for your report. This is already fixed in the Natty
Narwhal.

Have a nice day,

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Tsurumi, Kanagawa, Japan

** Changed in: emboss (Ubuntu)
   Status: New = Fix Released

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[Bug 624545] Re: package seaview (not installed) failed to install/upgrade: trying to overwrite '/usr/share/applications/seaview.desktop', which is also in package bio-linux-seaview 0:4.2-0

2010-10-24 Thread Charles Plessy
Hello,

the problem here is the bio-linux-seaview package. Since it is added
downstream of Ubuntu, we (the Debian maintainers who made the Ubuntu
package) can not prevent file conflicts. Given that currently the
version of Seaview is higher in Ubuntu than in Bio-Linux, I would simply
recommend to remove bio-linux-seaview if possible.

Do you mind if I close this bug, or would you like to keep it open until
an update of Bio Linux eventually resolves the problem?

Have a nice day,

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[Bug 526356] Re: restrict and remap segmentation faults - lucid version on karmic system

2010-10-24 Thread Charles Plessy
Fixed in the Natty Narwhal.

** Changed in: emboss (Ubuntu)
   Status: New = Fix Released

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[Bug 526347] Re: frestdist documentation should not be in emboss-doc

2010-10-24 Thread Charles Plessy
** Changed in: emboss (Ubuntu)
   Status: New = Fix Released

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frestdist documentation should not be in emboss-doc
https://bugs.launchpad.net/bugs/526347
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[Bug 525662] Re: Dependency on c shell necessary?

2010-10-24 Thread Charles Plessy
Fixed since the Maverick Meerkat.

** Changed in: emboss (Ubuntu)
   Status: Confirmed = Fix Released

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Dependency on c shell necessary?
https://bugs.launchpad.net/bugs/525662
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[Bug 588102] Re: perlprimer not up to date on repository

2010-10-24 Thread Charles Plessy
Hello,

the package was automatically synchronised with Debian since the
Maverick Meerkat.

Have a nice day,

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Tsurumi, Kanagawa, Japan

** Changed in: perlprimer (Ubuntu)
   Status: New = Fix Released

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perlprimer not up to date on repository
https://bugs.launchpad.net/bugs/588102
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[Bug 632446] Re: Please sync imagej (universe) 1.44e-1 from Debian unstable (main)

2010-10-23 Thread Charles Plessy
Hi,

it looks like imagej was synced to 1.44e-1 in the Natty Narwhal.

Have a nice day,

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Debian Med packaging team
Tsurumi, Kanagawa, Japan

** Changed in: imagej (Ubuntu)
   Status: New = Fix Released

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Please sync imagej (universe) 1.44e-1 from Debian unstable (main)
https://bugs.launchpad.net/bugs/632446
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[Bug 661545] Re: imagej refuses to quit

2010-10-23 Thread Charles Plessy
** Bug watch added: Debian Bug tracker #600997
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=600997

** Also affects: imagej via
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=600997
   Importance: Unknown
   Status: Unknown

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imagej refuses to quit
https://bugs.launchpad.net/bugs/661545
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[Bug 661573] [NEW] Reduction of the diff with Debian ?

2010-10-15 Thread Charles Plessy
Public bug reported:

Hello,

I wonder if it would be possible to reduce the diff between the Debian
and Ubuntu axis2c packages, in order to make its inspection easier:

 - Is it needed to keep Standards-Version at 3.8.0 in Ubuntu?
 - Including the contents of the NOTICE file in debian/copyright is necessary 
to comply with the Apache license 2.0.
 - The lintian overrides and the README.Debian notice about rpath, while not 
essential to Ubuntu, are probably better to be ignored than deleted.

Have a nice day,

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Debian pkg-eucalyptus team
http://wiki.debian.org/pkg-eucalyptus
Tsurumi, Kanagawa, Japan

** Affects: axis2c (Ubuntu)
 Importance: Undecided
 Status: New

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Reduction of the diff with Debian ?
https://bugs.launchpad.net/bugs/661573
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[Bug 298587] Re: xkbsel install problem

2010-08-06 Thread Charles Plessy
** Bug watch added: Debian Bug tracker #591592
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=591592

** Also affects: xkbsel (Debian) via
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=591592
   Importance: Unknown
   Status: Unknown

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xkbsel install problem
https://bugs.launchpad.net/bugs/298587
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[Bug 137847] Re: xview does not build correctly on amd64, causing treetool crashes on startup

2010-07-16 Thread Charles Plessy
For the record, treetool was removed from the Debian unstable and
testing branches, and will therefore not be part of future releases.

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Debian Med packaging team
http://www.debian.org/devel/debian-med/
Tsurumi, Kanagawa, Japan

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xview does not build correctly on amd64, causing treetool crashes on startup
https://bugs.launchpad.net/bugs/137847
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[Bug 423648] Re: Requestsync for ClustalX package

2010-03-24 Thread Charles Plessy
Hi all,

For the record, the reason why Debian's clustalx has not migrated in
testing is only the lack of autobuilders for non-free packages. There is
no release-critical problem in clustalx 2.0.12-2.

Cheers,

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Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

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Requestsync for ClustalX package
https://bugs.launchpad.net/bugs/423648
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[Bug 527019] Re: em_pscan and em_cons not found for jemboss

2010-02-25 Thread Charles Plessy
Dear Bela,

thank you for the report. pscan and cons are found under their original
name in /usr/lib/emboss. Jemboss (and any other application that calls
EMBOSS programs) needs to have this directory in its path to find them.
I will try to address that issue in the next upload.

Have a nice day,

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Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

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em_pscan and em_cons not found for jemboss
https://bugs.launchpad.net/bugs/527019
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[Bug 526350] Re: libfontconfig1 - high version in embassy-phylip

2010-02-23 Thread Charles Plessy
Dear Bela,

I think that this dependency is derived automatically at build time and
is quite conservative unless some detailed information about the library
symbols is provided. In other terms, if you rebuild embassy-phylip
against karmic (for instance through a Ubuntu personal package archive),
you will obtain a package that is installable on karmic.

Have a nice day

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Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

-- 
libfontconfig1 - high version in embassy-phylip
https://bugs.launchpad.net/bugs/526350
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[Bug 525662] Re: Dependency on c shell necessary?

2010-02-23 Thread Charles Plessy
Dear Bela,

this is a very good point. Since the emboss binary package does not
contain C shell scripts, this dependency is not needed. I will remove in
the next package update (to upstream version 6.2.0), which I hope to do
soon.

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

** Changed in: emboss (Ubuntu)
   Status: New = Confirmed

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Dependency on c shell necessary?
https://bugs.launchpad.net/bugs/525662
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[Bug 526356] Re: restrict and remap segmentation faults - lucid version on karmic system

2010-02-23 Thread Charles Plessy
Dear Bela,

have you also updated the libajax6 and libnucleus6 packages? Please let
me know if that solves your problem, so that I tighten the dependency of
the EMBOSS packages on these libraries.

Cheers,

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Debian Med packaging team
http:www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

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restrict and remap segmentation faults - lucid version on karmic system
https://bugs.launchpad.net/bugs/526356
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[Bug 471127] Re: ImageJ fails to run - /usr/share/imagej/jni/*: No such file or directory

2010-02-22 Thread Charles Plessy
Hello everybody,

This is fixed in Lucid since version 1.43l-1, that depends on
openjdk-6-jre | java2-runtime.

Have a nice day,

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Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

-- 
ImageJ fails to run - /usr/share/imagej/jni/*: No such file or directory
https://bugs.launchpad.net/bugs/471127
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[Bug 423648] Re: Package heavily out of date

2010-01-28 Thread Charles Plessy
Excellent! I added $(RM) moc_* to the clean target in debian/rules and
the package builds fine on Lucid:

https://launchpad.net/~plessy/+archive/plessy/+build/1472225

I will update the Debian package soon.

Have a nice day,

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Package heavily out of date
https://bugs.launchpad.net/bugs/423648
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