New issue 2908: Segfault when reading a GraphViz file with Pygraphviz
https://bitbucket.org/pypy/pypy/issues/2908/segfault-when-reading-a-graphviz-file-with
Shaun Jackman:
I installed Pypy3 6.0.0 and GraphViz 2.40.1 using Linuxbrew `brew install pypy3
graphviz`, and I installed Pygraphviz 1.5
[
https://issues.apache.org/jira/browse/SPARK-18778?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16368442#comment-16368442
]
Shaun Jackman commented on SPARK-18778:
---
I have this issue as well. spark-shell fails with Java 9
[
https://issues.apache.org/jira/browse/SPARK-18778?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16368442#comment-16368442
]
Shaun Jackman edited comment on SPARK-18778 at 2/18/18 5:25 AM:
I have
Hi, David. Two options:
1. Use Biomake, which is mostly compatible with GNU Make, and supports
submitting jobs to Slurm.
https://github.com/evoldoers/biomake
It can be installed with Linuxbrew on Linux or Homebrew on macOS.
brew install homebrew/science/biomake
2. Precede each command that you
Hi, Andreas. ABySS 2.0.1 is now GPL-3 without the non-commercial
restriction!
https://github.com/bcgsc/abyss/releases
Cheers,
Shaun
--
http://sjackman.ca
On September 6, 2016 at 09:13:44, Andreas Tille (andr...@an3as.eu) wrote:
Hi Shaun,
On Tue, Sep 06, 2016 at 03:49:16PM +, Shaun
, and we'll see how it goes.
Cheers,
Shaun
On Tue, 6 Sep 2016 at 08:34 Andreas Tille <andr...@an3as.eu> wrote:
> Hi Shaun,
>
> On Mon, Sep 05, 2016 at 01:50:57PM -0700, Shaun Jackman wrote:
> > The license of ABySS 2.0 is unchanged from ABySS 1.9. The license of
> ABySS
On April 20, 2016 at 13:37:01, Junio C Hamano
(gits...@pobox.com(mailto:gits...@pobox.com)) wrote:
> Shaun Jackman writes:
>
> > I'd like to insert a commit between two commits without changing
> > the committer date or author date of that commit or the subsequent
> &
I'd like to insert a commit between two commits without changing the committer
date or author date of that commit or the subsequent commits. I'd planned on
using `git rebase -i` to insert the commit. I believe it retains the author
date, but changes the committer date to the current time. I've
--- You are receiving this mail because: ---
You are on the CC list for the bug.
http://bugs.exim.org/show_bug.cgi?id=1525
Summary: RunTest fails with GCC 4.9.1
Product: PCRE
Version: 8.35
Platform: x86-64
URL:
Hi David,
Thanks for fixing this bug in avarice. Please do go ahead with the NMU.
avarice is up for adoption. See the RFA here: http://bugs.debian.org/732433
Would you like to adopt avarice?
Cheers,
Shaun
--
http://sjackman.ca
On 2013-Dec-22 at 10:39:11 , David Prévot (taf...@debian.org)
Hi David,
Thanks for fixing this bug in avarice. Please do go ahead with the NMU.
avarice is up for adoption. See the RFA here: http://bugs.debian.org/732433
Would you like to adopt avarice?
Cheers,
Shaun
--
http://sjackman.ca
On 2013-Dec-22 at 10:39:11 , David Prévot (taf...@debian.org)
Package: ftp.debian.org
Severity: normal
Hi,
Please remove pptview. It's quite dated (circa 1997), and there are
better free alternatives now. It has two open Ubuntu bugs.
installation fails for amd64
https://bugs.launchpad.net/ubuntu/+source/pptview/+bug/909447
PowerPoint viewer version 97
Package: ftp.debian.org
Severity: normal
Hi,
Please remove pocketpc-cab. I'm the upstream developer and the Debian
package maintainer, and it hasn't been maintained in many years.
Thanks,
Shaun
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with a subject of
From: Ma Xiaojun damage3...@gmail.com
Date: 17 December 2013 07:51
Subject: Remove or Fix Debian‘s pptview
To: sjack...@debian.org
Hi,
pptview is actually a pretty smart work. It offers a high level of
desktop integration, it somehow conforms to FHS, ...
However, it also have multiple issues
Package: wnpp
Please adopt avarice. A new upstream version is available: 2.13.
http://avarice.sourceforge.net/
Thanks,
Shaun
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Package: wnpp
Please adopt avarice. A new upstream version is available: 2.13.
http://avarice.sourceforge.net/
Thanks,
Shaun
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Archive:
VcdEIHjgSQREXKqOL68RaEryrxWVFXat16yEurUjbcvGhW1Lyb5m9V7osIBlxiXF
nBcrfEdC/q4CuHGBL8MP
=+D8f
-END PGP SIGNATURE-
-- Forwarded message --
From: Shaun Jackman sjack...@gmail.com
To: Submit@BTS sub...@bugs.debian.org
Cc:
Date: Wed, 6 Mar 2013 07:50:30 -0800
Subject: New upstream release available
Package: abyss
Hi Andreas,
My home machine is running OS X and I use Homebrew to manage packages, and
at work I don't have root access on the Linux servers, so I use Linuxbrew to
manage packages. To maintain a Debian package, there's a little extra effort
required to fire up a VM. I opened
I'm trying to build a data.frame row-by-row like so:
df - data.frame(rbind(list('a',1), list('b', 2), list('c', 3)))
I was surprised to see that the columns of the resulting data.frame
are stored in lists rather than vectors.
str(df)
'data.frame': 3 obs. of 2 variables:
$ X1:List of 3
..$ :
, which include the graphs generated
by the code. I believe there's also a base graphics version that you
can get from the gplots package, but I don't know a lot about it.
Dennis
On Thu, Jul 4, 2013 at 2:53 PM, Shaun Jackman sjack...@gmail.com wrote:
Hi,
I'd like to draw a lattice barchart
,
Shaun
On 5 July 2013 11:28, David Winsemius dwinsem...@comcast.net wrote:
On Jul 5, 2013, at 11:15 AM, Shaun Jackman wrote:
Hi Bert, Dennis,
I'll agree that using a barchart was a poor choice. I was in fact using a
notched bwplot to show the median and confidence interval of the median
.
Cheers,
Bert
On Fri, Jul 5, 2013 at 11:28 AM, David Winsemius dwinsem...@comcast.net
wrote:
On Jul 5, 2013, at 11:15 AM, Shaun Jackman wrote:
Hi Bert, Dennis,
I'll agree that using a barchart was a poor choice. I was in fact using a
notched bwplot to show the median and confidence interval
Hi,
I'd like to draw a lattice barchart of means with error bars to show
the standard deviation. I have the barchart, how do I add the error
bars?
require(datasets)
require(lattice)
x - aggregate(weight ~ Diet, ChickWeight, function(x) c(mean=mean(x),
sd=sd(x)))
barchart(weight[,'mean'] ~ Diet,
June 2013 05:50, Adams, Jean jvad...@usgs.gov wrote:
Shaun,
See the help on contrasts ...
?contr.treatment
Jean
On Tue, Jun 25, 2013 at 7:07 PM, Shaun Jackman sjack...@gmail.com wrote:
Hi,
I've used `lm` to create a linear model of a continuous variable
against a factor variable
Hi,
I've used `lm` to create a linear model of a continuous variable
against a factor variable with four levels using an example R data set
(see below). By default, it uses a treatment contrast matrix that
compares each level of the factor variable with the first reference
level (three
Package: abyss
Priority: wishlist
ABySS 1.3.5 is available.
Cheers,
Shaun
System.IO.MMap (mmapFileByteString) worked like a charm in loading
files larger than 2 GB on OS X. Using mmapFileByteString and strict
ByteString is roughly seven times faster for my program than using
getContents and ByteString.Lazy.
Cheers,
Shaun
On 11 June 2012 07:08, Gracjan Polak
Changed-By: Shaun Jackman sjack...@debian.org
Description:
gmap - spliced and SNP-tolerant alignment for mRNA and short reads
Changes:
gmap (2012-06-12-1) unstable; urgency=low
.
* New upstream release
Checksums-Sha1:
38c84f66c8d136e9845eb1e40edb98c1f1096509 1300 gmap_2012-06-12-1.dsc
build? That might have something to
do with it, if you're nearing 2^32 (or 2^31) bytes.
Erik
On Fri, Jun 8, 2012 at 2:25 AM, Shaun Jackman sjack...@gmail.com wrote:
Hi,
Data.ByteString.Char8.getContents fails for files 2GB on OS X. Is
there a fix for this?
$ cat getContents.hs
main
Hi,
Data.ByteString.Char8.getContents fails for files 2GB on OS X. Is
there a fix for this?
$ cat getContents.hs
main = getContents
$ ./getContents smallFile
$ ./getContents bigFile
getContents: stdin: hGetBuf: invalid argument (Invalid argument)
$ ghc --version
The Glorious Glasgow Haskell
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Format: 1.8
Date: Thu, 31 May 2012 11:39:13 -0700
Source: abyss
Binary: abyss
Architecture: source amd64
Version: 1.3.4-1
Distribution: unstable
Urgency: low
Maintainer: Shaun Jackman sjack...@debian.org
Changed-By: Shaun Jackman sjack...@debian.org
Hi Andreas,
I'd suggest using a scoped for loop rather than the original while loop.
Cheers,
Shaun
On 2012-04-23, at 1:30 AM, Andreas Tille wrote:
Hi Shaun,
as you know the Debian Med team has packaged plink for Debian. Recently
we received a bug report that the package does not build
No worries, Andreas. It's just a coding style suggestion. Your
solution is perfectly fine.
Cheers,
Shaun
On 23 April 2012 11:48, Andreas Tille ti...@debian.org wrote:
Hi Shaun,
On Mon, Apr 23, 2012 at 08:43:22AM -0700, Shaun Jackman wrote:
I'd suggest using a scoped for loop rather than
Hi Andreas,
Currently ABySS is maintained by me personally, not by Debian-med. Are you
proposing adopting the package?
Cheers,
Shaun
On 2012-03-31, at 23:20, Andreas Tille ti...@debian.org wrote:
Hi Shaun,
when checking the citations of our packages I stumbled upon abyss which
is not yet
Hi Andreas,
I haven't looked at your changes yet, but I trust your judgement. Go ahead and
upload. Thanks for your effort.
Cheers,
Shaun
On 2012-03-31, at 0:04, Andreas Tille andr...@an3as.eu wrote:
Hi Shaun,
you might have noticed that I updated jellyfish in Git. My main
motivation was
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Format: 1.8
Date: Tue, 13 Mar 2012 15:43:49 -0700
Source: abyss
Binary: abyss
Architecture: source amd64
Version: 1.3.3-1
Distribution: unstable
Urgency: low
Maintainer: Shaun Jackman sjack...@debian.org
Changed-By: Shaun Jackman sjack...@debian.org
-By: Shaun Jackman sjack...@debian.org
Description:
gmap - spliced and SNP-tolerant alignment for mRNA and short reads
Changes:
gmap (2011-12-28-1) unstable; urgency=low
.
* New upstream release.
Checksums-Sha1:
578fa447e864bb366b9729e9dde4642ef495e1d1 1272 gmap_2011-12-28-1.dsc
The following commit has been merged in the master branch:
commit 6d890ec11cda244af878bce40aaf28817d16fa87
Merge: fa026f0479f1ce52255c6f25dba299b7de54d5f6
e4c2005de55d41c725c009e2e1a008c3f46f6b1d
Author: Shaun Jackman sjack...@debian.org
Date: Thu Dec 29 12:32:02 2011 -0800
Merge commit
The following commit has been merged in the master branch:
commit 1c3f4475e101e5ff8f84e51ee2aa9773feddc1db
Author: Shaun Jackman sjack...@debian.org
Date: Thu Dec 29 12:56:00 2011 -0800
New upstream release.
diff --git a/debian/changelog b/debian/changelog
index 3809c40..a6732d3 100644
The annotated tag, upstream/2011-12-28 has been created
at a0ccf60d51aa5e17d17c5ec161236dd8558c5b80 (tag)
tagging e4c2005de55d41c725c009e2e1a008c3f46f6b1d (commit)
replaces upstream/2011-11-30
tagged by Shaun Jackman
on Thu Dec 29 12:32:02 2011 -0800
- Shortlog
-By: Shaun Jackman sjack...@debian.org
Description:
igv- Integrative Genomics Viewer
Changes:
igv (2.0.30-1) unstable; urgency=low
.
* New upstream release.
Checksums-Sha1:
ea93d96b13a083271cc33f2aba27ce81c923f10a 1628 igv_2.0.30-1.dsc
840b8d891a50d2885bcfdc8d3146fbf57e510a17 5774595
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Format: 1.8
Date: Tue, 13 Dec 2011 17:04:24 -0800
Source: abyss
Binary: abyss
Architecture: source i386
Version: 1.3.2-1
Distribution: unstable
Urgency: low
Maintainer: Shaun Jackman sjack...@debian.org
Changed-By: Shaun Jackman sjack...@debian.org
-By: Shaun Jackman sjack...@debian.org
Description:
gmap - spliced and SNP-tolerant alignment for mRNA and short reads
Changes:
gmap (2011-11-30-1) unstable; urgency=low
.
* New upstream release.
Checksums-Sha1:
11304ac3bee1dd5485d5c9b589fe8c0d27cff2aa 1272 gmap_2011-11-30-1.dsc
The following commit has been merged in the master branch:
commit fa026f0479f1ce52255c6f25dba299b7de54d5f6
Author: Shaun Jackman sjack...@debian.org
Date: Wed Dec 7 13:21:47 2011 -0800
New upstream release.
diff --git a/debian/changelog b/debian/changelog
index 758ddfb..3809c40 100644
The following commit has been merged in the pristine-tar branch:
commit 0a460b1ec9046adeea6f79f02b1dc3c800249dde
Author: Shaun Jackman sjack...@debian.org
Date: Wed Dec 7 10:46:06 2011 -0800
pristine-tar data for gmap_2011-11-30.orig.tar.gz
diff --git a/gmap_2011-11-30.orig.tar.gz.delta
b
The following commit has been merged in the master branch:
commit 3efcc56440643d5fdf174b9c05f0e19f7b9d3484
Merge: f9ff31c8c859f6aeee6045ae86eda7bf4b98b865
97f37c8aff7a03672cc366c437fd58ce1dd064de
Author: Shaun Jackman sjack...@debian.org
Date: Wed Dec 7 10:46:06 2011 -0800
Merge commit
The annotated tag, upstream/2011-11-30 has been created
at 94e7a81eb25188390d5180666c792d07044674e2 (tag)
tagging 97f37c8aff7a03672cc366c437fd58ce1dd064de (commit)
replaces upstream/2011-10-16
tagged by Shaun Jackman
on Wed Dec 7 10:46:06 2011 -0800
- Shortlog
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Format: 1.8
Date: Sat, 03 Dec 2011 12:23:50 -0800
Source: avarice
Binary: avarice
Architecture: source i386
Version: 2.11-1
Distribution: unstable
Urgency: low
Maintainer: Shaun Jackman sjack...@debian.org
Changed-By: Shaun Jackman sjack...@debian.org
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Format: 1.8
Date: Sat, 03 Dec 2011 12:48:15 -0800
Source: pptview
Binary: pptview
Architecture: source i386
Version: 8.0-7
Distribution: unstable
Urgency: low
Maintainer: Shaun Jackman sjack...@debian.org
Changed-By: Shaun Jackman sjack...@debian.org
pptview is a PE32 executable, so wine is necessary.
Cheers,
Shaun
On 29 November 2010 12:13, Frenchn00b frenchn...@yahoo.com wrote:
Package: pptview
Severity: important
Non non-substancial needed dependencies are in the deb file.
wine dependencies, could you avoid that too please ?
a#
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Format: 1.8
Date: Mon, 24 Oct 2011 11:32:59 -0700
Source: abyss
Binary: abyss
Architecture: source amd64
Version: 1.3.1-1
Distribution: unstable
Urgency: low
Maintainer: Shaun Jackman sjack...@debian.org
Changed-By: Shaun Jackman sjack...@debian.org
-By: Shaun Jackman sjack...@debian.org
Description:
gmap - spliced and SNP-tolerant alignment for mRNA and short reads
Changes:
gmap (2011-10-16-1) unstable; urgency=low
.
* New upstream release.
Checksums-Sha1:
a2cbfa392714cad475ebf0f6c6167c9ece9adb12 1272 gmap_2011-10-16-1.dsc
The following commit has been merged in the master branch:
commit a0a5398d71ef463913157876817c016e727bf6a5
Merge: 2d7fb22fd04e815078965cd2e7827bc7ae82cc67
9901f2c730069572df57ef5bbc05538a459c508d
Author: Shaun Jackman sjack...@debian.org
Date: Wed Oct 19 15:40:32 2011 -0700
Merge commit
The following commit has been merged in the master branch:
commit f9ff31c8c859f6aeee6045ae86eda7bf4b98b865
Author: Shaun Jackman sjack...@debian.org
Date: Wed Oct 19 16:57:17 2011 -0700
New upstream release.
diff --git a/debian/changelog b/debian/changelog
index c348c40..758ddfb 100644
The following commit has been merged in the pristine-tar branch:
commit 3273d61e4cf5005e041b9b3913a5767ef9936caf
Author: Shaun Jackman sjack...@debian.org
Date: Wed Oct 19 15:40:32 2011 -0700
pristine-tar data for gmap_2011-10-16.orig.tar.gz
diff --git a/gmap_2011-10-16.orig.tar.gz.delta
Changed-By: Shaun Jackman sjack...@debian.org
Description:
jellyfish - count k-mers in DNA sequences
Closes: 644925
Changes:
jellyfish (1.1.2-1) unstable; urgency=low
.
* Initial release. Closes: #644925.
Checksums-Sha1:
7d2b5587036d6a6a93252e912c5dab7fa0b58515 1281 jellyfish_1.1.2-1.dsc
Package: wnpp
Severity: wishlist
Package name: jellyfish
Version: 1.1.2
Upstream author: Guillaume Marçais gmarc...@umd.edu
License: GPL-3+
Description: count k-mers of DNA
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting
Package: wnpp
Severity: wishlist
Package name: jellyfish
Version: 1.1.2
Upstream author: Guillaume Marçais gmarc...@umd.edu
License: GPL-3+
Description: count k-mers of DNA
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting
The branch, master has been created
at 50f2f49253b432acdb224e4cc94ce856c4d6991a (commit)
- Shortlog
commit 50f2f49253b432acdb224e4cc94ce856c4d6991a
Author: Shaun Jackman sjack...@gmail.com
Date: Mon Oct 10 11:33:20 2011 -0700
The following commit has been merged in the master branch:
commit 6529ac1a2916faf781c227cd16dfab240bc57611
Author: Shaun Jackman sjack...@gmail.com
Date: Mon Oct 10 14:04:37 2011 -0700
Initial release.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 000
The annotated tag, upstream/1.1.2 has been created
at 3ae3d0681c314eda00ebdf430bed9d58f0a06753 (tag)
tagging 50f2f49253b432acdb224e4cc94ce856c4d6991a (commit)
tagged by Shaun Jackman
on Mon Oct 10 11:33:22 2011 -0700
- Shortlog
The branch, pristine-tar has been created
at 0fb0e92af013dd85e336476e91296f865f677b65 (commit)
- Shortlog
commit 0fb0e92af013dd85e336476e91296f865f677b65
Author: Shaun Jackman sjack...@gmail.com
Date: Mon Oct 10 11:33:22 2011
The branch, upstream has been created
at 50f2f49253b432acdb224e4cc94ce856c4d6991a (commit)
- Shortlog
---
--
count k-mers of DNA
The tag, debian/1.1.2-1 has been created
at 6529ac1a2916faf781c227cd16dfab240bc57611 (commit)
- Shortlog
commit 6529ac1a2916faf781c227cd16dfab240bc57611
Author: Shaun Jackman sjack...@gmail.com
Date: Mon Oct 10 14:04:37 2011
-By: Shaun Jackman sjack...@debian.org
Description:
gmap - spliced and SNP-tolerant alignment for mRNA and short reads
Changes:
gmap (2011-09-14-1) unstable; urgency=low
.
* New upstream release.
Checksums-Sha1:
f4c32a863e6b0a5cc632555b49fc903328ce87fb 1272 gmap_2011-09-14-1.dsc
The following commit has been merged in the master branch:
commit 6d902e0e8aae3db3b68fb16608fd242426196e59
Merge: ce800895fb3da208229f877b5e8025fd72d80ae2
2ab08afc5f80572c59ddf6bde8222aa65ee41ab2
Author: Shaun Jackman sjack...@debian.org
Date: Thu Sep 15 14:36:32 2011 -0700
Merge commit
The following commit has been merged in the master branch:
commit 2d7fb22fd04e815078965cd2e7827bc7ae82cc67
Author: Shaun Jackman sjack...@debian.org
Date: Thu Sep 15 14:43:17 2011 -0700
New upstream release.
diff --git a/debian/changelog b/debian/changelog
index e8cfaf8..c348c40 100644
The annotated tag, upstream/2011-09-14 has been created
at 641e76314761451bd0d32600d3d2cfde27c72c13 (tag)
tagging 2ab08afc5f80572c59ddf6bde8222aa65ee41ab2 (commit)
replaces upstream/2011-09-09
tagged by Shaun Jackman
on Thu Sep 15 14:36:32 2011 -0700
- Shortlog
-By: Shaun Jackman sjack...@debian.org
Description:
gmap - spliced and SNP-tolerant alignment for mRNA and short reads
Changes:
gmap (2011-09-09-1) unstable; urgency=low
.
* New upstream release.
Checksums-Sha1:
fee2c5b42e7b1b60246ebbc62a9e23454f165d35 1272 gmap_2011-09-09-1.dsc
The following commit has been merged in the master branch:
commit e7e10a2c7b4941e79bd3703532cee5c83d6df0a3
Merge: e21796d88ba8cf78ddbb3c851e412329ee96b25b
a50c159e265f15a53ab51ddc19ee77962be73a4f
Author: Shaun Jackman sjack...@debian.org
Date: Wed Sep 14 17:08:07 2011 -0700
Merge commit
The following commit has been merged in the master branch:
commit ce800895fb3da208229f877b5e8025fd72d80ae2
Author: Shaun Jackman sjack...@debian.org
Date: Wed Sep 14 17:44:09 2011 -0700
New upstream release.
diff --git a/debian/changelog b/debian/changelog
index c3c12ac..e8cfaf8 100644
The following commit has been merged in the pristine-tar branch:
commit 494d0320cfdb45911699db2569175950eb7323d5
Author: Shaun Jackman sjack...@debian.org
Date: Wed Sep 14 17:08:07 2011 -0700
pristine-tar data for gmap_2011-09-09.orig.tar.gz
diff --git a/gmap_2011-09-09.orig.tar.gz.delta
The annotated tag, upstream/2011-09-09 has been created
at f15661026d0ca5f7e875bc0196921a3863fc28a1 (tag)
tagging a50c159e265f15a53ab51ddc19ee77962be73a4f (commit)
replaces upstream/2011-08-15
tagged by Shaun Jackman
on Wed Sep 14 17:08:07 2011 -0700
- Shortlog
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Format: 1.8
Date: Sun, 11 Sep 2011 10:00:13 -0700
Source: abyss
Binary: abyss
Architecture: source amd64
Version: 1.3.0-1
Distribution: unstable
Urgency: low
Maintainer: Shaun Jackman sjack...@debian.org
Changed-By: Shaun Jackman sjack...@debian.org
-By: Shaun Jackman sjack...@debian.org
Description:
gmap - spliced and SNP-tolerant alignment for mRNA and short reads
Changes:
gmap (2011-08-15-1) unstable; urgency=low
.
* New upstream release.
* Bump Standards-Version to 3.9.2.
Checksums-Sha1
The following commit has been merged in the master branch:
commit 3094fe8acfc2dc083edd82725214c7e97cdc7eb6
Merge: 95ea5b7cc34322fd2106a539c605d63304554905
76e4b00922a1232a84bdf9e60525fc4c084d7eff
Author: Shaun Jackman sjack...@debian.org
Date: Tue Aug 23 14:34:57 2011 -0700
Merge commit
The following commit has been merged in the master branch:
commit e21796d88ba8cf78ddbb3c851e412329ee96b25b
Author: Shaun Jackman sjack...@debian.org
Date: Tue Aug 23 14:54:38 2011 -0700
New upstream release.
diff --git a/debian/changelog b/debian/changelog
index 9cb0e8c..c3c12ac 100644
The annotated tag, upstream/2011-08-15 has been created
at 1451005dcd7a0238f7d87c915f3e16b588b63840 (tag)
tagging 76e4b00922a1232a84bdf9e60525fc4c084d7eff (commit)
replaces upstream/2011-03-11
tagged by Shaun Jackman
on Tue Aug 23 14:34:56 2011 -0700
- Shortlog
The branch, pristine-tar has been created
at 126fe8513e7f2cf69b4b90e980a4425a364f94c1 (commit)
- Shortlog
commit 126fe8513e7f2cf69b4b90e980a4425a364f94c1
Author: Shaun Jackman sjack...@debian.org
Date: Tue Aug 23 14:34:56
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Format: 1.8
Date: Mon, 15 Aug 2011 11:07:19 -0700
Source: abyss
Binary: abyss
Architecture: source amd64
Version: 1.2.7-3
Distribution: unstable
Urgency: low
Maintainer: Shaun Jackman sjack...@debian.org
Changed-By: Shaun Jackman sjack...@debian.org
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi,
I'm the upstream and Debian maintainer of abyss, which
is a bioinformatics software package. Its license is free for academic
use and licensed to commercial users. The license currently reads
Debian may redistribute this software package.
Is
On 25 July 2011 17:13, Charles Plessy ple...@debian.org wrote:
Le Mon, Jul 25, 2011 at 05:03:55PM -0700, Shaun Jackman a écrit :
I used git-import-orig from git-buildpackage 0.5.26, but it didn't
update the pristine-tar branch by default. I'll read the man page
tomorrow and see if I can get
On 26 July 2011 10:02, Shaun Jackman sjack...@gmail.com wrote:
On 25 July 2011 17:13, Charles Plessy ple...@debian.org wrote:
Le Mon, Jul 25, 2011 at 05:03:55PM -0700, Shaun Jackman a écrit :
I used git-import-orig from git-buildpackage 0.5.26, but it didn't
update the pristine-tar branch
-By: Shaun Jackman sjack...@debian.org
Description:
igv- Integrative Genomics Viewer
Changes:
igv (2.0.6-1) unstable; urgency=low
.
* New upstream release.
* debian/control: Depend and Build-Depend on libcommons-logging-java,
libhttpclient-java, libhttpcore-java, libjcommon-java
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Format: 1.8
Date: Thu, 21 Jul 2011 09:55:52 -0700
Source: abyss
Binary: abyss
Architecture: source i386
Version: 1.2.7-2
Distribution: unstable
Urgency: low
Maintainer: Shaun Jackman sjack...@debian.org
Changed-By: Shaun Jackman sjack...@debian.org
Hi all,
I work with the author of Circos and am a Debian developer. I'm happy
to help if you need a contact inside.
Cheers,
Shaun
On 21 July 2011 22:33, Olivier Sallou olivier.sal...@irisa.fr wrote:
Hi,
I have contacted upstream author, and he will remove copyright issues on
fonts in next
Hi Charles,
I've just uploaded IGV 2.0.6-1.
What do I do with the pristine-tar and meta branches? These branches
are new to me.
Cheers,
Shaun
On 28 June 2011 10:38, Shaun Jackman sjack...@gmail.com wrote:
Hi Charles,
I'm going to be pretty busy for about two weeks. I probably won't have
On 25 July 2011 16:12, Charles Plessy ple...@debian.org wrote:
Le Mon, Jul 25, 2011 at 12:56:01PM -0700, Shaun Jackman a écrit :
Hi Charles,
I've just uploaded IGV 2.0.6-1.
What do I do with the pristine-tar and meta branches? These branches
are new to me.
Hi Shaun,
thanks a lot
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Format: 1.8
Date: Fri, 24 Jun 2011 12:16:36 -0700
Source: abyss
Binary: abyss
Architecture: source i386
Version: 1.2.7-1
Distribution: unstable
Urgency: low
Maintainer: Shaun Jackman sjack...@debian.org
Changed-By: Shaun Jackman sjack...@debian.org
Hi Charles,
I'm going to be pretty busy for about two weeks. I probably won't have
time to look into this until then. If 1.5.65 compiles cleanly and
works, there's no harm in uploading that in the mean time. I can take
a look into the 2.0 log4j issue two weeks from now. The
RollingFileAppender
Package: wnpp
Severity: wishlist
Package name: abyss
Version: 1.2.7
Upstream Author: sjack...@bcgsc.ca
URL: http://www.bcgsc.ca/platform/bioinfo/software/abyss
License: free for academic use
Description: a de novo, parallel, paired-end sequence assembler
ABySS is a de novo, parallel, paired-end
Package: wnpp
Severity: wishlist
Package name: abyss
Version: 1.2.7
Upstream Author: sjack...@bcgsc.ca
URL: http://www.bcgsc.ca/platform/bioinfo/software/abyss
License: free for academic use
Description: a de novo, parallel, paired-end sequence assembler
ABySS is a de novo, parallel, paired-end
, Shaun Jackman wrote:
When using mkdir
-pm, the specified mode is applied only to the final directory and not
the parent directories
That behavior is required by POSIX; see
http://pubs.opengroup.org/onlinepubs/9699919799/utilities/mkdir.html.
Perhaps an argument could be made for a new
On Tue, 2011-05-31 at 13:06 -0700, Paul Eggert wrote:
On 05/31/11 11:12, Shaun Jackman wrote:
My use case is working in a directory shared amongst a group of users.
My umask is 022. I run
mkdir -pm775 project/subproject
You're typing stuff like that by hand? I'd expect that sort
On Tue, 2011-05-31 at 15:49 -0700, Bob Proulx wrote:
Shaun Jackman wrote:
My use case is working in a directory shared amongst a group of users.
My umask is 022. I run
If you are working among a group of users then you should set your
umask to be 02 instead of 022. That is probably
On Tue, 2011-05-31 at 15:49 -0700, Bob Proulx wrote:
Shaun Jackman wrote:
My use case is working in a directory shared amongst a group of users.
My umask is 022. I run
If you are working among a group of users then you should set your
umask to be 02 instead of 022. That is probably
:46 -0700, Bob Proulx wrote:
Shaun Jackman wrote:
My primary use case for this feature is to create a shell alias:
alias mkdir='mkdir --reference=.'
so that in interactive shells, new directories are created with the same
permissions as their parent directory.
If your primary purpose
Hi,
mkdir has an option -m to set the permission mode of the directory. I
would find it useful for mkdir to have a --reference=FILE option that
works identically to chmod.
My primary use case for this feature is to create a shell alias:
alias mkdir='mkdir --reference=.'
so that in
...@lists.alioth.debian.org
Changed-By: Shaun Jackman sjack...@debian.org
Description:
libsam-java - Java library to manipulate SAM and BAM files
picard-tools - Command line tools to manipulate SAM and BAM files
Closes: 619201
Changes:
picard-tools (1.41-1) unstable; urgency=low
.
* New upstream release
-By: Shaun Jackman sjack...@debian.org
Description:
gmap - spliced and SNP-tolerant alignment for mRNA and short reads
Changes:
gmap (2011-03-11-1) unstable; urgency=low
.
* New upstream release.
Checksums-Sha1:
1e2c4fec8dc3bd980e5b25c79edd571ca65b69c0 1269 gmap_2011-03-11-1.dsc
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