Re: Altitude value of the point in context menu

2018-12-06 Thread Florent Angly
But barometric altitude is not something OsmAnd does. It would be cool if it did... -- You received this message because you are subscribed to the Google Groups "Osmand" group. To unsubscribe from this group and stop receiving emails from it, send an email to

Re: [Rd] Undefined behavior of head() and tail() with n = 0

2017-01-27 Thread Florent Angly
Dunlap > TIBCO Software > wdunlap tibco.com > > > On Thu, Jan 26, 2017 at 1:53 AM, Martin Maechler > <maech...@stat.math.ethz.ch> wrote: >>>>>>> Florent Angly <florent.an...@gmail.com> >>>>>>> on Wed, 25 Jan 2017 16:31:45 +010

[Rd] Undefined behavior of head() and tail() with n = 0

2017-01-25 Thread Florent Angly
Hi all, The documentation for head() and tail() describes the behavior of these generic functions when n is strictly positive (n > 0) and strictly negative (n < 0). How these functions work when given a zero value is not defined. Both GNU command-line utilities head and tail behave differently

Re: [Rd] Very small numbers in hexadecimal notation parsed as zero

2016-12-24 Thread Florent Angly
Hi Martin, Thanks for the Bugzilla account. I have filed this bug under number 17199. Cheers, Florent On 21 December 2016 at 12:28, Martin Maechler <maech...@stat.math.ethz.ch> wrote: >>>>>> Florent Angly <florent.an...@gmail.com> >>>>>> on Tue,

Re: [Rd] Unexpected I(NULL) output

2016-12-24 Thread Florent Angly
Thank you for the feedback, Martin. Of course, deprecating would be a sensible way to go. I filed this issue on BugZilla under # 17198. Florent On 22 December 2016 at 10:24, Martin Maechler <maech...@stat.math.ethz.ch> wrote: >>>>>> Florent Angly <florent.an...@gmail

[Rd] Unexpected I(NULL) output

2016-12-20 Thread Florent Angly
Hi all, I believe there is an issue with passing NULL to the function I(). class(NULL) # "NULL" (as expected) print(NULL) # NULL (as expected) is.null(NULL) # TRUE (as expected) According to the documentation I() should return a copy of its input with class "AsIs" preprended:

[Rd] Very small numbers in hexadecimal notation parsed as zero

2016-12-20 Thread Florent Angly
Hi all, I have noticed incorrect parsing of very small hexadecimal numbers like "0x1.dp-987". Such a hexadecimal representation can can be produced by sprintf() using the %a flag. The return value is incorrectly reported as 0 when coercing these numbers to double using

Re: [R] Bugzilla account request

2016-12-20 Thread Florent Angly
at 17:41, David Winsemius <dwinsem...@comcast.net> wrote: > >> On Dec 19, 2016, at 12:25 AM, Florent Angly <florent.an...@gmail.com> wrote: >> >> Hi, >> >> I have identified a couple of bugs that I would like to file on >> https://bugs.r

[R] Bugzilla account request

2016-12-19 Thread Florent Angly
Hi, I have identified a couple of bugs that I would like to file on https://bugs.r-project.org/ . Reading the archives, I found that the bugzilla account creation is not automated anymore and must be mannually requested on this mailing list. Can an administrator please create an account for me?

Bug#730672: gnote: Gnote startup causes GNOME crash

2013-11-28 Thread Florent Angly
On Thu, Nov 28, 2013 at 8:22 PM, Emilio Pozuelo Monfort po...@debian.org wrote: Please attach ~/.cache/gdm/session.log and ~/.cache/gdm/session.log.old after a GNOME crash. /etc/gdm3/Xsession: Beginning session setup... localuser:floflooo being added to access control list gnome-session[4831]:

Bug#730672: gnote: Gnote startup causes GNOME crash

2013-11-27 Thread Florent Angly
Package: gnote Version: 3.10.1-1 Severity: normal Dear Maintainer, I updated my software packages with apt-get upgrade and apt-get dist-upgrade about a week ago. Since then, when I log in GNOME (3.8.4), GNOME crashes with the message Oh no, something went wrong and I have no other choice than

Bug#730672:

2013-11-27 Thread Florent Angly
Now that Gnote is uninstalled, I got the same problem trying to print something from Firefox. Thus it seems that the problem is upstream from Gnote and Firefox. Still not sure what log file is relevant. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of

Re: [galaxy-dev] Best practices for a local install of Galaxy for only 1 user on a Mac

2013-06-18 Thread Florent Angly
Hi Paul, I have Galaxy running on a small Mac workstation. I have made a specific user, 'galaxy', for it. It is cleaner, but probably overkill for 1 person. Note also that you can install a daemon to start Galaxy automatically when your computer starts:

Re: [Rd] [R] gettext weirdness

2013-02-04 Thread Florent Angly
for translation depends on the language, including how trailing spaces are handled. There is no reason to expect domains intended for C code to work in R-level gettext(), nor in stop() etc. This was really an R-devel question: see the posting guide. On Mon, 4 Feb 2013, Florent Angly wrote

Re: [Rd] [R] gettext weirdness

2013-02-04 Thread Florent Angly
On 05/02/13 00:02, Prof Brian Ripley wrote: On 04/02/2013 11:14, Florent Angly wrote: Hi Brian, I appreciate your clarifications. I am sending this reply to the R-devel, as per you suggestion. As mentioned in my post, I have no prior experience with this R function and logically, I looked

[R] gettext weirdness

2013-02-03 Thread Florent Angly
Hi, I am trying to use the gettext() function to translate some text. I have never used this function before, so, it's entirely possible that I am doing something wrong. The issue that I am encountering is that gettext() properly translates some text, but not some other. Natural language

Bug#587733: (no subject)

2013-02-03 Thread Florent Angly
The issue was resolved upstream in the Pod-Parser distribution, version 1.60 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Bug#587733: (no subject)

2013-01-13 Thread Florent Angly
I am affected by this issue as well. I reported the bug upstream: https://rt.cpan.org/Ticket/Display.html?id=82682 Cheers, Florent -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

[med-svn] [SCM] grinder annotated tag, upstream/0.4.4, created. upstream/0.4.4

2012-05-03 Thread Florent Angly
+1h9w4L1TvRYgZDaB9Mpyban+5NZOPg9FQelBpT 3hmCqgwlNj5OCKaWZeBDo6ftEOQDDxTCTYfWFdeeHJ+3mZsv0BsYtZAB9dRNUSqQ OzXY7g9yGXBcNZzg4sVxx3iH6qbG6fYbDD+NSgkbfxiFthClLyaoh3a3CObtkBbt hiQsUg4EJV/kNCiWYHWq2pRi43FEmmRkhE25psxxWxEK3UfRgLpd4LIIzfxO6aQW ZMZ2jJtBa00lOPUdSfbn =F1ZO -END PGP SIGNATURE- Florent Angly (1

Re: Scrunched up string literals in Pod::Simple tests

2012-02-21 Thread Florent Angly
Hi Sean, You are right that Pod::Simple has problems with multiline POD strings contained into a variable or heredoc section: https://rt.cpan.org/Ticket/Display.html?id=36404 https://rt.cpan.org/Ticket/Display.html?id=69390 In that second link, David Wheeler wrote that the

Re: .pod files

2012-02-10 Thread Florent Angly
I doubt you'll ever see a distribution which has POD in both Foo/Bar.pm and Foo/Bar.pod, because the perldoc tool will only see one or the other when a user types 'perldoc Foo::Bar'. Thank you David, this is very useful. My conclusion is that it is not explicitly forbidden, but it is not

.pod files

2012-02-09 Thread Florent Angly
Dear all, I had a look at the perlsyn, perldoc and perldocspec documents but cannot seem to find the answer to the following questions. The POD content of a module can be written into its Perl file or into a separate .pod file. There are quite a few examples of modules around that use one

Re: [galaxy-dev] Existing efforts to convert the QIIME pipeline to Galaxy?

2012-02-07 Thread Florent Angly
Hi Amanda, I would certainly be interested in using your helpful QIIME wrappers if you put them on the Toolshed. Best, Florent On 06/02/12 06:22, Amanda Zuzolo wrote: Hello, all. I have been working on getting the Qiime scripts into Galaxy as mentioned before, and they are working with Qiime

Re: Initial Grinder package

2012-01-30 Thread Florent Angly
Charles Plessy-12 wrote: Florent, since the files in /inc are also distributed as Debian packages: are they strictly neeeded, or could they be omitted? That would reduce the code duplication in our archive. Thanks for the help with the package upload, Charles. What you ask is a good

[med-svn] [SCM] grinder branch, master, updated. debian/0.4.4-1-2-g7af62fd

2012-01-28 Thread Florent Angly
The following commit has been merged in the master branch: commit 7af62fd1a0cb2c35507ec59684610a92554099ae Author: Florent Angly florent.an...@gmail.com Date: Sun Jan 29 12:37:21 2012 +1000 Added copyright information for files in inc/*, part of the modules: Module::Install, Module

Re: Initial Grinder package

2012-01-26 Thread Florent Angly
Hi Andreas, Thank you for your advices. The only thing I would like you to change is the authorship of the manpages. While it is correct that you can claim yourself as the author of the manpage it would be more precise to inform that you did this by the help of help2man for the Debian

[med-svn] [SCM] grinder branch, master, updated. 66d39bf5a8cb2d98f859e65ee0f25c931cec5e61

2012-01-26 Thread Florent Angly
The following commit has been merged in the master branch: commit 66d39bf5a8cb2d98f859e65ee0f25c931cec5e61 Author: Florent Angly florent.an...@gmail.com Date: Fri Jan 27 13:57:27 2012 +1000 Removed manpage authorship because the manpages are automatically generated by help2man diff --git

[med-svn] [SCM] grinder branch, master, updated. 5ac272e9a4b93ae4534ed158e80368ccd9041f27

2012-01-26 Thread Florent Angly
The following commit has been merged in the master branch: commit 5ac272e9a4b93ae4534ed158e80368ccd9041f27 Author: Florent Angly florent.an...@gmail.com Date: Fri Jan 27 14:39:40 2012 +1000 Added a basic load test diff --git a/debian/rules b/debian/rules index 30a7b58..1c06364 100755

Re: [galaxy-user] Recent problematic change in the Galaxy Toolshed

2012-01-19 Thread Florent Angly
instance with no problems, so I believe your grinder repository is now in a good state. Thanks very much for reporting this issue. Greg Von Kuster On Jan 17, 2012, at 8:43 PM, Florent Angly wrote: Hi, I just tried to upload a new version of the Grinder Galaxy wrapper to the Galaxy ToolShed

[med-svn] [SCM] grinder branch, master, created. 1405e42527d1a9780f6073900e0cd29038355adb

2012-01-19 Thread Florent Angly
The branch, master has been created at 1405e42527d1a9780f6073900e0cd29038355adb (commit) - Shortlog commit 1405e42527d1a9780f6073900e0cd29038355adb Author: Florent Angly florent.an...@gmail.com Date: Fri Jan 20 10:48:41 2012

[med-svn] [SCM] grinder branch, upstream, created. 1405e42527d1a9780f6073900e0cd29038355adb

2012-01-19 Thread Florent Angly
The branch, upstream has been created at 1405e42527d1a9780f6073900e0cd29038355adb (commit) - Shortlog commit 1405e42527d1a9780f6073900e0cd29038355adb Author: Florent Angly florent.an...@gmail.com Date: Fri Jan 20 10:48:41

[med-svn] [SCM] grinder branch, master, updated. 9de4e2efcea986af73e865b962db06c33a7f68d2

2012-01-19 Thread Florent Angly
The following commit has been merged in the master branch: commit 9de4e2efcea986af73e865b962db06c33a7f68d2 Author: Florent Angly florent.an...@gmail.com Date: Fri Jan 20 11:42:07 2012 +1000 grinder-0.4.4 ready for unstable diff --git a/debian/changelog b/debian/changelog index ba96811

[med-svn] [SCM] grinder branch, master, updated. 9de4e2efcea986af73e865b962db06c33a7f68d2

2012-01-19 Thread Florent Angly
The following commit has been merged in the master branch: commit 25e50a71264cc6857ecd5cd3e43ed7451d777527 Author: Florent Angly florent.an...@gmail.com Date: Fri Jan 20 11:33:01 2012 +1000 Using gbp.conf file diff --git a/debian/gbp.conf b/debian/gbp.conf new file mode 100644 index

[galaxy-user] Recent problematic change in the Galaxy Toolshed

2012-01-17 Thread Florent Angly
Hi, I just tried to upload a new version of the Grinder Galaxy wrapper to the Galaxy ToolShed and am encountering difficulties that I did have in previous versions. When I upload my .tar.gz file, the upload is aborted and I get the error: 'GalaxyWebUITransaction' object has no attribute

[rt.cpan.org #73785] scandeps -c fails on modules that depend on Getopt::Euclid

2012-01-06 Thread Florent Angly via RT
Fri Jan 06 03:02:15 2012: Request 73785 was acted upon. Transaction: Ticket created by FANGLY Queue: Module-ScanDeps Subject: scandeps -c fails on modules that depend on Getopt::Euclid Broken in: 1.07 Severity: (no value) Owner: Nobody Requestors:

Bug#653133: ITP: libmath-random-mt-perl-perl -- Pure-Perl Mersenne-Twister module to generate random numbers

2012-01-05 Thread Florent Angly
On 04/01/12 01:34, Ansgar Burchardt wrote: On 01/03/2012 03:43 PM, Florent Angly wrote: Good question! I see three advantages of the Pure-perl approach: 1/ It should work on all platforms, including the hurd-i386, where the C/XS approach does not work The failure on hurd-i386 is trivial

Bug#653133: ITP: libmath-random-mt-perl-perl -- Pure-Perl Mersenne-Twister module to generate random numbers

2012-01-05 Thread Florent Angly
On 04/01/12 01:34, Ansgar Burchardt wrote: On 01/03/2012 03:43 PM, Florent Angly wrote: Good question! I see three advantages of the Pure-perl approach: 1/ It should work on all platforms, including the hurd-i386, where the C/XS approach does not work The failure on hurd-i386 is trivial

Bug#654394: ITP: grinder -- Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms

2012-01-03 Thread Florent Angly
Package: wnpp Severity: wishlist Owner: Florent Angly florent.an...@gmail.com * Package name: grinder Version : 0.4.2 Upstream Author : Florent Angly florent.an...@gmail.com * URL : http://sourceforge.net/projects/biogrinder/ * License : GPL Programming Lang

Bug#654394: ITP: grinder -- Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms

2012-01-03 Thread Florent Angly
Package: wnpp Severity: wishlist Owner: Florent Angly florent.an...@gmail.com * Package name: grinder Version : 0.4.2 Upstream Author : Florent Angly florent.an...@gmail.com * URL : http://sourceforge.net/projects/biogrinder/ * License : GPL Programming Lang

Bug#653133: ITP: libmath-random-mt-perl-perl -- Pure-Perl Mersenne-Twister module to generate random numbers

2012-01-03 Thread Florent Angly
On 03/01/12 21:58, Ansgar Burchardt wrote: Hi, On 12/24/2011 12:32 PM, Florent Angly wrote: * Package name: libmath-random-mt-perl-perl This module implements the same pseudorandom number generator found in Math::Random::MT (libmath-random-mt-perl Debian package), which is implemented

Unidentified subject!

2012-01-03 Thread Florent Angly
-- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4f02e850.8010...@gmail.com

Bug#654394: ITP: grinder -- Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms

2012-01-03 Thread Florent Angly
Package: wnpp Severity: wishlist Owner: Florent Angly florent.an...@gmail.com * Package name: grinder Version : 0.4.2 Upstream Author : Florent Angly florent.an...@gmail.com * URL : http://sourceforge.net/projects/biogrinder/ * License : GPL Programming Lang

Bug#653133: ITP: libmath-random-mt-perl-perl -- Pure-Perl Mersenne-Twister module to generate random numbers

2012-01-03 Thread Florent Angly
On 03/01/12 21:58, Ansgar Burchardt wrote: Hi, On 12/24/2011 12:32 PM, Florent Angly wrote: * Package name: libmath-random-mt-perl-perl This module implements the same pseudorandom number generator found in Math::Random::MT (libmath-random-mt-perl Debian package), which is implemented

Introduction

2011-12-30 Thread Florent Angly
Dear DebianMed list, I just joined the group. I am a computational biologist, a microbial ecologist specifically, who uses mostly Perl when coding. I have been using Debian-based Linux distros for quite some time (Linux Mint Debian Edition at the moment) and became interested in packaging

Re: [galaxy-dev] amplicon reads(with errors)

2011-12-30 Thread Florent Angly
Hi Bassam, Try Grinder, which is available from the Galaxy Toolshed at http://toolshed.g2.bx.psu.edu/. Regards, Florent On 30/12/11 04:23, Bassam Tork wrote: Dear All, Is there a way to generate 454 simulated amplicon reads with errors using galaxy. Happy New Year, Bassam Tork.

Bug#653133: ITP: libmath-random-mt-perl-perl -- Pure-Perl Mersenne-Twister module to generate random numbers

2011-12-24 Thread Florent Angly
Package: wnpp Severity: wishlist Owner: Florent Angly florent.an...@gmail.com * Package name: libmath-random-mt-perl-perl Version : 1.06 Upstream Author : Dr James Freeman airmedi...@gmail.com * URL : hhttp://search.cpan.org/dist/Math-Random-MT-Perl/ * License

Bug#653133: ITP: libmath-random-mt-perl-perl -- Pure-Perl Mersenne-Twister module to generate random numbers

2011-12-24 Thread Florent Angly
Package: wnpp Severity: wishlist Owner: Florent Angly florent.an...@gmail.com * Package name: libmath-random-mt-perl-perl Version : 1.06 Upstream Author : Dr James Freeman airmedi...@gmail.com * URL : hhttp://search.cpan.org/dist/Math-Random-MT-Perl/ * License

Bug#653133: ITP: libmath-random-mt-perl-perl -- Pure-Perl Mersenne-Twister module to generate random numbers

2011-12-24 Thread Florent Angly
Package: wnpp Severity: wishlist Owner: Florent Angly florent.an...@gmail.com * Package name: libmath-random-mt-perl-perl Version : 1.06 Upstream Author : Dr James Freeman airmedi...@gmail.com * URL : hhttp://search.cpan.org/dist/Math-Random-MT-Perl/ * License

Re: [galaxy-user] Patch for better FASTQ description handling

2011-11-29 Thread Florent Angly
On 19/10/11 23:31, Daniel Blankenberg wrote: Sorry for the delay. I did try the patch out shortly after you contributed it, but it caused the functional to fail. I was able to fix the issue and allow the existing tests to start passing, but I've been bogged down lately and haven't been

Re: [galaxy-user] FASTQ Quality Trimmer for PE Illumina?

2011-10-25 Thread Florent Angly
Hi Joanna, During trimming, some of the reads may be removed from your dataset. Depending on what you need to do, you may or may not want to discard reads that don't have a mate mate anymore. If so, you might consider using the FASTQ de-interlacer and interlacer tools. Florent On 26/10/11

Re: [galaxy-user] Patch for better FASTQ description handling

2011-10-19 Thread Florent Angly
Peter and Daniel, thanks for the comments. On 19/10/11 23:49, Peter Cock wrote: On Wed, Oct 19, 2011 at 2:31 PM, Daniel Blankenbergd...@bx.psu.edu wrote: Hi Florent, Sorry for the delay. I did try the patch out shortly after you contributed it, but it caused the functional to fail. I was

Re: [galaxy-user] Patch for better FASTQ description handling

2011-10-18 Thread Florent Angly
I have had the chance to try the patch on several datasets and it looks good :) I reiterate my suggestion to pull the patch in galaxy-central. Best, Florent On 05/10/11 18:28, Florent Angly wrote: Hi, I have found some issue with the way FASTQ read description is handled by Galaxy

Re: [galaxy-dev] [galaxy-user] Problem with new tool shed

2011-10-13 Thread Florent Angly
On 14/10/11 06:45, Greg Von Kuster wrote: Hello Forent, On Oct 13, 2011, at 2:48 AM, Florent Angly wrote: But maybe I need a little bit of guidance with this because the example shown, the user is given a _limited_ number of output datasets to choose from. The Grinder case seems simple: give

Re: [galaxy-user] Problem with new tool shed

2011-10-04 Thread Florent Angly
additional problems. Thanks for finding this! Greg Von Kuster On Oct 4, 2011, at 2:53 AM, Florent Angly wrote: Hi all, I tried the latest stable version of Galaxy: http://wiki.g2.bx.psu.edu/News%20Briefs/2011_08_30. This page has links to how to use the new tool shed including how

Re: [galaxy-dev] [galaxy-user] Problem with new tool shed

2011-10-04 Thread Florent Angly
additional problems. Thanks for finding this! Greg Von Kuster On Oct 4, 2011, at 2:53 AM, Florent Angly wrote: Hi all, I tried the latest stable version of Galaxy: http://wiki.g2.bx.psu.edu/News%20Briefs/2011_08_30. This page has links to how to use the new tool shed including how

Re: [galaxy-user] Simulating sequencing and removing redundant sequences

2011-09-20 Thread Florent Angly
For read simulation, you may also want to give Grinder a try. I made a Galaxy wrapper for it (see in the toolshed: http://toolshed.g2.bx.psu.edu/) Florent On 20/09/11 18:46, Kevin Lam wrote: Hi Daniel, You would have multiple names for each sequence and that would be quite hard to display. I

Re: [galaxy-dev] outputting different numbers of files based on variables?

2011-09-16 Thread Florent Angly
Thanks for the pointer Ross. It was really useful. I also found more information about multiple output datasets on the wiki: http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files?highlight=%28dataset%29 I plan on writing a script that renames the output of the Grinder tool I am

Re: [galaxy-dev] outputting different numbers of files based on variables?

2011-09-15 Thread Florent Angly
Hi, I too would be interested in knowing how to handle tools that might generate multiple output files for the Grinder wrapper I am developing. Any news on this? Has a ticket been recorded? How about when the tool generate an number of files that cannot be determined from the values the

[Artemis-users] Bitten by multiFASTA annotation bug

2011-08-01 Thread Florent Angly
Hi, I was trying Artemis to view some annotations I have in a multiFASTA and GFF3 file. In my use case, it is not common to have this type of data. I noticed a problem though, in that Artemis assigns all the GFF features to the first sequence in the FASTA file (see attached screenshot). After

Re: [Artemis-users] Bitten by multiFASTA annotation bug

2011-08-01 Thread Florent Angly
Hi Tim, Thank you for your feedback. I will definitely try the two workarounds you described for this dataset. However, in the future, it would be great if Artemis were capable of handling all use-cases, including the one where the multiple sequences are loaded before the GFF3 features.

Re: [galaxy-user] filtering fastq file according to qual score

2011-07-31 Thread Florent Angly
for removing bases. After your reply, I got suspicious. Am I trying to do something wrong in theory? Thanks in advance. On Sun, Jul 31, 2011 at 6:07 AM, Florent Angly florent.an...@gmail.com mailto:florent.an...@gmail.com wrote: Hi Haluk, By filtering, you mean removing reads? trimming

Re: [galaxy-user] filtering fastq file according to qual score

2011-07-30 Thread Florent Angly
Hi Haluk, By filtering, you mean removing reads? trimming their ends? or masking some of their bases? There are 3 tools under Generic FASTQ manipulation that may help you: Filter FASTQ reads by quality score and length FASTQ Quality Trimmer by sliding window FASTQ Masker by quality

Re: [galaxy-dev] Fwd: Request for pulling the updated FASTQ (de-)interlacer tool

2011-06-02 Thread Florent Angly
tried this patch? Feedback would be appreciated. Thanks, K On Fri, May 27, 2011 at 1:27 AM, Florent Angly florent.an...@gmail.com mailto:florent.an...@gmail.com wrote: Can anyone comment on my email please? Florent On 22/05/11 14:03, Florent Angly wrote: Let me know if you

Re: [galaxy-dev] stdout and stderr

2011-05-26 Thread Florent Angly
On 27/05/11 00:04, Peter Cock wrote: I regard fixing issue 325 as one of the top priorities in Galaxy Can't agree more with you Peter! This bug and other tool wrapper related bugs make it harder and more tedious to contribute tool wrappers. It's a big turn off for me. Florent

Re: [galaxy-dev] Fwd: Request for pulling the updated FASTQ (de-)interlacer tool

2011-05-26 Thread Florent Angly
Can anyone comment on my email please? Florent On 22/05/11 14:03, Florent Angly wrote: Let me know if you have any questions about this. Thanks, Florent Original Message Subject:Request for pulling the updated FASTQ (de-)interlacer tool Date: Tue, 17 May 2011 17:47

[galaxy-user] Fwd: Workflows with conditional statements

2011-05-21 Thread Florent Angly
Date: Wed, 18 May 2011 10:31:21 +1000 From: Florent Angly florent.an...@gmail.com To: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu Hi all, I was wondering if there is a way to put conditional statements in a Galaxy workflow. This would be useful, for example, in the case

[galaxy-dev] Fwd: Request for pulling the updated FASTQ (de-)interlacer tool

2011-05-21 Thread Florent Angly
Let me know if you have any questions about this. Thanks, Florent Original Message Subject:Request for pulling the updated FASTQ (de-)interlacer tool Date: Tue, 17 May 2011 17:47:13 +1000 From: Florent Angly florent.an...@gmail.com To: galaxy-dev

Re: [galaxy-dev] Wrapper generator.

2011-05-15 Thread Florent Angly
Hi Jeroen, The idea of having a tool to automatically generate Galaxy wrappers is attractive, and in some cases, possible. For example, I know that the tools in QIIME (http://qiime.sourceforge.net/) use some sort of argument declaration and a Python module to read it and deal with the

Re: [galaxy-dev] Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?

2011-04-23 Thread Florent Angly
Hi Jeff Some of these tools can be installed easily on Mac OS using MacPorts port search gnuplot Of course, you have to install MacPorts first. Florent On 23/04/11 01:25, Whyte, Jeffrey wrote: Hi Everyone, I'm having trouble getting some of the tools to work on my local installation of

Re: [galaxy-dev] Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?

2011-04-23 Thread Florent Angly
:03 PM, Florent Angly wrote: Hi Jeff Some of these tools can be installed easily on Mac OS using MacPorts port search gnuplot Of course, you have to install MacPorts first. Florent On 23/04/11 01:25, Whyte, Jeffrey wrote: Hi Everyone, I'm having trouble getting some of the tools to work

Re: [galaxy-dev] Ratings on Tool Shed broken?

2011-04-05 Thread Florent Angly
Hi Peter, I get the same error here. Florent On 06/04/11 01:50, Peter Cock wrote: Hi all, I had wondered why none of the tools on the Galaxy Tool Shed had a rating, and had assumed it was just that so far no-one had bothered. I have a new theory, it doesn't work? I just viewed Brad's BAM to

Re: [galaxy-user] GTF-to-GFF3

2011-03-22 Thread Florent Angly
Speaking of which, could a Galaxy developer look at adding these changes, please? https://bitbucket.org/galaxy/galaxy-central/issue/447/new-tools-to-de-interlace-fastq-mate-pair Thanks, Florent On 23/03/11 12:02, Jeremy Goecks wrote: Alternatively, we welcome community contributions to the

Re: [galaxy-dev] [galaxy-user] Galaxy does not find my executables

2011-02-15 Thread Florent Angly
. Florent Angly wrote: Indeed, this workaround works! Thank you. I added these lines to the beginning of my run.sh: PATH=/opt/local/bin:/opt/local/sbin:$PATH export $PATH Now, Galaxy can find Grinder, Velvet, etc Could Galaxy detect and use ~/.profile automatically if it exists

Re: [OctDev] Bug : sym or Pi in GNUoctave

2010-10-06 Thread Florent Angly
Digvijay, Did you report this bug to Fedora? If so, can you provide a link to it the bug report please? Florent On 14/09/10 05:33, Tatsuro MATSUOKA wrote: Hello The issue what you met is specific to the Fedora distributions. The octave-dev ML list is a place to discuss about the

Re: [OctDev] Bug : sym or Pi in GNUoctave

2010-09-12 Thread Florent Angly
Hi, The Fedora bug report page is here: https://bugzilla.redhat.com/buglist.cgi?quicksearch=octave I have Fedora 13 as well and was able to reproduce the crash: Linux bombadil 2.6.34.6-54.fc13.x86_64 #1 SMP Sun Sep 5 17:16:27 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux Name: octave Arch

Re: [OctDev] lists in 'optim'

2010-03-20 Thread Florent Angly
On 12/03/10 06:51, Søren Hauberg wrote: The main problem seems to be that both Octave and 'optim' comes with an implementation of 'fminbnd'. I don't know which is better, but I don't like the duplication. Ok. I found that the new fminbnd function is part of the development version of

Bug#550163: (no subject)

2009-11-05 Thread Florent Angly
After an upgrade to openoffice.org 1:3.1.1-6, all is well again; the bug is gone. Thank you. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Bug#550163: (no subject)

2009-11-05 Thread Florent Angly
After an upgrade to openoffice.org 1:3.1.1-6, all is well again; the bug is gone. Thank you. -- To UNSUBSCRIBE, email to debian-openoffice-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Bug#550163: (no subject)

2009-10-14 Thread Florent Angly
I upgraded to: Zotero 2.0b7.4 Zotero OpenOffice Integration 3.0a5 The crash still happens. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Bug#550163: (no subject)

2009-10-14 Thread Florent Angly
I upgraded to: Zotero 2.0b7.4 Zotero OpenOffice Integration 3.0a5 The crash still happens. -- To UNSUBSCRIBE, email to debian-openoffice-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Bug#550163: (no subject)

2009-10-12 Thread Florent Angly
My version of python-uno is 1:3.1.1-4 I tested your suggestion and found out that the email-merge function crashes 100% of the time too. In a new text document, I did: Tools Mail merge wizard At step 3 (insert block address), substep 1 (select address list), I clicked on Create, and when

Bug#550163: (no subject)

2009-10-12 Thread Florent Angly
My version of python-uno is 1:3.1.1-4 I tested your suggestion and found out that the email-merge function crashes 100% of the time too. In a new text document, I did: Tools Mail merge wizard At step 3 (insert block address), substep 1 (select address list), I clicked on Create, and when

Bug#550163: Zotero plugin makes OpenOffice.org crash

2009-10-07 Thread Florent Angly
Package: openoffice.org Version: 1:3.1.1-4 Inserting a bibliography with the Zotero plugin in a text document makes OpenOffice.org 3.1.1-4 crash without error message. I needed to have Zotero working, thus I downgraded to OpenOffice.org 3.1.1-2 and everything works again. Sorry I didn't manage

Bug#550163: Zotero plugin makes OpenOffice.org crash

2009-10-07 Thread Florent Angly
Package: openoffice.org Version: 1:3.1.1-4 Inserting a bibliography with the Zotero plugin in a text document makes OpenOffice.org 3.1.1-4 crash without error message. I needed to have Zotero working, thus I downgraded to OpenOffice.org 3.1.1-2 and everything works again. Sorry I didn't manage

Bug#548771: openoffice.org-kde: Checkbox description not showing in the File Save as dialog

2009-09-28 Thread Florent Angly
Package: openoffice.org-kde Version: 1:3.1.1-2 Severity: normal With the openoffice.org-kdei package, when I click on the File Save as, the saving dialog opens but seems to have problems. Under the Name and Filter input text boxes, there are 4 checkboxes. The last one is a checkbox followed

Bug#548771: openoffice.org-kde: Checkbox description not showing in the File Save as dialog

2009-09-28 Thread Florent Angly
And how does this differ from 544691? Correct, it doesn't. (BTW, that bug only seems to happen with the Oxygen theme) And that bug is already forwarded to the upstream developer for the KDE4 stuff. Thanks. Good to know. Plese check whether bugs already were reported, thanks. I must

Bug#548771: openoffice.org-kde: Checkbox description not showing in the File Save as dialog

2009-09-28 Thread Florent Angly
Package: openoffice.org-kde Version: 1:3.1.1-2 Severity: normal With the openoffice.org-kdei package, when I click on the File Save as, the saving dialog opens but seems to have problems. Under the Name and Filter input text boxes, there are 4 checkboxes. The last one is a checkbox followed

Bug#548771: openoffice.org-kde: Checkbox description not showing in the File Save as dialog

2009-09-28 Thread Florent Angly
And how does this differ from 544691? Correct, it doesn't. (BTW, that bug only seems to happen with the Oxygen theme) And that bug is already forwarded to the upstream developer for the KDE4 stuff. Thanks. Good to know. Plese check whether bugs already were reported, thanks. I must

Bug#547954: icedove: Attachement name stripped

2009-09-22 Thread Florent Angly
Package: icedove Version: 2.0.0.22-1 Severity: normal The name of the attachements received in an email on my Gmail account got seriously stripped. Name of multiple attachements received in a email received on Gmail: plos bio review for florent.pdf plos bio review for florentS1 plos bio review

Re: [OctDev] optimization function strategy

2009-07-23 Thread Florent Angly
Hi, Oh, I never realized that fminbnd is a core function of Matlab and not in the core. I guess that's because you don't have to explicitely load toolboxes. Anyways, I know, because I had plans of working on it, that the fminbnd in Octave is much slower than the fminbnd in Matlab, because the

[Catalyst] Example of a simple repeatable field and button

2009-03-10 Thread Florent Angly
Hi list, I have created a small Catalyst webapp that uses a form that is based on a FormFu YML configuration file. I would like to have some repeatable fields, along with a button to click in order generate more of these fields on the fly. I have read the Catalyst tutorial, the FormFu

Re: [Catalyst] Re: System call problem

2008-12-24 Thread Florent Angly
;' Returns: 0 I'm not sure what you mean with using $class-handle_request; in Catalyst/Engine/HTTP.pm. My Catayst app runs using the Catalyst test server at the moment. I haven't deployed it on a standalone webserver yet. Cheers, Florent Tomas Doran wrote: On 19 Dec 2008, at 16:21, Florent Angly

[Catalyst] Re: Upload problem

2008-12-23 Thread Florent Angly
I still haven't made any progress on this issue... Any hint on where to look to debug this problem? Thanks, Florent Florent Angly wrote: Hi all, I am designing my first Catalyst application. I am using a form to upload some documents. Although it works fine for a file of ~60MB, it doesn't

Re: [Catalyst] Re: Upload problem

2008-12-23 Thread Florent Angly
...@digitalcraftsmen.net wrote: On 23/12/08 10:33, Florent Angly wrote: I still haven't made any progress on this issue... Any hint on where to look to debug this problem? Thanks, Florent Hi Florent, I suspect this is not working because the file is too big. Web uploads are really meant

Re: [Catalyst] How to run self-tests from within the application

2008-12-20 Thread Florent Angly
Concerning wrong exit status, I've had this problem but could fix it. See here: http://www.gossamer-threads.com/lists/catalyst/users/21925?page=last Regards, Florent Peter Edwards wrote: 2008/12/20 Ashley a...@sedition.com mailto:a...@sedition.com What am I doing wrong? This code

[Catalyst] Upload problem

2008-12-19 Thread Florent Angly
Hi all, I am designing my first Catalyst application. I am using a form to upload some documents. Although it works fine for a file of ~60MB, it doesn't work at all for another file that is almost 3GB. It seems that the form isn't submitted; there is just some very brief activity in the

[Catalyst] System call problem

2008-12-19 Thread Florent Angly
Hi all, My Catalyst application uses an external Perl module that needs to call an external application using the Perl system() command. This Perl module works fine on its own (no error message when the external app is called). However, whenever used from within my Catalyst application

Re: [html-formfu] Config::General select form field

2008-12-17 Thread Florent Angly
Carl Franks wrote: 2008/12/15 Florent Angly florent.an...@gmail.com: Hi all, I have trouble creating Config::General code for a form select field. For example, how does the following YAML config translate into Config::General? elements: - type: Select name: sex options

[html-formfu] Config::General select form field

2008-12-15 Thread Florent Angly
Hi all, I have trouble creating Config::General code for a form select field. For example, how does the following YAML config translate into Config::General? elements: - type: Select name: sex options: - [ 'm', 'Male' ] - [ 'f', 'Female' ] I've tried many syntaxes

Re: [OctDev] Problem committing in SVN

2008-06-21 Thread Florent Angly
I uploaded my ssh key. Initially it didn't solve my problem. I retried several times today, and now finally it worked and I could commit. Thanks for your assistance David, Florent David Bateman wrote: Florent Angly wrote: Hi, I was given access to the SVN repository yesterday but have

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