'
Subject: Re: [Bioc-devel] Biostrings: substitution matrices disappeared?
Good. I also just pushed 2 additional small tweaks (commits 0e98500 and
84c8ed5) right after you pushed yours. Hopefully I didn't step on your toes.
H.
On 4/25/24 01:04, Ulrich Bodenhofer wrote:
Great, thanks, Hervé! I
?
I'm done. Please resync you GitHub repo.
Best,
H.
On 4/25/24 00:14, Ulrich Bodenhofer wrote:
Great, thanks, Hervé, so I’ll simply wait for the update. If there is anything
I should do, just let me know.
Thanks and best regards,
Ulrich
From: Hervé Pagès <mailto:hpages.on.
: Re: [Bioc-devel] Biostrings: substitution matrices disappeared?
Hi Ulrich,
Yes the substitution matrices are now in pwalign. I'm taking care of msa. Sorry
for that.
Best,
H.
On 4/24/24 23:25, Ulrich Bodenhofer wrote:
Ah, thank you very much, sorry for having overlooked this! Yes
://stat.ethz.ch/pipermail/bioc-devel/2024-April/020395.html
I thought it might be related to your problem.
Regards,
Martin
On Thu, Apr 25, 2024 at 8:23 AM Ulrich Bodenhofer
<mailto:ulrich.bodenho...@gmail.com> wrote:
Dear colleagues, dear BioC core team,
One of my packages in the devel branch, th
Dear colleagues, dear BioC core team,
One of my packages in the devel branch, the msa package seems broken since
yesterday. The vignette does not run anymore (therefore, the package does
not build), and the reason is that the BLOSUM62 substitution matrix cannot
be loaded form the Biostrings
& Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
*From:* Bioc-devel on behalf of
Ulrich Bodenhofer
*Sent:* Monday, February 20, 2023 10:22 AM
*To:* bioc-devel@r-project.org
*Subject:* [Bioc-devel] Can
Hi,
I am the maintainer of the 'msa' package which has been in Bioconductor for
eight years now. The package is hosted on github and synchronized with the BioC
git repo. Today I merged a pull request that had been contributed by a github
user. I further updated the package's DESCRIPTION and
Hi,
I am the maintainer of the 'msa' package which has been in Bioconductor
for eight years now. The package is hosted on github and synchronized
with the BioC git repo. Today I merged a pull request that had been
contributed by a github user. I further updated the package's
DESCRIPTION and
proceed with the deprecation
process.
Martin
On 7/28/20, 6:02 AM, "Bioc-devel on behalf of Ulrich Bodenhofer"
wrote:
Dear Lori, dear Martin, dear Hervé,
[I am mentioning you personally, since you are the Core Team members I
had personal contact with in the past]
Dear Lori, dear Martin, dear Hervé,
[I am mentioning you personally, since you are the Core Team members I
had personal contact with in the past]
dear Bioconductor Core Team,
This is an open letter to you and the Bioconductor community ... my
letter concerns the 'msa' package of which I am
: bioc-devel@r-project.org; Ulrich Bodenhofer ; Kurt
Hornik
Betreff: Re: [Bioc-devel] Biostrings: unicode character ("compact ellipsis") in
print()/show() output (2nd attempt, rephrased)
you are not wrong ... thanks for pointing this out
https://github.com/Bioconductor/Biostrin
Dear colleagues,
As noted in my previous message, I have encountered problems with the
new way of displaying sequences/sequence sets that now use a UTF-8
ellipsis character (internally defined as R object 'compact_ellipsis' in
the package) when the output is included in a LaTeX document
Dear colleagues,
Apart from my Bioconductor packages, I am also the maintainer of the
CRAN package 'apcluster'. This package's vignette includes an example in
which biological sequences are clustered. To this end, it uses the
'Biostrings' package. It seems that the latest version of the
Hi Hervé,
Thanks a lot for your very helpful and insightful reply!
[...]
I think this looks indeed like a leftover/stale .o file but I think the
file is in the source tarball produced by the BUILD stage
(msa_1.17.0.tar.gz). If you look at your cleanup.win script, it doesn't
remove the stuff in
Dear colleagues,
I have two issues with the Windows BUILD BIN of our 'msa' package. (to
my horror, I figured out that the first problem has existed for quite a
while; I am deeply sorry for that!)
The main problem can be seen on
ot be pushed to the release
version because of this error?
Thank you,
David
On Apr 14, 2017, at 12:50 PM, Martin Morgan
<martin.mor...@roswellpark.org<mailto:martin.mor...@roswellpark.org>>
wrote:
On 04/07/2017 11:26 AM, Ulrich Bodenhofer wrote:
Hi,
The devel version of our
Hi,
The devel version of our package 'msa' currently does not compile on
veracruz2 (R 3.4.0 alpha under OS X 10.11.6 El Capitan), but it seems to
work on toluca2 (R-devel on OS X 10.9.5 Mavericks). I also checked on my
Mac at home (R 3.3.3 under macOS 10.12.3 Sierra using the very latest
Hi Natalie,
Sorry, there is presently no such function in the 'msa' package and, as
far as I know, there is no such thing in 'Biostrings' either. If you can
specify us an exact formula how to compute the score you are
particularly interested in (or at least point us to a reference), we can
Hi all,
I have a subtle question related to how R CMD SHLIB handles variables in
make child processes. In more detail: I am the maintainer of the 'msa'
package which has been in Bioconductor since April 2015. This package
integrates three open-source libraries for multiple sequence alignment.
-
From: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>
To: "Ulrich Bodenhofer" <bodenho...@bioinf.jku.at>
Cc: "bioc-devel" <bioc-devel@r-project.org>, "msa" <m...@bioinf.jku.at>,
keb...@bioinf.jku.at
Sent: Tuesday, M
).
Best,
Leonardo
On Tue, May 17, 2016 at 4:18 AM, Ulrich Bodenhofer
<bodenho...@bioinf.jku.at> wrote:
Hi all,
I just noticed that the version numbers of many (yet not all) packages have
recently been incremented from x.y.0 to x.y.2 both in the devel and in the
release branch. Ac
list.
Thanks in advance and best regards,
Ulrich
*Dr. Ulrich Bodenhofer*
Associate Professor / Institute of Bioinformatics
*JOHANNES KEPLER
UNIVERSITY LINZ*
Altenberger Str. 69
4040 Linz, Austria
P +43 732 2468 4526
F
Dear BioC Core Team members,
As you know, we have submitted a package 'msa' for Bioconductor 3.1
which has been accepted last week. After having fixed some other
cross-platform problems, we are still having issues on the Mavericks
build server morelia (see
/Rsamtools/inst/doc/Rsamtools-UsingCLibraries.pdf
It was a breaking change in how Rsamtools reverse dependencies are
supposed to find the libraries prompted by the new R CMD check
warnings re: GNU make-specific extensions in non-Windows Makevars.
On 03/19/2015 07:59 AM, Ulrich Bodenhofer wrote
It was a breaking change in how Rsamtools reverse dependencies are
supposed to find the libraries prompted by the new R CMD check warnings
re: GNU make-specific extensions in non-Windows Makevars.
On 03/19/2015 07:59 AM, Ulrich Bodenhofer wrote:
Hi,
I am currently finishing
Hi,
I am currently finishing a package for submission to Bioconductor 3.1
and, therefore, I am trying to make everything work on the latest
R-devel, but I have an issue with linking to Rsamtools. It seems that
Rsamtools installs the libraries libbam, libbcf, and libtabix to the
? At least I could not find anything in the current
development branch.
Thanks and best regards,
Ulrich
*Dr. Ulrich Bodenhofer*
Associate Professor
Institute of Bioinformatics
*Johannes Kepler University*
Altenberger Str. 69
On 03/27/2014 06:31 PM, Hervé Pagès wrote:
On 03/27/2014 02:13 AM, Ulrich Bodenhofer wrote:
[...]
For the time being, it seems I have three options:
1) not supplying the sort() function yet (it is not yet in the release,
but only in my internal devel version)
2) including a dependency
,
Ulrich
--
Dr. Ulrich Bodenhofer
Associate Professor
Institute of Bioinformatics
Johannes Kepler University
Altenberger Str. 69
4040 Linz, Austria
Tel. +43 732 2468 4526
Fax +43 732 2468 4539
bodenho...@bioinf.jku.at
http://www.bioinf.jku.at/
___
Bioc
kind of help!
Best regards,
Ulrich
*Dr. Ulrich Bodenhofer*
Associate Professor
Institute of Bioinformatics
*Johannes Kepler University*
Altenberger Str. 69
4040 Linz, Austria
Tel. +43 732 2468 4526
Fax +43 732 2468 4539
On 03/26/2013 12:18 PM, Laurent Gatto wrote:
On 26 March 2013 09:26, Ulrich Bodenhofer bodenho...@bioinf.jku.at wrote:
Dear colleagues,
One of my students is currently working on a package that we plan to submit
to Bioconductor. I want him to adhere to the Bioconductor coding standards
which I
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