gorov'
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, t
isappeared?
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 <ma
rg
Subject: 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
://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 pa
Great, Martin, thanks!
Best regards, Ulrich
From: Martin Grigorov
Sent: Wednesday, June 7, 2023 12:04 PM
To: bodenho...@bioinf.jku.at
Cc: bioc-devel@r-project.org; Hervé Pagès
Subject: Re: [Bioc-devel] Rhtslib on arm64
Hi Ulrich,
The issue with the LOCK files and folders have been addressed
Dear Hervé, dear Rhtslib developers, dear BioC core team,
I am regularly checking all BioC check results in order to make sure that I
do not miss any issues of the four Bioconductor packages that I am
maintaining. It seems that the podkat package in BioC 3.17 release has not
been built for arm64
& 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 ins
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 i
Hi,
The vignette of my package 'podkat' loads the
'BSgenome.Mmusculus.UCSC.mm10.masked' package. Currently, my package fails
on all three BioC 3.14 servers because of this package. On nebbiolo2 and
riesling1, the package is not available, while the package is available, but
fails to load, on merid
Thanks a lot for your swift and helpful reply, Henrik! Yes, I could reproduce
the error on my local system by adding "_R_CHECK_LENGTH_1_LOGIC2_=verbose" to
my .Renviron file. I will fix the errors and push fixes soon.
Thanks again,
Ulrich
-Original Message-
From: Henrik Bengtsson
Sen
Dear colleagues,
It seems to me that, starting with the latest BioC devel branch (3.14), the
build systems have become more pedantic about logical vectors of length > 1
in conditions. Two of the packages I am maintaining, 'kebabs' and 'procoil'
currently fail to build. Surely I want to fix this. H
hen we can 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
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 the
0 20:50
An: Shepherd, Lori
Cc: 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.c
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 (which
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
'Bios
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 s
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
http://bioconductor.org/checkResults/3.10/bioc-LATEST/msa/to
related to this thread. Will my package not be pushed to the release
version because of this error?
Thank you,
David
On Apr 14, 2017, at 12:50 PM, Martin Morgan
mailto:martin.mor...@roswellpark.org>>
wrote:
On 04/07/2017 11:26 AM, Ulrich Bodenhofer wrote:
Hi,
The devel version of
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
vers
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
tr
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.
riginal Message -
From: "Kasper Daniel Hansen"
To: "Ulrich Bodenhofer"
Cc: "bioc-devel" , "msa" ,
keb...@bioinf.jku.at
Sent: Tuesday, May 17, 2016 7:15:35 AM
Subject: Re: [Bioc-devel] Version numbers incremented?
Ulrich, "svn log" does not h
).
Best,
Leonardo
On Tue, May 17, 2016 at 4:18 AM, Ulrich Bodenhofer
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. Actually, this affected all four packages I
devel 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 4
Thanks for your message! I am out of office until August 10, 2015. Your
message will be answered after I return to office on August 11, 2015. Thank
you in advance for your kind patience!
Best regards,
Ulrich Bodenhofer
___
Bioc-devel@r-project.org
Hi Dan,
Thanks for your reply!
On our Mavericks machine (10.9.5 with XCode 6.1), there was no OpenMP
installed at all. The configure script correctly found that out and
compiled our package without OpenMP support. On morelia, however, the
configure script seems to enforce OpenMP or at least t
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
http://bioconductor.org/checkResults
ent to configure is
adding the intermediate subdirectory. It is my fault the current (Linux)
recommendation does not account for that. I was not aware ${R_ARCH} was
ever non-empty string on Linux. I will update the documentation. Thanks
for pointing it out!
On 03/20/2015 06:39 AM, Ulrich Bode
u seen the updated recommendations for linking to the libraries
> in the Rsamtools Using samtools C libraries vignette?
> http://bioconductor.org/packages/devel/bioc/vignettes/Rsamtools/inst/doc/Rsamtools-UsingCLibraries.pdf
>
> It was a breaking change in how Rsamtools reverse dependencie
amtools-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
se 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 a package for submission to Bioconductor 3.1
and, therefore, I a
ckages/devel/bioc/vignettes/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
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 a package for submission to Bioconductor 3.1
and, therefore, I am trying to make everything work on the latest
R-devel, but I
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
usrlib/x86_64/
I.hg38 and
BSgenome.Hsapiens.NCBI.hg38.masked available.
I'll prepare the 2 packages in the next couple of weeks and post back
here when they are ready for download.
Cheers,
H.
On 02/06/2015 06:13 AM, Ulrich Bodenhofer wrote:
Hi,
The latest human genome build GRCh38 has been around in Biocon
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
Dear Rodrigo,
We recently released our 'kebabs' package as part of the Bioconductor
3.0 release. Though this package is aimed at providing sequence kernels
for classification, regression, and other tasks such as similarity-based
clustering, the package includes functionality that exactly match
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 to
Michael
On Wed, Mar 26, 2014 at 4:26 AM, Ulrich Bodenhofer
mailto:bodenho...@bioinf.jku.at>
> wrote:
> [cross-posted to R-devel and bioc-devel]
>
> Hi,
>
> I am trying to implement a 'sort' metho
her. Any ideas are gratefully appreciated!
Thanks a lot,
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 <mailto:bodenho..
is probably what users would not expect - given the
misleading "LB" in the name of the function.
Regards,
Ulrich
*Dr. Ulrich Bodenhofer*
Associate Professor
Institute of Bioinformatics
*Johannes Kepler Univers
r kind assistance!
Kind 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
bodenho...@bioinf.jku.at
On 03/26/2013 12:18 PM, Laurent Gatto wrote:
On 26 March 2013 09:26, Ulrich Bodenhofer 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 thought were available
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
to resort to a
conversion to character vectors anyway.
Thanks a lot in advance for your inputs!
Best regards,
Ulrich
----
*Dr. Ulrich Bodenhofer*
Associate Professor
Institute of Bioinformatics
*Johannes Kepler University
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