ST_1.34.0progress_1.2.2 tidyselect_1.1.1
> [4] purrr_0.3.4vctrs_0.3.8generics_0.1.1
> [7] stats4_4.1.1 BiocFileCache_2.2.0utf8_1.2.2
> [10] blob_1.2.2 XML_3.99-0.8 rlang_0.4.12
> [13] pillar_1.6.4
Hej!
The easyRNASeq package fails with the following error on nebbiolo2:
easyRNASeq RUnit Tests - 20 test functions, 1 error, 0 failures
ERROR in test_getAnnotation_BiomaRt: Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function
'%in%'
tgenie.org/Tutorials/RnaSeqTutorial/data/star/unitTest/213.1_subset_sortmerna_trimmomatic_sorted.bam.bai";
> BiocFileCache::bfcrpath(rnames = url)
>
> which downloads (once) and returns the path to the cached file.
>
> Martin
>
> On 11/25/19, 8:24 AM, "Bioc-devel on behalf
I have faced the same issue as described in this post and I agree with Aaron,
that it would be nice if the doc on the website where extended to specify the
version as in "BiocManager::install(version='3.10’)"
Best,
Nico
> On 15 Nov 2019, at 00:32, Aaron Lun
> wrote:
>
> I would assume that
Hej!
The easyRNASeq package is not building on tokay1, with what seems to be a file
decompression issue?
https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/easyRNASeq/tokay1-buildsrc.html
It works fine on the other OSs.
The error is triggered while downloading a small dataset durin
Hej Lori!
Indeed. Thanks for answering though. Now, it seems to be an error propagating
through from biomaRt, so I'll wait for that to be fixed.
Best,
Nico
---
Nicolas Delhomme, PhD
UPSC bioinformatics facility Manager
Umeå
nks,
Nico
-------
Nicolas Delhomme, PhD
UPSC bioinformatics facility Manager
Umeå Plant Science Center,
Swedish University for Agricultural
Sciences (SLU) and Umeå University
Tel: +46 90 786 5478
Email: nicolas.delho...@umu.se
SLU - Umeå universitet
Ume
Nico
---
Nicolas Delhomme, PhD
Acting Manager
UPSC bioinformatics core facility
Umeå Plant Science Center,
Swedish University for Agricultural
Sciences (SLU) and Umeå University
Tel: +46 90 786 5478
Email: nicolas.delho...@umu.se
SLU - Umeå univer
[31] xtable_1.8-0 RCurl_1.95-4.7
Am I overlooking something or is it just that I got slightly out of sync
packages?
Cheers,
Nico
-------
Nicolas Delhomme, PhD
Acting Manager
UPSC bioinformatics core facility
Umeå
Hej Martin!
Changing the Import from IRanges to S4Vectors fixed it.
Thanks again,
Nico
---
Nicolas Delhomme, PhD
Acting Manager
UPSC bioinformatics core facility
Umeå Plant Science Center,
Swedish University for Agricultural
Sciences
1.23.7ShortRead_1.29.1
[43] SummarizedExperiment_1.1.11 xtable_1.8-0
[45] RCurl_1.95-4.7
Thanks!
Nico
PS Have a good Christmas time!
---
Nicolas Delhomme, PhD
Acting Manager
UPSC bioinformatics core fa
Thanks for the quick action :-)
Nico
---
Nicolas Delhomme, PhD
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 5478
Email: nicolas.delho...@umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
now, so no sessionInfo(), but I'm
using R3.2.1 on OSX 10.10.3 (Yosemite), and the latest devel packages (updated
today; SummarizedExperiment version is 0.3.0).
Cheers,
Nico
-------
Nicolas Delhomme, PhD
The Street Lab
Department of
of least resistance ;-)
Thanks for the feedback, I'll come back to you if the point raised by Michael
occurs.
Cheers,
Nico
-------
Nicolas Delhomme
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
T
hem in the
easyRNASeq package.
Cheers,
Nico
-------
Nicolas Delhomme
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 5478
Email: nicolas.delho...@umu.
dered/considering downgrading it. This is mere speculation, but I
guess the newer OSX have not been developed and tested for "classic"
harddrives, so I'm afraid that this situation is not going to improve.
HTH,
Nico
----
outdated and I'm preparing
a dataset with much more recent and more comprehensive data.
Cheers,
Nico
---
Nicolas Delhomme
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 5478
Email: nicolas.
That did it, sorry for whining too early :-\
Nico
---
Nicolas Delhomme
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 5478
Email: nicolas.delho...@umu.se
SLU - Umeå universitet
Umeå S-901 87
enbaum wrote:
>
> I think we'd need to see your files in order to try to reproduce this.
> Dan
>
>
> ----- Original Message -
>> From: "Nicolas Delhomme"
>> To: "bioC-devel"
>> Sent: Friday, March 27, 2015 11:04:17 AM
>> Sub
neplotter_1.45.0
lambda.r_1.1.7 edgeR_3.9.14
[26] intervals_0.15.0 genomeIntervals_1.23.2 splines_3.2.0
xtable_1.7-4 RCurl_1.95-4.5
---
Nicolas Delhomme
The Street Lab
Department of Plant Physiology
Hej Valerie!
Yes, it did fix the issue, but only after I also installed the snow package.
Could it be that that's another dependency that has been overlooked in
BiocParallel?
Nico
---
Nicolas Delhomme
The Street Lab
Departme
-26
RColorBrewer_1.1-2 tools_3.2.0
[11] Biobase_2.27.2
Cheers,
Nico
-------
Nicolas Delhomme
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 5478
Email: nicolas.delho...@um
I do
understand their point.
Cheers,
Nico
---
Nicolas Delhomme
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 5478
Email: nicolas.delho...@plantphys.umu.se
SLU - Umeå universitet
Umeå S-901 87
:
>
>
> - Original Message -
>> From: "Nicolas Delhomme"
>> To: bioc-devel@r-project.org
>> Sent: Tuesday, May 6, 2014 7:24:08 AM
>> Subject: [Bioc-devel] Is roxygen2 version 4.0.0 supported on the devel build
>> system?
>>
>> Hej!
>>
Hej!
I was wondering if the version 4.0.0 of roxygen2 is supported on the devel
build system.
Cheers,
Nico
---
Nicolas Delhomme
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 5478
Email
Hej Dan!
Thanks for the details and the super quick answer :-)
Nico
---
Nicolas Delhomme
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 7989
Email: nicolas.delho...@umu.se
SLU - Umeå
can also take turn to answer them
:-)
Nico
---
Nicolas Delhomme
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 7989
Email: nicolas.delho...@umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
but got a workaround from the package developers - and this since Maverick is
out (October last year).
Cheers,
Nico
---
Nicolas Delhomme
The Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 7989
Hej Martin!
On 11 Dec 2013, at 12:19, Martin Morgan wrote:
> On 12/03/2013 12:50 PM, Martin Morgan wrote:
>> On 12/03/2013 12:30 PM, Nicolas Delhomme wrote:
>>> Hej Martin!
>>>
>>> I’d like to have multi-line comments in my vignette and the easiest way I
analyse these alignments, so I’m bound to
see how it works out in R :-)
Cheers,
Nico
---
Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310
Email: nicolas.delho
every comment line?
Cheers,
Nico
---
Nicolas Delhomme
Nathaniel Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 7989
Email: nicolas.delho...@umu.se
SLU - Umeå universitet
Umeå S-901 87
admit I haven’t though about this
in detail, but I already can think of use cases where such a function would
come in handy.
Nico
---
Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel
people would benefit from an equivalent rtracklayer
implementation. If you’re interested, I could do a performance comparison -
based on my usual use case - between both packages.
Nico
---
Nicolas Delhomme
Genome Biology Computational
o the even=stable; odd=devel
paradigm that is useful to us developers. I may as well just be a creature of
habits ;-)
Nico
-------
Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49
do_install_source(pkg_name, instdir, pkg, desc)
46: do_install(pkg)
47: tools:::.install_packages()
aborting ...
/Users/delhomme/opt/R-3.0.2_SRC/../R-3.0.2/R.framework/Resources/bin/INSTALL:
line 34: 63387 Doneecho 'tools:::.install_packages()'
63388 Segmentation fault
22:02, Laurent Gatto wrote:
> Dear Nico,
>
> On 5 September 2013 20:39, Nicolas Delhomme wrote:
> > Hej Bioc!
> >
> > I'd like to update the data in that data package:
> >
> > https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RnaSeqTutorial/
Thanks,
Nico
-------
Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310
Email: nicolas.delho...@embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
___
Bioc-devel@r-project.o
it might have to be set to "NULL" by default.
Alejandro - I've seen that in DEXSeq you conserve only these exons you can test
- what you call testable exons - does that include a size filter?
What's your take?
Nico
----
Fantastic!
Cheers,
Nico
---
Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310
Email: nicolas.delho...@embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg
r03 ... scaffold_99 scaffold_991
NANANA ...NANA
What do you say?
Cheers,
Nico
-------
Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Labor
ce (and not attached):
[1] stats4_3.0.1
So I'm not sure what happened; so far, I can only imagine an NFS / RAID related
issue.
Doing it with my own data gives the same results as above.
Sorry for bothering you with that and many thanks for the help.
Cheers,
Nico
-
Hej Hervé!
---
Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310
Email: nicolas.delho...@embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
Hi Martin,
On Jul 10, 2013, at 8:40 PM, Martin Morgan wrote:
>
> - Nicolas Delhomme wrote:
>> Hej Bioc Core!
>>
>> There was some discussion last year about implementing a BamStreamer (à la
>> FastqStreamer), but I haven't seen anything like it in the
ttached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] BiocInstaller_1.11.3 Rsamtools_1.13.22 Biostrings_2.29.12
[4] GenomicRanges_1.13.26 XVector_0.1.0 IRanges_1.19.15
[7] BiocGenerics_0.7.2
load
Hi Martin,
On 8 Jan 2013, at 19:53, Martin Morgan wrote:
> On 01/07/2013 12:32 PM, Nicolas Delhomme wrote:
>> Hi Martin, Marc,
>>
>> I'm now implementing the use of BamFile objects in easyRNASeq and I like
>> them. I think it would be very useful if when constru
Just to clarify. I don't mean it needs to validate the BAM file (i.e. checking
that it's properly formatted), so using file.exists on the provided file paths
would be sufficient.
-------
Nicolas Delhomme
Genome Biology Com
14 Biostrings_2.27.8 GenomicRanges_1.11.21
[4] IRanges_1.17.24 BiocGenerics_0.5.6BiocInstaller_1.9.6
loaded via a namespace (and not attached):
[1] bitops_1.0-5 stats4_2.16.0 tools_2.16.0 zlibbioc_1.5.0
Cheers,
Nico
---
Nico
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