Re: [Bioc-devel] biocLite “no packages in repository” error

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

Re: [Bioc-devel] [BioC] Can\'t load new BioC packages

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

Re: [Bioc-devel] biocLite “no packages in repository” error

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

[Bioc-devel] Is roxygen2 version 4.0.0 supported on the devel build system?

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

Re: [Bioc-devel] Is roxygen2 version 4.0.0 supported on the devel build system?

: > > > - 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! >>

Re: [Bioc-devel] Bug tracker for Bioconductor?

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

[Bioc-devel] ShortRead srdistance is broken

-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

Re: [Bioc-devel] ShortRead srdistance is broken

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

[Bioc-devel] "forceAndCall" is not a SPECIAL function ERROR when using ShortRead readAligned function

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

Re: [Bioc-devel] "forceAndCall" is not a SPECIAL function ERROR when using ShortRead readAligned function

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

Re: [Bioc-devel] "forceAndCall" is not a SPECIAL function ERROR when using ShortRead readAligned function

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

Re: [Bioc-devel] "forceAndCall" is not a SPECIAL function ERROR when using ShortRead readAligned function

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.

Re: [Bioc-devel] R 3.3 for snow leopard

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 ----

[Bioc-devel] seqnames as a candidate for BiocGenerics

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.

Re: [Bioc-devel] seqnames as a candidate for BiocGenerics

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

[Bioc-devel] SummarizedExperiment initialisation and manipulation question.

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

Re: [Bioc-devel] SummarizedExperiment initialisation and manipulation question.

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

[Bioc-devel] as.table not available for HitsList anymore?

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

Re: [Bioc-devel] as.table not available for HitsList anymore?

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

[Bioc-devel] summarizeOverlaps provide a non existing algorithm argument to findOverlaps

[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

Re: [Bioc-devel] summarizeOverlaps provide a non existing algorithm argument to findOverlaps

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

[Bioc-devel] Build time-out on malbec1

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

Re: [Bioc-devel] Build time-out on malbec1

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

[Bioc-devel] Problem with uncompressing files on tokay1?

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

Re: [Bioc-devel] BiocManager not installing latest release version of DepecheR

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

Re: [Bioc-devel] Problem with uncompressing files on tokay1?

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

[Bioc-devel] SSL certificate error on nebbiolo2

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%'

Re: [Bioc-devel] SSL certificate error on nebbiolo2

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

[Bioc-devel] BamFile validation

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

Re: [Bioc-devel] BamFile validation

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

Re: [Bioc-devel] BamFile validation

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

[Bioc-devel] appending 2 GappedAlignments using "c" takes long

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

Re: [Bioc-devel] appending 2 GappedAlignments using "c" takes long

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

Re: [Bioc-devel] appending 2 GappedAlignments using "c" takes long

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

Re: [Bioc-devel] appending 2 GappedAlignments using "c" takes long

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 -

[Bioc-devel] the character to collapse the geneNames when using the disjointExons function with aggregateGenes=TRUE

r03 ... scaffold_99 scaffold_991 NANANA ...NANA What do you say? Cheers, Nico ------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Labor

Re: [Bioc-devel] the character to collapse the geneNames when using the disjointExons function with aggregateGenes=TRUE

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

Re: [Bioc-devel] the character to collapse the geneNames when using the disjointExons function with aggregateGenes=TRUE

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 ----

[Bioc-devel] How to update the data in a data package?

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

Re: [Bioc-devel] How to update the data in a data package?

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/

[Bioc-devel] memory not mapped error when installing Bioc 2.13 packages on R 3.0.2

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

Re: [Bioc-devel] SUGGESTION: BioC version (e.g. 2.13) to also follow the x.y(.z) version scheme of Bioc packages

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

Re: [Bioc-devel] [BioC] GTF file error when using easyRNAseq

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

Re: [Bioc-devel] [BioC] GTF file error when using easyRNAseq

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

[Bioc-devel] Conflict between BiocStyle and the verbatim package

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

Re: [Bioc-devel] GenomicRanges: Storing 'seqlengths' as numeric

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

Re: [Bioc-devel] Conflict between BiocStyle and the verbatim package

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