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

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 glue_1.4.2 DBI_1.1.

[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

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

/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 of Nicolas Del

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

[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

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 Plant

[Bioc-devel] Build time-out on malbec1

--- 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 Umeå S-901 87

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

--- 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 universitet

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

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 Plant Scie

[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

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] SummarizedExperiment initialisation and manipulation question.

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 Plant Physiology Umeå Plant Science Center Tel: +46 90 786

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

;-) 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 Tel: +46 90 786 5478 Email

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

/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 --- Nicolas Delhomme

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

[Bioc-devel] ShortRead srdistance is broken

] 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...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden

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 Department

[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?

wrote: - Original Message - From: Nicolas Delhomme nicolas.delho...@umu.se 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! I was wondering if the version 4.0.0

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

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

Hej Martin! On 11 Dec 2013, at 12:19, Martin Morgan mtmor...@fhcrc.org 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 know is to use the “comment

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

around this other than using % on 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

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

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

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

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

Chr03 ... scaffold_99 scaffold_991 NANANA ...NANA What do you say? Cheers, Nico --- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology

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 delho...@embl.de 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 current devel. I've

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

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

[7] BiocGenerics_0.7.2 loaded via a namespace (and not attached): [1] bitops_1.0-5 stats4_3.0.1 zlibbioc_1.7.0 Cheers, Nico --- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel