Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

ards, Felix -Ursprüngliche Nachricht- Von: Bioc-devel Im Auftrag von Leonardo Collado Torres Gesendet: Montag, 27. April 2020 18:07 An: Charlotte Soneson Cc: Bioc-devel Betreff: Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: m

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

--Ursprüngliche Nachricht- Von: Bioc-devel Im Auftrag von Leonardo Collado Torres Gesendet: Montag, 27. April 2020 18:07 An: Charlotte Soneson Cc: Bioc-devel Betreff: Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble Hi, I also ran more tests, which

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

nd >Windows (again, this doesn't fail on the Bioconductor devel docker). >Here's for example the error on Windows > > https://github.com/leekgroup/derfinderPlot/runs/620055131?check_suite_focus=true#step:12:1077. >Immediately after, GenomeInfoDbData does

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

the error on Windows >> >> https://github.com/leekgroup/derfinderPlot/runs/620055131?check_suite_focus=true#step:12:1077. >>Immediately after, GenomeInfoDbData does get installed >> >> https://github.com/leekgroup/derfinderPlot/runs/620055131?check_suite_f

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

l/016671.html. > > Best, > Leo > > > > On Sun, Apr 26, 2020 at 10:30 AM Martin Morgan wrote: > > > > Thanks Charlotte for the detective work. > > > > > > > >

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

> >>Likely this issue only happens on Windows and macOS because of the >>availability of some packages in source form and others in binary >>form, unlike only using source versions in the Bioconductor docker >>run. However, maybe I need some other code to get all the >>d

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

as source – this was a decision made quite a > while (years) ago, to save disk space (some of these packages are large, and > hosting macOS and Windows binaries in addition to source triple disk space > requirements) and on the rationale that the packages do not have C-level > source co

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

users have temporary or library paths with spaces or non-ASCII characters. I believe that this upstream bug (in R’s handling of Windows paths) has been fixed in the 4.0.0 release, but the details are quite complicated and I have not been able to follow the discussion fully. > >

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

t; > > > Martin > > > > From: Charlotte Soneson > Date: Sunday, April 26, 2020 at 5:32 AM > To: Martin Morgan > Cc: Leonardo Collado Torres , Bioc-devel > > Subject: Re: [Bioc-devel] GenomicFeatures and/or > TxDb.Hsapiens.UCSC.hg19.knownGene issue: missin

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

been able to follow the discussion fully. Martin From: Charlotte Soneson Date: Sunday, April 26, 2020 at 5:32 AM To: Martin Morgan Cc: Leonardo Collado Torres , Bioc-devel Subject: Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble Hi Leo, Martin

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

Hi Leo, Martin, it looks like this is related to an issue with the remotes package: https://github.com/r-lib/remotes/issues/296 . It gets the installation order wrong, and tries to install source packages before binaries. This can be a problem with

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

tibble is not a direct dependency of TxDb*. > db = available.packages(repos = BiocManager::repositories()) > deps = tools::package_dependencies("TxDb.Hsapiens.UCSC.hg19.knownGene", db) > deps $TxDb.Hsapiens.UCSC.hg19.knownGene [1] "GenomicFeatures" "AnnotationDbi" but it is an indirect dependency

[Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

Hi Bioc-devel, I think that there's a potential issue with either GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene or an upstream package. On a fresh R 4.0 Windows installation with BioC 3.11, I get the following error message when installing TxDb.Hsapiens.UCSC.hg19.knownGene as shown at https

Re: [Bioc-devel] GenomicFeatures export request

Awesome, thanks Hervé! Best, Leo On Wed, Dec 5, 2018 at 1:55 PM Pages, Herve wrote: > Hi Leo, > > This is done in GenomicFeatures 1.35.4: > > > https://github.com/Bioconductor/GenomicFeatures/commit/0b596c18b69f55d097aff0c6cdbbfc0b2993c4aa > > Cheers, > > H. > > > On 11/15/18 09:25, Leonardo Co

Re: [Bioc-devel] GenomicFeatures export request

Hi Leo, This is done in GenomicFeatures 1.35.4: https://github.com/Bioconductor/GenomicFeatures/commit/0b596c18b69f55d097aff0c6cdbbfc0b2993c4aa Cheers, H. On 11/15/18 09:25, Leonardo Collado Torres wrote: > Hi Hervé, > > Looking into the details of GenomicFeatures::exonicParts() I see that >

[Bioc-devel] GenomicFeatures export request

Hi Hervé, Looking into the details of GenomicFeatures::exonicParts() I see that this function runs GenomicFeatures:::.tidy_exons(). Would it be possible to export this function? Looks like it'll be useful for some work we are doing. We can start using it without the function being exported, and w

Re: [Bioc-devel] GenomicFeatures

FYI I've temporarily disabled the makeTxDbFromBiomart() examples in GenomicFeatures that have been responsible for this 'R CMD check' TIMEOUT for 2-3 days in a row: https://bioconductor.org/checkResults/3.8/bioc-LATEST/GenomicFeatures/malbec1-checksrc.html Hopefully GenomicFeatures will pass CH

Re: [Bioc-devel] GenomicFeatures

Historically we used to flush the repos before a release. At some point we stopped and I could not remember why. The situation you describe below is probably it. When preparing for 3.8, we ran into the case where we had quite a few stale packages in the repos. Their 'staleness' was due to being

Re: [Bioc-devel] GenomicFeatures

Lates BiocManager It is not flagging GenomicFeatures as out of date, presumably because it doesn't exists in the repos. So in some sense it is all internally consistent. I was just surprised to not see it flagged as being out of date. I guess I am also confused about what happens at release. Is

Re: [Bioc-devel] GenomicFeatures

For which BiocManager::version() is this? BiocManager::valid() checks within versions, and if there's no GenomicFeatures to reference, then there is no way to flag it as out-of-date, sort of like a package you'd installed that was in neither CRAN nor Bioconductor. Though of course we'd like Gen

Re: [Bioc-devel] GenomicFeatures

Thanks Kasper. I'm looking into the error in GenomicFeatures. Martin or Marcel may have more to add but I think BiocManager::install() can only report what versions are in the repo. GenomicFeatures 1.34.0 has not built so doesn't yet exist in the repo. We archive all versions in release but not

[Bioc-devel] GenomicFeatures

Seem broken in release. And btw., because it is broken, when I run BiocManager::valid() it doesn't report GenomicFeatures as out of date, despite the fact that I have version 1.33.2 installed, and there are newer versions in the 1.33.x hierarchy and the "right" (but broken) version in Bioc 3.8 i

Re: [Bioc-devel] GenomicFeatures::makeTxDbFromGFF leads to a S4Vectors error

Awesome, thanks Hervé! On Mon, Jan 30, 2017 at 12:22 PM, Hervé Pagès wrote: > Hi Leonardo, > > You need the latest version of rtracklayer: 1.35.3. Unfortunately this > version didn't propagate because of an issue that is not related to > this: > > > https://bioconductor.org/checkResults/3.5/bioc-

Re: [Bioc-devel] GenomicFeatures::makeTxDbFromGFF leads to a S4Vectors error

Hi Leonardo, You need the latest version of rtracklayer: 1.35.3. Unfortunately this version didn't propagate because of an issue that is not related to this: https://bioconductor.org/checkResults/3.5/bioc-LATEST/rtracklayer/malbec2-checksrc.html In the mean time you can fetch and install rtrac

[Bioc-devel] GenomicFeatures::makeTxDbFromGFF leads to a S4Vectors error

Hi, I think that a recent change in S4Vectors broke GenomicFeatures::makeTxDbFromGFF(). I ran this code about a week ago without problems, but it's failing now. Best, Leo ## Unevaluated code library('GenomicFeatures') library('devtools') txdb <- makeTxDbFromGFF('ftp://ftp.sanger.ac.uk/pub/genc

Re: [Bioc-devel] GenomicFeatures::extractTranscriptSeqs setMethod suggestion

Thanks Hervé! I’ll check it out but don’t expect any problems. cheers, jo > On 19 Jan 2016, at 22:31, Hervé Pagès wrote: > > Hi Jo, > > In GenomicFeatures 1.23.18 I've modified the default > "extractTranscriptSeqs" method so it can be called with additional > arguments when the 2nd argument i

Re: [Bioc-devel] GenomicFeatures::extractTranscriptSeqs setMethod suggestion

Hi Jo, In GenomicFeatures 1.23.18 I've modified the default "extractTranscriptSeqs" method so it can be called with additional arguments when the 2nd argument in not a GRangesList object. These additional arguments then get passed to the internal call to exonsBy(). With this change, the user shou

[Bioc-devel] GenomicFeatures::extractTranscriptSeqs setMethod suggestion

Dear all, I’m having hard times to extend the extractTranscriptSeqs method implemented in GenomicFeatures. Basically, I would like to implement a method for signature(x="ANY”, transcripts="EnsDb”), so that I can re-use the method from GenomicFeatures and add the optional parameter “filter” whic

[Bioc-devel] GenomicFeatures::getChromInfoFromBiomart

Shouldn't this be deprecated and replaced by getSeqinfoFromBiomart? Michael [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] GenomicFeatures LoadDb Path

On 08/08/2013 07:00 PM, Dario Strbenac wrote: It's not documented by ?loadDb, but providing an absolute path doesn't work, and shows an unusual error message. genes17 <- loadDb("/nb/dario/genes/gencode17.db") Error in loadDb(file, dbType, dbPackage, ...) : error in evaluating the argument

[Bioc-devel] GenomicFeatures LoadDb Path

It's not documented by ?loadDb, but providing an absolute path doesn't work, and shows an unusual error message. > genes17 <- loadDb("/nb/dario/genes/gencode17.db") Error in loadDb(file, dbType, dbPackage, ...) : error in evaluating the argument 'dbType' in selecting a method for function 'lo

Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

Hi Marc, Thanks a lot for your help, I will keep you updated on this. Tengfei On Mon, Feb 11, 2013 at 4:21 PM, Marc Carlson wrote: > ** > Hi Tengfei, > > Ugh. It seems that they have cooked up yet another new way to represent > that same kind of data inside of a gff file. :(I am sad to s

Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

Hi Tengfei, Ugh. It seems that they have cooked up yet another new way to represent that same kind of data inside of a gff file. :(I am sad to say that this is exactly the sort of thing that I was worried about. If you can't specify a field from your gff attribute field that contains the

Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

Hi Marc, Thanks a lot for your advice. I think as far as I know the gff3 file is the only way I can use to get Gmax's latest build for annotation from phytozome(http://www.phytozome.net/). Now it's publicly available ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Gmax/annotation/Gmax_189_gene_

Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

From: Marc Carlson [mailto:mcarl...@fhcrc.org] .Sent: Saturday, February 09, 2013 3:57 AM .To: Cook, Malcolm .Cc: 'bioc-devel@r-project.org' .Subject: Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file . .Hi Malcolm, . .In

Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

Hi Malcolm, In general I have found ensembl to be really great and I expect that their gtf files are probably fine. Usually the exon rank is the 1st thing you will see left out when a gtf file is cutting corners, and you are correct that they seem to be including that. I ran the one for Homo

Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

.Hi Tengfei, . .Yes that looks like an oversight. Thanks for reporting that! I will .extend makeTxDbPackage so that it's more accommodating of these newer .transcriptDbs. If you want to help me out, you could call saveDb() on .your gmax189 object and send me the .sqlite file that you save i

Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

Hi Tengfei, Yes that looks like an oversight. Thanks for reporting that! I will extend makeTxDbPackage so that it's more accommodating of these newer transcriptDbs. If you want to help me out, you could call saveDb() on your gmax189 object and send me the .sqlite file that you save it to.

[Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

Dear all, I am trying to build a txdb object from gff3 for soybean data and try to make it a package. Code used like this gmax189 <- makeTranscriptDbFromGFF("~/Gmax_189_gene_exons.gff3", format = "gff3", species = "Glycine max",