Re: [Bioc-devel] workflow builder error: winbuilder1 says "pdflatex is not available"

Thank you for the quick fix and reply Andrzej. best, Mike On Thu, Sep 14, 2017 at 6:30 PM, Andrzej Oleś wrote: > Hi Mike, > > thanks for reporting this. Strange, not sure what the problem was because > now I was able to rebuild the workflow without actually reinstalling

Re: [Bioc-devel] Identical methods in two packages

On 09/14/2017 02:23 PM, Laurent Gatto wrote: On 14 September 2017 15:15, Hervé Pagès wrote: Hi, Note that right now the name of the Ontology getter matches the name of the corresponding field in all our annotations: > library(org.Hs.eg.db) > org.Hs.egGO[["92610"]][["GO:0005622"]]

Re: [Bioc-devel] workflow builder error: winbuilder1 says "pdflatex is not available"

Hi Mike, thanks for reporting this. Strange, not sure what the problem was because now I was able to rebuild the workflow without actually reinstalling or reconfiguring anything on the builder. Maybe this was a transient issue related to the fact that I updated the LaTeX distro on the builder

Re: [Bioc-devel] Identical methods in two packages

On 14 September 2017 15:15, Hervé Pagès wrote: > Hi, > > Note that right now the name of the Ontology getter matches the > name of the corresponding field in all our annotations: > >> library(org.Hs.eg.db) > >> org.Hs.egGO[["92610"]][["GO:0005622"]] >$GOID >[1] "GO:0005622" > >

Re: [Bioc-devel] Hsapiens in bioconductor

Dear Herve, Your solution worked out, no 'R CMD check' warning. -- Tomasz On Thu, 14 Sep 2017 18:09:44 +0200, wrote: Hi Tomasz, The name of the BSgenome object defined in a BSgenome data package is the name of the package itself. Hsapiens is just an

[Bioc-devel] Fwd: Getting w+r access for my package (IntEREst); svn/git transfer problem (Problem remains unsloved)

You are welcome. Begin forwarded message: From: "Oghabian, Ali" > Subject: Re: Getting w+r access for my package (IntEREst); svn/git transfer problem (Problem remains unsloved) Date: September 14, 2017 at 12:19:37 PM EDT To: "Turaga,

[Bioc-devel] workflow builder error: winbuilder1 says "pdflatex is not available"

hi, I pushed a change to rnaseqGene workflow and only winbuilder1 had a problem: * checking PDF version of manual ...Warning: running command '"C:/Progra~1/R/R-3.4.0/bin/x64/Rcmd.exe" Rd2pdf --batch --no-preview --build-dir="C:/Windows/TEMP/RtmpE9T1fB/Rd2pdff6059a733c8" --no-clean -o

Re: [Bioc-devel] Identical methods in two packages

Hi, Note that right now the name of the Ontology getter matches the name of the corresponding field in all our annotations: > library(org.Hs.eg.db) > org.Hs.egGO[["92610"]][["GO:0005622"]] $GOID [1] "GO:0005622" $Evidence [1] "IEA" $Ontology [1] "CC" > library(GO.db) >

Re: [Bioc-devel] Hsapiens in bioconductor

Hi Tomasz, The name of the BSgenome object defined in a BSgenome data package is the name of the package itself. Hsapiens is just an convenient "alias" for the long name. So you could do: importFrom(BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19)

Re: [Bioc-devel] SSH keys

Hi, That is an invalid key. Please regenerate your key with the instructions provided in the http://bioconductor.org/developers/how-to/git/faq/ (FAQ section). Resubmit to the google-form. Best, Nitesh > On Sep 14, 2017, at 8:12 AM, Vojtech Kulvait wrote: > > Hi, > I

Re: [Bioc-devel] Hsapiens in bioconductor

Hello Tomaszu, On 9/14/17 2:14 PM, Tomasz Stokowy wrote: Could you suggest how to avoid this warning? I would like to use both hg19 and hg38 references in my package. super easy: library(BSgenome.Hsapiens.UCSC.hg19) suppressMessages(library(BSgenome.Hsapiens.UCSC.hg38))

[Bioc-devel] non-ASCII strings in data for a developing package

The Cell Line Ontology includes tokens like CSMaß1H cell which trigger warnings if included in .rda files in data folder. They can be masked using iconv but it seems unfortunate to do this. The offending .rda files can be kept elsewhere and loaded by function. Is that the appropriate

[Bioc-devel] Hsapiens in bioconductor

Dear bioc-devel, I would like to import Hsapiens objects from both BSgenome.Hsapiens.UCSC.hg19 and BSgenome.Hsapiens.UCSC.hg38 this is currently handled in the namespace of my package by import(BSgenome.Hsapiens.UCSC.hg19) import(BSgenome.Hsapiens.UCSC.hg38) I get warning (because I assign

[Bioc-devel] assay dimnames in SingleCellExperiment / SummarizedExperiment

Dear all, I cc-ed to this email individual package maintainer to directly 'notify' them of this thread and have their respective opinions, but I thought the common use of SummarizedExperiment was worth involving the community as well. Background: I was updating one of my workflow from SCESet to