Re: [Bioc-devel] Windows specific error during CHECK

Thanks Herve! -Ursprüngliche Nachricht- Von: Hervé Pagès Gesendet: Dienstag, 26. Oktober 2021 21:53 An: Felix Ernst ; bioc-devel@r-project.org Betreff: Re: [Bioc-devel] Windows specific error during CHECK Hi Felix, On 26/10/2021 12:10, Felix Ernst wrote: > Hi Bioc-Team, > &g

[Bioc-devel] Windows specific error during CHECK

Hi Bioc-Team, I have got a problem with an error on Windows, which I am not able to debug. http://bioconductor.org/checkResults/devel/bioc-LATEST/mia/riesling1-checksrc.html The testthat.out.fail output doesn't indicate any problems and the testthat.out on other systems looks the same. Can

[Bioc-devel] Testthat problem - version info

Hi all, I have been notified about some issues and it is quite clear that they are from testthat https://master.bioconductor.org/checkResults/3.14/bioc-LATEST/RNAmodR/nebbiolo2-checksrc.html Can somebody let me know which testthat version was used for the last check run? I want to raise the

Re: [Bioc-devel] BSgenome changes

Hi Leonard, Hi Herve, I followed your conversation, since I have noticed the same problem. Thanks, Herve, for the explanation of the recent changes on hg19. The GRCh37.P13 report states in its last line: MT assembled-molecule MT Mitochondrion J01415.2=

[Bioc-devel] AnnotationHubData -> rBiopaxParser -> nem dependency issue

Hi, I have a bit of a strange error on my Travis-CI build reports and strange in the sense, that they are not picked up by the Bioc build report. https://travis-ci.com/github/FelixErnst/RNAmodR The package "rBiopaxParser" is reported as not available during the dependency install step. I

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

Hi, Thanks for the discussion and the insight into possible solutions. I currently have the same problem with settings up an RNAmodR GitHub Action. This fails because the RNAmodR requires RNAmodR.Data, which suggests GenomicRanges, which then leads to GenomeInfoDb and GenomeInfoDbData. What

Re: [Bioc-devel] R Dependency Warning

Hi Sunny, I would venture a guess and suggest that is about the too fined grained version you defined in the DESCRIPTION file. I would suggest, that you try to define an R version, which follows the format x.y and not x.y.z. So for you that would be R (>= 4.0). Hope that works, Felix

Re: [Bioc-devel] Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased)

Hi, If you can replicate the latex/knitr/sweave issue locally, try installing Biostrings from my GitHub fork used in the PR. This should solve the issue, if it is about the ellipsis character causing problems on windows only. If it doesn't, it probably has more to do with the way unicode

Re: [Bioc-devel] warning: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic

Hi, I am certainly not a roxygen expert, but if \code{\link{\%>\%}} is to implicit for anyone's taste, \code{\link[magrittr:pipe]{\%>\%}} should also work in this case. The case above is used for a package external link. For an internal explicit link use \code{\link[=something]{or other}}.

Re: [Bioc-devel] New bioconductor_docker image officially released

Hi Nitesh, Thanks for the new image. I have a question regarding the behavior of encountering logicals with a length higher than 1 and its coercion to logical(1) for an if statement. I encountered a bit of a problem, when a unit test returned an error running R CMD check using the

[Bioc-devel] error regarding splitAsList from IRanges packages

Hi I have a build error for RNAmodR package, which was just added to the Bioc git repo and was build for the first time for 3.10. https://bioconductor.org/checkResults/3.10/bioc-LATEST > No methods found in package �IRanges� for request: �splitAsList� when loading > �ensembldb� > Error:

[Bioc-devel] BiocManager for BioC 3.9/R 3.6

Hi, I just installed R 3.6, but everything I try to get a BiocManager Version, which works with R 3.6 were so far not successful. I installed BiocManager from CRAN � > install.packages("BiocManager") � and from GitHub � > devtools::install_github("Bioconductor/BiocManager") � but both times

[Bioc-devel] Single Package Builder

still valid? Best regards, Felix --- Felix Ernst, PhD Universit� Libre de Bruxelles RNA MOLECULAR BIOLOGY BIOPARK Charleroi Brussels-South CAMPUS Rue Profs Jeener & Brachet, 12 B-6041 Charleroi - Gosselies BELGIUM +32(2)650 9774 (office phone) <mailto:felix.er...@ul

Re: [Bioc-devel] EXTERNAL: troubles with fetching Bioconductor github

ying cause for the behaviour is. It is more a fix for the symptom, not a cure. Hope this helps some people. Best regards, Felix --- Felix Ernst, PhD Université Libre de Bruxelles RNA MOLECULAR BIOLOGY BIOPARK Charleroi Brussels-South CAMPUS Rue Profs Jeener & Brachet, 12 B-6041 Charleroi - Gosselies BEL

[Bioc-devel] DOI information

Dear BioC-Team, Just as little bug report. I don't want to make a big deal about it: I just imported the citation information for my package tRNAscanImport into Citavi using the doi number and the last name was not imported correctly. Is this due to the middle name(s)? On the package page

[Bioc-devel] AAString - Amino acid code enforced?

Dear all, probably this is for Hervé Pagès: I tried the following code, which should according to ?AAString not work, since ÜÖÄ are not part of any AA code. > AAString("ÜÄÖ") 3-letter "AAString" instance seq: ÜÄÖ > sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-w64-mingw32/x64

[Bioc-devel] SummarizedExperiment: duplication of metadata, when modifying colData

ata(se)) List of 4 $ meep: chr "meep" $ meep: chr "meep" $ meep: chr "meep" $ meep: chr "meep" > colData(se[, 2])$xyz <- "abc" > str(metadata(se)) List of 8 $ meep: chr "meep" $ meep: chr "meep" $ meep: c