[Bioc-devel] ChIPseeker failing on r-devel on CRAN checks

[Hervé Pagès]

Hi Onur,

AFAICT ChIPseeker is currently available on all platforms in BioC devel:

   https://bioconductor.org/packages/3.13/ChIPseeker

Same for all the other Bioconductor packages that the CRAN check results 
for cinaR say are not available:

- CRAN check results:
 
https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/cinaR-00check.html
 
https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/cinaR-00check.html
 
https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/cinaR-00check.html
 
https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/cinaR-00check.html

- Packages reported as not available are available:

   pkgs_reported_as_not_available <- c(
       'ChIPseeker',
       'DESeq2',
       'TxDb.Hsapiens.UCSC.hg38.knownGene',
       'TxDb.Hsapiens.UCSC.hg19.knownGene',
       'TxDb.Mmusculus.UCSC.mm10.knownGene')

   library(BiocManager)
   # Bioconductor version 3.13 (BiocManager 1.30.11), 
?BiocManager::install for help

   available_pkgs <- 
rownames(available.packages(contrib.url(repositories())))

   pkgs_reported_as_not_available %in% available_pkgs
   # [1] TRUE TRUE TRUE TRUE TRUE

So to me it looks like some hiccup in the CRAN builds.

H.


On 3/23/21 3:12 PM, Onur Karakaslar wrote:
> Hi all,
> 
> I have a CRAN package called cinaR which depends on ChIPseeker. Yet, I
> recently learned that ChIPseeker is actually failing on r-devel checks of
> CRAN, which possibly fails my package as well. You can find the detailed
> info here:
> 
> https://support.bioconductor.org/p/9135778/
> 
> Can anyone help me figure this out?
> 
> Thank you very much for your help!
> Best,
> Onur
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Hervé Pagès

Bioconductor Core Team
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