Why is DMRcate not available for Bioconductor version 3.18?
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@daniel-e-weeks-10677
Last seen 12 weeks ago
Pittsburgh, Pennsylvania, United States…

According to the Bioconductor web page for DMRcate, it looks like it is available for Bioconductor version 3.18 but this installation fails:

> BiocManager::install("DMRcate")
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Installing package(s) 'DMRcate'
Warning message:
package 'DMRcate' is not available for Bioconductor version '3.18'

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so;  LAPACK version 3.8.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/New_York
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.22

loaded via a namespace (and not attached):
[1] compiler_4.3.2
DMRcate • 856 views
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That's a good question. On the DMRcate landing page, one can see that the "Source package" file is missing, meaning that installation in Unix will fail: https://bioconductor.org/packages/DMRcate

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If we hover over the tiny little red icon next to the Linux build report, we can see that the source package isn't being distributed because the DSS package, on which it depends, is also not available on Linux.

It seem like that is probably because DSS uses edgeR in in it's vignette, but doesn't declare this in the DESCRIPTION file: https://bioconductor.org/checkResults/release/bioc-LATEST/DSS/nebbiolo2-checksrc.html

I think the options are either:

  • pester the DSS authors to fix their package, or
  • try to convince the DMRcate authors to drop their dependence on DSS.
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The DSS package authors just need to add edgeR to their Suggest of their DESCRIPTION. They have been contacted about it but have not acted or responded about it.

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Thanks Daniel, Gordon and Lori for flagging this. DSS is only needed for the vignette so I'll remove that section, plus the dependency, some time this week.

Best wishes, Tim

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Thank you for the explanation and contacting the DSS package authors.

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Hi Daniel,

All updated with the dependency dropped. Thanks again for bringing this to my attention.

Cheers, Tim

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