Question

Why is DMRcate not available for Bioconductor version 3.18?

1

Entering edit mode

Daniel E. Weeks ▴ 30

@daniel-e-weeks-10677

Last seen 11 months 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 • 1.8k views

ADD COMMENT • link written 12 months ago by Daniel E. Weeks ▴ 30

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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

ADD REPLY • link 12 months ago Gordon Smyth 51k

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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.

ADD REPLY • link 12 months ago Mike Smith ★ 6.6k

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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.

ADD REPLY • link 12 months ago shepherl 4.1k

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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

ADD REPLY • link 11 months ago Tim Peters ▴ 200

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Entering edit mode

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

ADD REPLY • link 11 months ago Daniel E. Weeks ▴ 30

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Entering edit mode

Hi Daniel,

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

Cheers, Tim

ADD REPLY • link 11 months ago Tim Peters ▴ 200