dmrseq installation failed
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guy.bioinfo ▴ 10
@guybioinfo-18190
Last seen 3.5 years ago

Hello,

 dmrseq installtiont failed due to dependencies.

It looks like bumphunter is not included in Bioconductor 3.8.

 

BiocManager::install("dmrseq", version = "3.8")
Bioconductor version 3.8 (BiocManager 1.30.3), R 3.5.1 (2018-07-02)
Installing package(s) 'dmrseq'
Warning: dependency ‘bumphunter’ is not available
trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/dmrseq_1.2.1.tar.gz'
Content type 'application/x-gzip' length 2942106 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

ERROR: dependency ‘bumphunter’ is not available for package ‘dmrseq’
* removing ‘/home/guyho/R/x86_64-pc-linux-gnu-library/3.5/dmrseq’

The downloaded source packages are in
    ‘/tmp/RtmpxyY6iT/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘dmrseq’ had non-zero exit status

 

installation problem dmrseq bumphunter • 663 views
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shepherl 3.1k
@lshep
Last seen 6 hours ago
United States

bumphumper has yet to build cleanly after the Bioconductor 3.8 release as indicated on the build report. Until the package builds it will be unavailable for installations. Once the package builds it will be available via BiocManager

A temporary work around could be to either clone and install manually bumphunter despite the package currently being broken

git clone https://git@git.bioconductor.org/packages/bumphunter
R CMD INSTALL bumphunter

Or you could see if bumphunter has a github repository that could be installed temporarily.

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2
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Just as a follow up, I believe the Github repo is at https://github.com/rafalab/bumphunter and you can install directly from there via:

BiocManager::install('rafalab/bumphunter')
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1
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Thanks Mike, it worked after 

BiocManager::install('remotes')
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If you're using github and the release branch, be sure to add the argument ref = "RELEASE_3_8" to the install command. Likewise, be sure to git checkout RELEASE_3_8 in the git clone.

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Looks like this issue has now been resolved and bumphunter is passing build in Bioconductor 3.8.

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