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guy.bioinfo
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@guybioinfo-18190
Last seen 6.0 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
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:
Thanks Mike, it worked after
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.Looks like this issue has now been resolved and bumphunter is passing build in Bioconductor 3.8.