dmrseq installation failed
1
0
Entering edit mode
guy.bioinfo ▴ 10
@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

 

installation problem dmrseq bumphunter • 1.6k views
ADD COMMENT
2
Entering edit mode
shepherl 4.1k
@lshep
Last seen just now
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.

ADD COMMENT
2
Entering edit mode

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')
ADD REPLY
1
Entering edit mode

Thanks Mike, it worked after 

BiocManager::install('remotes')
ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 921 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6