Question

dmrseq installation failed

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 • link updated 6.0 years ago by shepherl 4.1k • written 6.0 years ago by guy.bioinfo ▴ 10

score 2 · Accepted Answer · 2018-11-05

2

Entering edit mode

shepherl 4.1k

@lshep

Last seen 5 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.

ADD COMMENT • link 6.0 years ago shepherl 4.1k

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 • link 6.0 years ago Mike Smith ★ 6.6k

1

Entering edit mode

Thanks Mike, it worked after

BiocManager::install('remotes')

ADD REPLY • link 6.0 years ago guy.bioinfo ▴ 10

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 • link 6.0 years ago Martin Morgan 25k

0

Entering edit mode

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

ADD REPLY • link 6.0 years ago keegan ▴ 60