Question: dmrseq installation failed
0
gravatar for guy.bioinfo
13 months ago by
guy.bioinfo10
guy.bioinfo10 wrote:

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

 

ADD COMMENTlink modified 13 months ago by shepherl ♦♦ 1.7k • written 13 months ago by guy.bioinfo10
Answer: dmrseq installation failed
2
gravatar for shepherl
13 months ago by
shepherl ♦♦ 1.7k
United States
shepherl ♦♦ 1.7k wrote:

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 COMMENTlink written 13 months ago by shepherl ♦♦ 1.7k
2

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 REPLYlink written 13 months ago by Mike Smith4.0k
1

Thanks Mike, it worked after 

BiocManager::install('remotes')
ADD REPLYlink written 13 months ago by guy.bioinfo10
1

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 REPLYlink written 13 months ago by Martin Morgan ♦♦ 24k

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

ADD REPLYlink written 13 months ago by keegan60
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