Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Cann't install chromVAR successfully on Linux #91

Open
whui2bioinformatics opened this issue Jun 4, 2021 · 3 comments
Open

Cann't install chromVAR successfully on Linux #91

whui2bioinformatics opened this issue Jun 4, 2021 · 3 comments

Comments

@whui2bioinformatics
Copy link

whui2bioinformatics commented Jun 4, 2021

Hi, I have tried some times but not install this successfully yet. Can anyone help me?

first, I create a conda environment: conda create -n r
and then activate r to install R and packages: conda install -c conda-forge r-base #R4.1
finally, try to install chromVAR with this command, BiocManager::install("chromVAR")
but I got the error information as follows

1: In .inet_warning(msg) :
  installation of package ‘RSQLite’ had non-zero exit status
2: In .inet_warning(msg) :
  installation of package ‘AnnotationDbi’ had non-zero exit status
3: In .inet_warning(msg) :
  installation of package ‘annotate’ had non-zero exit status
4: In .inet_warning(msg) :
  installation of package ‘GO.db’ had non-zero exit status
5: In .inet_warning(msg) :
  installation of package ‘CNEr’ had non-zero exit status
6: In .inet_warning(msg) :
  installation of package ‘TFBSTools’ had non-zero exit status
7: In .inet_warning(msg) :
  installation of package ‘chromVAR’ had non-zero exit status

before using R created by conda, I have tried installation chromVAR so many times by R installed by source code in my linux account, but unfortunately I also got some errors, such as fatal error: gsl/gsl_rng.h: No such file or directory, I guess may be I have lacked some shared file in my R program, so I newly create a new conda env and install R, but I still cann't install this(the error information are above)

@whui2bioinformatics
Copy link
Author

whui2bioinformatics commented Jun 4, 2021

Hi, this installation problem has solved.
cann't install RSQLite by install.packages("RSQLite"), try to used a low RSQLite version.

require(devtools)
install_version("RSQLite", version = "2.2.5")

and then BiocManager::install("chromVAR")

@candacelei
Copy link

Hi,
Did you successfully install chromVAR? I got the following error message when I followed your step:

install_version("RSQLite", version = "2.2.5")
--- Please select a CRAN mirror for use in this session ---
Error in download_version_url(package, version, repos, type) :
version '2.2.5' is invalid for package 'RSQLite'

@whui2bioinformatics
Copy link
Author

Yes, I installed it successfully. May be you need to debug according to all errors emerged.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants