Comments (3)
Hi Redmar,
I set up your environment and the best way I found to continue is to install xbioc within your R session:
install.packages("remotes") # to install remotes pkg
remotes::install_github("renozao/xbioc")
also you will need to install the single reference data package which is hosted in my github:
install.packages("seAMLessData", repos = "https://eonurk.github.io/drat/")
then you should be able to follow the documentation. Let me know if you have any other questions.
I will update the documentation and close this issue, if you don't have further comments.
Best, Onur
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When I'm trying to install xbioc, I get a bunch of errors:
The downloaded source packages are in
‘/tmp/Rtmp82hMss/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Skipping install of 'pkgmaker' from a github remote, the SHA1 (48185132) has not changed since last install.
Use `force = TRUE` to force installation
Running `R CMD build`...
* checking for file ‘/tmp/Rtmp82hMss/remotes2458dceb5e/renozao-xbioc-1354168/DESCRIPTION’ ... OK
* preparing ‘xbioc’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘xbioc_0.1.19.tar.gz’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘xbioc’
* removing ‘/usr/local/lib/R/library/xbioc’
Warning messages:
1: In i.p(...) : installation of package ‘RCurl’ had non-zero exit status
2: In i.p(...) :
installation of package ‘GenomeInfoDb’ had non-zero exit status
3: In i.p(...) :
installation of package ‘Biostrings’ had non-zero exit status
4: In i.p(...) :
installation of package ‘KEGGREST’ had non-zero exit status
5: In i.p(...) :
installation of package ‘AnnotationDbi’ had non-zero exit status
6: In i.p(...) :
installation of package ‘/tmp/Rtmp82hMss/file243881bb4e/xbioc_0.1.19.tar.gz
I'm running this inside the biocontainer for r-seamless, so there should be no interference from local libraries etc.
docker://quay.io/biocontainers/r-seamless:0.1.0--r41h3121a25_0
from seamless.
#2 closing with this.
from seamless.
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