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eonurk avatar eonurk commented on August 27, 2024

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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Redmar-van-den-Berg avatar Redmar-van-den-Berg commented on August 27, 2024

When I'm trying to install xbioc, I get a bunch of errors:

The downloaded source packages are in/tmp/Rtmp82hMss/downloaded_packagesUpdating 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
* preparingxbioc:
* 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 adata/datalistfile should be added
* buildingxbioc_0.1.19.tar.gzERROR: dependencyAnnotationDbiis not available for packagexbioc* removing/usr/local/lib/R/library/xbiocWarning messages:
1: In i.p(...) : installation of packageRCurlhad non-zero exit status
2: In i.p(...) :
  installation of packageGenomeInfoDbhad non-zero exit status
3: In i.p(...) :
  installation of packageBiostringshad non-zero exit status
4: In i.p(...) :
  installation of packageKEGGRESThad non-zero exit status
5: In i.p(...) :
  installation of packageAnnotationDbihad 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

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eonurk avatar eonurk commented on August 27, 2024

#2 closing with this.

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