No package called xbioc

[Redmar-van-den-Berg]

I'm trying to follow along with the readme, but I get the following error

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(seAMLess)
> library(xbioc)
Error in library(xbioc) : there is no package called ‘xbioc’

I'm testing in a clean conda environment that only contains r-seamless: environment.zip

[eonurk]

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

[Redmar-van-den-Berg]

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

[eonurk]

#2 closing with this.