Installation fails in R 4.1

[remomomo]

Hi,

I've followed the steps to install CONQUER, at the final step of the installation, I get the following error:

> devtools::install_github("roderickslieker/CONQUER")
Downloading GitHub repo roderickslieker/CONQUER@HEAD
Skipping 6 packages not available: BiocGenerics, clusterProfiler, IRanges, org.Hs.eg.db, GenomicRanges, conquer.db
✓  checking for file ‘/private/var/folders/dg/9g8hxb3n1wbdv89mc5nc5gjw0000gn/T/RtmpUGUpoL/remotesa6a34a3f471c/roderickslieker-CONQUER-1dd72eb/DESCRIPTION’ ...
─  preparing ‘CONQUER’:
✓  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘CONQUER_1.1.3.tar.gz’

* installing *source* package ‘CONQUER’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB

Warning: namespace ‘CONQUER’ is not available and has been replaced
by .GlobalEnv when processing object ‘KEGG_DATA’
Warning: namespace ‘CONQUER’ is not available and has been replaced
by .GlobalEnv when processing object ‘KEGG_DATA’
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'get_eQTL_bulk(genesx = genes_versioned, ': unused argument (genesx = genes_versioned) 
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘CONQUER’ in namespaceExport(ns, exports):
 undefined exports: extract.pathways
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/CONQUER’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/dg/9g8hxb3n1wbdv89mc5nc5gjw0000gn/T//RtmpUGUpoL/filea6a355a559/CONQUER_1.1.3.tar.gz’ had non-zero exit status

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13     magrittr_2.0.1      usethis_2.0.1       devtools_2.4.2      pkgload_1.2.1       R6_2.5.1            rlang_0.4.12       
 [8] fastmap_1.1.0       tools_4.1.0         pkgbuild_1.2.0      sessioninfo_1.1.1   cli_3.0.1           withr_2.4.2         ellipsis_0.3.2     
[15] remotes_2.4.0       rprojroot_2.0.2     lifecycle_1.0.1     crayon_1.4.1        processx_3.5.2      BiocManager_1.30.16 purrr_0.3.4        
[22] callr_3.7.0         fs_1.5.0            ps_1.6.0            curl_4.3.2          testthat_3.0.3      memoise_2.0.0       glue_1.4.2         
[29] cachem_1.0.6        compiler_4.1.0      desc_1.3.0          prettyunits_1.1.1  

[roderickslieker]

Thank you for raising the issue. I will have a look into this and come back to you!

[roderickslieker]

Hi, can you try again? You may also want to install GTEx.Data: devtools::install_github("roderickslieker/GTEx.Data")