Error: object 'homologene_download' is not exported by 'namespace:OmnipathR'

[jjacob12]

Hi there, I am struggling to install liana. I initially followed the install instructions on GitHub but got this error:

 remotes::install_github('saezlab/liana')
Error: Failed to install 'unknown package' from GitHub:
  Line starting 'Config/testthat/edit ...' is malformed!

However, this seemed more promising:

git clone https://github.com/saezlab/liana.git

I downloaded it but on attempting to install it from inside the liana directory with install.packages(".", repos = NULL, type = "source") I got this error: ERROR: dependencies 'OmnipathR', 'basilisk.utils', 'basilisk' are not available for package 'liana'

• removing '/gpfs3/well/ludwig/users/ikb229/R/4.1/skylake/liana' Warning message: In install.packages(".", repos = NULL, type = "source") : installation of package '.' had non-zero exit status"

So I successfully installed basilisk.utils, basilisk. and OmnipathR:

> find.package("OmnipathR")
[1] "/gpfs3/well/ludwig/users/ikb229/R/4.2/skylake/OmnipathR"
> find.package("basilisk")
[1] "/gpfs3/apps/eb/2020b/skylake/software/R-bundle-Bioconductor/3.15-foss-2022a-R-4.2.1/basilisk"
> find.package("basilisk.utils")
[1] "/gpfs3/apps/eb/2020b/skylake/software/R-bundle-Bioconductor/3.15-foss-2022a-R-4.2.1/basilisk.utils"

However on then attempting to install liana again, I got this message:

> install.packages(".", repos = NULL, type = "source")
Installing package into '/gpfs3/well/ludwig/users/ikb229/R/4.2/skylake'
(as 'lib' is unspecified)
* installing *source* package 'liana' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object 'homologene_download' is not exported by 'namespace:OmnipathR'
Execution halted
ERROR: lazy loading failed for package 'liana'
* removing '/gpfs3/well/ludwig/users/ikb229/R/4.2/skylake/liana'
Warning message:
In install.packages(".", repos = NULL, type = "source") :
  installation of package '.' had non-zero exit status

So in R I tried:

> library(OmnipathR)
?homologene_download
No documentation for 'homologene_download' in specified packages and libraries:
you could try '??homologene_download'
> ??homologene_download
No vignettes or demos or help files found with alias or concept or
title matching 'homologene_download' using regular expression matching.

These are the modules I am using on an HPC cluster:

[ikb229@rescomp1 liana]$ module load R/4.2.1-foss-2022a 
[ikb229@rescomp1 liana]$ module load R-bundle-Bioconductor/3.15-foss-2022a-R-4.2.1

Session info below:

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /gpfs3/apps/eb/2020b/skylake/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64/libflexiblas.so.3.2

locale:
[1] C

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

loaded via a namespace (and not attached):
[1] compiler_4.2.1 tools_4.2.1    curl_4.3.2     remotes_2.4.2

I can't find a solution. What do you suggest? Thanks!

[deeenes]

Hello, Please update to the latest version of OmnipathR:

remotes::install_github('saezlab/OmnipathR')

[jjacob12]

Thanks. Will try it out and feedback. Appreciate the swift response!

On 7 Apr 2024, at 12:55, deeenes @.***> wrote:

Hello, Please update to the latest version of OmnipathR:

remotes::install_github('saezlab/OmnipathR') — Reply to this email directly, view it on GitHub https://github.com/saezlab/liana/issues/144#issuecomment-2041444745, or unsubscribe https://github.com/notifications/unsubscribe-auth/APEFENFXPISXGR66JP2H4ODY4EX27AVCNFSM6AAAAABF2YYWUWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBRGQ2DINZUGU. You are receiving this because you authored the thread.

[jjacob12]

This has worked and I can launch Liana, but first there were other dependencies that I had to update first, which basically involved updating the tidyverse package. Many thanks!