installation of package ‘depmap’ had non-zero exit status

[Mango1235]

if(!"depmap" %in% installed.packages()) BiocManager::install("depmap") remotes::install_github("UCLouvain-CBIO/depmap", ref = "4a9f52ed6cf9c3821891ebdd9db317194d6518c9") BiocManager::install("depmap",version = "3.17")

these three methods didn't work.

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/ Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16 ucrt) Installing package(s) 'depmap' installing the source package ‘depmap’

trying URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/depmap_1.14.0.tar.gz' Content type 'application/x-gzip' length 1379521 bytes (1.3 MB) downloaded 1.3 MB

• installing source package 'depmap' ... using staged installation R inst byte-compile and prepare package for lazy loading ** help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use Error: package or namespace load failed for 'depmap': .onLoad failed in loadNamespace() for 'depmap', details: call: h(simpleError(msg, call)) error: error in evaluating the argument 'x' in selecting a method for function 'query': Invalid Cache: sqlite file Hub has not been added to cache Run again with 'localHub=FALSE' Error: loading failed Execution halted ERROR: loading failed
• removing 'D:/00000/R4.3.1/R-4.3.1/library/depmap'

The downloaded source packages are in ‘C:\Users\M\AppData\Local\Temp\RtmpaeE4pj\downloaded_packages’ Warning message: In install.packages(...) : installation of package ‘depmap’ had non-zero exit status

[lgatto]

This could be linked to network issues - you were able to download the package, but then, can't access ExperimentHub (that hosts the data).

Could you try again. The following is enough

BiocManager::install("depamap")

[Mango1235]

Thanks for your suggestion. I tried several times, but failed with the same error. It's weird, because I could install other bio-conductor packages using the same method, and the same network. I tried to install locally in R Studio, but it didn't work as well. Maybe I need a better network environment, or any other suggestions? Thanks!

install.packages("D:/CRISPR_in_R/depmap_1.14.0.tar.gz", repos = NULL, type = "source")

• installing source package 'depmap' ... using staged installation R inst byte-compile and prepare package for lazy loading ** help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use Error: package or namespace load failed for 'depmap': .onLoad failed in loadNamespace() for 'depmap', details: call: h(simpleError(msg, call)) error: error in evaluating the argument 'x' in selecting a method for function 'query': Invalid Cache: sqlite file Hub has not been added to cache Run again with 'localHub=FALSE' Error: loading failed Execution halted ERROR: loading failed
• removing 'D:/00000/R4.3.1/R-4.3.1/library/depmap' Warning in install.packages : installation of package ‘D:/CRISPR_in_R/depmap_1.14.0.tar.gz’ had non-zero exit status

[lgatto]

Could you try to delete the ExperimentHub cache. You can find it with tools::R_user_dir("ExperimentHub")

[homerzpq]

I am also meeting the same problem when i install depmap. It can not connect to Experimenthub server. I could not use Experimenthub directly. But when I run this code:

proxy <- httr::use_proxy(Sys.getenv('http_proxy'))
httr::set_config(proxy)
ExperimentHub::setExperimentHubOption("PROXY", proxy)

this could make Experimenthub work, but R still not able to install depmap. Have you solved the problem?

[lgatto]

What I think happens is that the installation fails because the http proxy isn't set when installing depmap. Could you try to set these options in your .Rprofile.

[homerzpq]

It's done when I followed your advice! Thanks

[Mango1235]

Sorry for late reply. I tried the same method, but still failed to install the "depmap" package. Could you please share the code with me. Thanks!

[Mango1235]

Sorry for late reply. I tried the same method, but still failed to install the "depmap" package. Could you please share the code with me. Thanks! @homerzpq