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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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installation of package ‘pathfindR’ had non-zero exit status / Error: callr subprocess failed: Invalid parent_resolve callback #93

Closed yotammarton closed 3 years ago

yotammarton commented 3 years ago

Describe the bug Unable to install pathfindR

R Session Information: R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.4

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] processx_3.5.2 compiler_4.1.0 R6_2.5.0 cli_3.0.1 tools_4.1.0 htmltools_0.5.1.1 rstudioapi_0.13
[8] crayon_1.4.1 knitr_1.33 callr_3.7.0 xfun_0.25 digest_0.6.27 ps_1.6.0 rlang_0.4.11
[15] pak_0.1.2.1

Additional context Cannot get pathfindR to install properly, have tried the following code, attached is the returned errors:

install.packages("pathfindR") Warning in install.packages : installation of package ‘pathfindR’ had non-zero exit status

install.packages("pak") # if you have not installed "pak" pak::pkg_install("pathfindR") Error: callr subprocess failed: Invalid parent_resolve callback

Thank you

egeulgen commented 3 years ago

Hey can you try installing via devtools:

install.packages("devtools") # if you have not installed "devtools" 
devtools::install_github("egeulgen/pathfindR")
yotammarton commented 3 years ago

Thanks @egeulgen

install.packages("devtools") # if you have not installed "devtools" devtools::install_github("egeulgen/pathfindR") yields: > devtools::install_github("egeulgen/pathfindR") Downloading GitHub repo egeulgen/pathfindR@HEAD Error in utils::download.file(url, path, method = method, quiet = quiet, : download from 'https://api.github.com/repos/egeulgen/pathfindR/tarball/HEAD' failed

egeulgen commented 3 years ago

this seems to be an issue with the download.file.method option. Maybe try setting it to something else (the default should be "auto"):

options(download.file.method = "libcurl")

If this does not work, please open up an issue on devtools as this is an issue related to that package. Best, -E

yotammarton commented 3 years ago

Thanks, options(download.file.method = "curl") worked for me. (and ofcourse the java installation was missing too)