The package provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database
Hello! I have an updated version of R and Bioconductor. paxtoolsr fails with a segmentation fault with installation from biocLite("paxtoolsr"). All of the prerequisites are installed and R CMD javareconf command has been run. Please let me know which log information would be helpful.
(R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
> library(devtools)
> install_github("BioPAX/paxtoolsr")
Downloading GitHub repo BioPAX/paxtoolsr@master
from URL https://api.github.com/repos/BioPAX/paxtoolsr/zipball/master
Installing paxtoolsr
'/opt/maths/R/R-3.4.0/home/bin/R' --no-site-file --no-environ --no-save \
--no-restore --quiet CMD INSTALL \
'/tmp/Rtmpb9C8gU/devtools17b13e9ba7c8/BioPAX-paxtoolsr-3559497' \
--library='/opt/maths/R/R-3.4.0/home/library' --install-tests
* installing *source* package ‘paxtoolsr’ ...
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
sh: line 1: 6088 Segmentation fault '/opt/maths/R/R-3.4.0/home/bin/R' --no-save --slave 2>&1 < '/tmp/RtmppSfPL0/file17c658a60e1e'
ERROR: loading failed
* removing ‘/opt/maths/R/R-3.4.0/home/library/paxtoolsr’
Installation failed: Command failed (1)
Hello! I have an updated version of R and Bioconductor. paxtoolsr fails with a segmentation fault with installation from biocLite("paxtoolsr"). All of the prerequisites are installed and R CMD javareconf command has been run. Please let me know which log information would be helpful.