Just to follow up with my question about R extensions failing sanity
check. I wrote my own sanity check tester. The extensions flagged by EB
as failing were installed and loaded without errors. test script is
inline, Easyconfig is in github.
#!/bin/bash
list='RcppArmadillo data.table batchtools Hmisc scidb taxize rms TraMineR
csvy rio car cvAUC mediation mlr unbalanced extRemes qgraph diveRsity
regtools partools alr3 haplo.stats its tables dbplyr sparklyr'
for pkg in $list; do
echo R package $pkg
Rscript -e "if(\"$pkg\" %in% rownames(installed.packages()) == FALSE) {
stop(\"error\") }"
if [ $? != 0 ]; then
echo Package $pkg Not installed;
fi
done
this is a link to my Easyconfig:
easybuild-life-sciences
<https://github.com/FredHutch/easybuild-life-sciences>/fh_easyconfigs
<https://github.com/FredHutch/easybuild-life-sciences/tree/master/fh_easyconfigs>
/*R-3.5.1-foss-2016b-fh1.eb*
John Dey
[email protected]
