PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference
GNU Affero General Public License v3.0
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Cannot install Kaphi on cluster (CentOS) #140

Closed mavino closed 5 years ago

mavino commented 5 years ago

After having installed all the necessary packages I ran:

sudo R CMD INSTALL pkg

and I got:

* installing to library ‘/usr/lib64/R/library’
* installing *source* package ‘Kaphi’ ...
** libs
make: Nothing to be done for `all'.
installing to /usr/lib64/R/library/Kaphi/libs
** R
Error in parse(outFile) : 
  /home/marianoavino/Kaphi/pkg/R/treekernel.R:210:29: unexpected '{'
209:   # use reorder() instead of postorder() to support `ape` version < 5.0
210:   for (n1 in .postorder(t1) {
                                 ^
ERROR: unable to collate and parse R files for package ‘Kaphi’
* removing ‘/usr/lib64/R/library/Kaphi’
mavino commented 5 years ago

OK after I ran this command to update Kaphi repository and try to reinstall it on BEVi

git pull origin master
sudo R CMD INSTALL pkg

I got:

* installing to library ‘/usr/lib64/R/library’
* installing *source* package ‘Kaphi’ ...
** libs
make: Nothing to be done for `all'.
installing to /usr/lib64/R/library/Kaphi/libs
** R
Error in parse(outFile) : 
  /home/marianoavino/Kaphi/pkg/R/treekernel.R:213:84: unexpected ')'
212:       if (V(g1)$production[n1] == V(g2)$production[n2]) {
213:         res = lambda * exp(-1/rbf.var * (V(g1)$ssq.bl[n1] + V(g2)$ssq.bl[n2] - 2 * )
                                                                                        ^
ERROR: unable to collate and parse R files for package ‘Kaphi’