I know very little about R and am currently attempting to run a pre-written R script.
My key issue is that one of the libraries (lme4 - linear mixed-effects library) doesn't seem to be installing.
The script starts with the following dependencies -
options(repos=structure(c(CRAN="http://cran.cnr.berkeley.edu/")))
library(rbundler)
bundle('.')
library(lme4)
And the output is as follows, with the error occurring at the very end.
Loading required package: devtools
Attaching package: ‘rbundler’
The following object is masked from ‘package:devtools’:
install_version
R_LIBS_USER=~/R/x86_64-redhat-linux-gnu-library/3.0:./.Rbundle
.libPaths() =/home/jeeves/my_script/.Rbundle/usr/lib64/R/library/usr/share/R/library
Bundling package /home/jeeves/my_script dependencies into library ./.Rbundle
Downloading lme4_1.1-7.tar.gz from http://cran.cnr.berkeley.edu/src/contrib/lme4_1.1-7.tar.gz
Installing package from /tmp/Rtmp3SzgSS/lme4_1.1-7.tar.gz
Installing lme4
'/usr/lib64/R/bin/R' --vanilla CMD INSTALL '/tmp/Rtmp3SzgSS/lme4' \
--library='/home/jeeves/my_script/.Rbundle' --with-keep.source \
--install-tests
* installing *source* package 'lme4' ...
** package 'lme4' successfully unpacked and MD5 sums checked
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/home/jeeves/my_script/.Rbundle/Rcpp/include" -I"/home/jeeves/my_script/.Rbundle/RcppEigen/include" -DNDEBUG -DEIGE
N_DONT_VECTORIZE -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c external.cpp -o external.o
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/home/jeeves/my_script/.Rbundle/Rcpp/include" -I"/home/jeeves/my_script/.Rbundle/RcppEigen/include" -DNDEBUG -DEIGE
N_DONT_VECTORIZE -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c glmFamily.cpp -o glmFamily.o
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/home/jeeves/my_script/.Rbundle/Rcpp/include" -I"/home/jeeves/my_script/.Rbundle/RcppEigen/include" -DNDEBUG -DEIGE
N_DONT_VECTORIZE -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c mcmcsamp.cpp -o mcmcsamp.o
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/home/jeeves/my_script/.Rbundle/Rcpp/include" -I"/home/jeeves/my_script/.Rbundle/RcppEigen/include" -DNDEBUG -DEIGE
N_DONT_VECTORIZE -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c optimizer.cpp -o optimizer.o
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/home/jeeves/my_script/.Rbundle/Rcpp/include" -I"/home/jeeves/my_script/.Rbundle/RcppEigen/include" -DNDEBUG -DEIGE
N_DONT_VECTORIZE -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c predModule.cpp -o predModule.o
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/home/jeeves/my_script/.Rbundle/Rcpp/include" -I"/home/jeeves/my_script/.Rbundle/RcppEigen/include" -DNDEBUG -DEIGE
N_DONT_VECTORIZE -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c respModule.cpp -o respModule.o
g++ -m64 -shared -L/usr/local/lib64 -o lme4.so external.o glmFamily.o mcmcsamp.o optimizer.o predModule.o respModule.o -L/usr/lib64/R/lib -lR
installing to /home/jeeves/my_script/.Rbundle/lme4/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'lme4'
finding HTML links ... done
Dyestuff html
GHrule html
GQN html
GQdk html
InstEval html
NelderMead-class html
Nelder_Mead html
Pastes html
Penicillin html
VarCorr html
VerbAgg html
bootMer html
cake html
cbpp html
confint.merMod html
devcomp html
drop1.merMod html
dummy html
expandDoubleVerts html
findbars html
fixef html
fortify html
getME html
glmFamily-class html
glmFamily html
glmer html
glmer.nb html
golden-class html
golden html
grouseticks html
isNested html
isREML html
lmList-class html
lmList html
lmResp-class html
lmResp html
lme4-package html
lmer html
lmerControl html
finding level-2 HTML links ... done
merMod-class html
merPredD-class html
merPredD html
mkMerMod html
mkReTrms html
mkRespMod html
mkVarCorr html
mkdevfun html
modular html
ngrps html
nlformula html
nlmer html
nloptwrap html
nobars html
plot.merMod html
plots.thpr html
predict.merMod html
profile-methods html
pvalues html
ranef html
rePos-class html
rePos html
refit html
refitML html
residuals.merMod html
sigma html
simulate.merMod html
sleepstudy html
subbars html
varianceProf html
** building package indices
** installing vignettes
'PLSvGLS.Rnw'
'Theory.Rnw'
'lmer.Rnw' using 'UTF-8'
Error in match.arg(options$results, c("verbatim", "tex", "hide")) :
'arg' should be one of "verbatim", "tex", "hide"
ERROR: installing vignettes failed
* removing '/home/jeeves/my_script/.Rbundle/lme4'
Error: Command failed (1)
Execution halted
I tried looking up anything related to match.arg and where it might be setting an option other than "verbatim", "tex", "hide" but had no luck.
Any ideas on what could be the source of the error?
Thanks!
