Omics Academy

> install.packages("RcppEigen") Installing package into ‘/home/xie186/R/x86_64-redhat-linux-gnu-library/3.3’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/src/contrib/RcppEigen_0.3.3.3.0.tar.gz' Content type 'unknown' length 1634023 bytes (1.6 MB) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = downloaded 1.6 MB * installing *source* package ‘RcppEigen’ ... ** package ‘RcppEigen’ successfully unpacked and MD5 sums checked ** libs g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/home/xie186/R/x86_64-redhat-linux-gnu-library/3.3/Rcpp/include" -I../inst/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppEigen.cpp -o RcppEigen.o g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/home/xie186/R/x86_64-redhat-linux-gnu-library/3.3/Rcpp

I encountered this problem when using Bookdown. accepted ! I can't write on file `bioinfBookXIE186.pdf'. (Press Enter to retry, or Control-D to exit; default file extension is `.pdf') Please type another file name for output ! Emergency stop. \AtBegShi@Output ...ipout \box \AtBeginShipoutBox                                                    \fi \fi  l.199 \maketitle ! Emergency stop. \AtBegShi@Output ...ipout \box \AtBeginShipoutBox                                                    \fi \fi  l.199 \maketitle Error: Failed to compile bioinfBookXIE186.tex. See bioinfBookXIE186.log Here is the answer from stackexchange: accepted ! I can't write on file `skills.pdf'. In this case, the error is caused by not having enough memory. The  clone(...) = -1 ENOMEM (Cannot allocate memory)  error from strace prompted me to check my ram usage. Running xelatex with 150M of free ram provokes the write/clone() error. Running with a