I am currently trying to run some R code that originally ran under 2.11.0 . The version of R that I am using 2.14.1 does not run the code. I am unfamiliar with R and how backwards compatible it is. (My issue could have nothing to do versions for all I know; I will be happy to learn that it is something that I am doing wrong.) The rest of the code is irrelevant; my installs are failing even when I run by themselves.
#these fail
install.packages("gtools",repos="http://cran.r-project.org")
install.packages("minet", repos="http://cran.r-project.org")
#these work
install.packages("psych", repos="http://cran.r-project.org")
install.packages("qvalue",repos="http://cran.r-project.org")
install.packages("R2HTML",repos="http://cran.r-project.org")
I have tried other installation methods in addition to the one I listed above. I have tried installing and compiling earlier versions of gtools and minet. I have tried getting current versions of the package from other repos (biocLite). However all installation attempts produce identical failures. For a little more background, I am not a superuser on the machine that I am trying to run this code on. I can ask the person who is the superuser for small favors (ones that do not affect other users of the machine). I have been able to install other packages just fine; though as I said early if I have a simple problem I will be pleased. Here are some failures.
* installing *source* package ‘gtools’ ...
** libs
Warning: R include directory is empty -- perhaps need to install R-devel.rpm or similar
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c setTCPNoDelay.c -o setTCPNoDelay.o
setTCPNoDelay.c:1:15: error: R.h: No such file or directory
setTCPNoDelay.c:2:24: error: Rinternals.h: No such file or directory
setTCPNoDelay.c: In function ‘checkStatus’:
setTCPNoDelay.c:66: warning: implicit declaration of function ‘strncpy’
setTCPNoDelay.c:66: warning: incompatible implicit declaration of built-in function ‘strncpy’
setTCPNoDelay.c:72: warning: implicit declaration of function ‘strerror’
setTCPNoDelay.c:72: warning: passing argument 2 of ‘strncpy’ makes pointer from integer without a cast
make: *** [setTCPNoDelay.o] Error 1
ERROR: compilation failed for package ‘gtools’
This error arose because the particular machine that i was logged into did not have the development headers. My system admin directed me to login into a different machine that did. What was rather odd about this is that R would allow me to install some packages without the headers. If you intermittently get this complaint when attempting to install R packages, it may have to do with the development headers as Joshua Ulrich mention in the comments.