I’m trying to install rstan on a CentOS cluster so that I can run map_rect, but I’m running into problems with the installation. It appears it might have less to do with rstan itself though, but one of its dependencies, processx. If anyone has any suggestions on how to remedy this, please let me know! The error message is the following:
* installing *source* package ‘processx’ ...
** package ‘processx’ successfully unpacked and MD5 sums checked
** libs
icc -std=gnu99 -g -O2 -std=c99 -Wall tools/px.c -o tools/px
icc -std=gnu99 -g -O2 -std=c99 supervisor/supervisor.c supervisor/utils.c \
-o supervisor/supervisor
icc -std=gnu99 -I/share/apps/r/3.4.2/intel/lib64/R/include -DNDEBUG -I/share/apps/intel/17.0.1/include -I/share/apps/r/3.4.2/intel/lib64/R/include -I/share/apps/intel/17.0.1/mkl/include -I/share/apps/jdk/1.8.0_111/include -fpic -g -O2 -std=c99 -c init.c -o init.o
icc -std=gnu99 -I/share/apps/r/3.4.2/intel/lib64/R/include -DNDEBUG -I/share/apps/intel/17.0.1/include -I/share/apps/r/3.4.2/intel/lib64/R/include -I/share/apps/intel/17.0.1/mkl/include -I/share/apps/jdk/1.8.0_111/include -fpic -g -O2 -std=c99 -c poll.c -o poll.o
icc -std=gnu99 -I/share/apps/r/3.4.2/intel/lib64/R/include -DNDEBUG -I/share/apps/intel/17.0.1/include -I/share/apps/r/3.4.2/intel/lib64/R/include -I/share/apps/intel/17.0.1/mkl/include -I/share/apps/jdk/1.8.0_111/include -fpic -g -O2 -std=c99 -c processx-connection.c -o processx-connection.o
icc -std=gnu99 -I/share/apps/r/3.4.2/intel/lib64/R/include -DNDEBUG -I/share/apps/intel/17.0.1/include -I/share/apps/r/3.4.2/intel/lib64/R/include -I/share/apps/intel/17.0.1/mkl/include -I/share/apps/jdk/1.8.0_111/include -fpic -g -O2 -std=c99 -c processx-vector.c -o processx-vector.o
In file included from processx-vector.c(3):
processx-types.h(13): error: identifier "pid_t" is undefined
pid_t *stor_begin;
^
In file included from processx-vector.c(3):
processx-types.h(14): error: identifier "pid_t" is undefined
pid_t *stor_end;
^
In file included from processx-vector.c(3):
processx-types.h(15): error: identifier "pid_t" is undefined
pid_t *end;
^
In file included from processx-vector.c(3):
processx-types.h(24): error: identifier "pid_t" is undefined
void processx_vector_push_back(processx_vector_t *v, pid_t e);
^
In file included from processx-vector.c(3):
processx-types.h(25): error: identifier "pid_t" is undefined
int processx_vector_find(const processx_vector_t *v, pid_t e, size_t from, size_t *idx);
^
In file included from processx-vector.c(3):
processx-types.h(26): error: identifier "pid_t" is undefined
void processx_vector_rooted_tree(pid_t root, const processx_vector_t *nodes,
^
processx-vector.c(8): error: identifier "pid_t" is undefined
v->stor_begin = (pid_t*) R_alloc(alloc_size, sizeof(pid_t));
^
processx-vector.c(8): error: expected an expression
v->stor_begin = (pid_t*) R_alloc(alloc_size, sizeof(pid_t));
^
processx-vector.c(8): error: expected a ";"
v->stor_begin = (pid_t*) R_alloc(alloc_size, sizeof(pid_t));
^
processx-vector.c(21): error: identifier "pid_t" is undefined
pid_t *tmp;
^
processx-vector.c(21): error: identifier "tmp" is undefined
pid_t *tmp;
^
processx-vector.c(24): error: expected an expression
tmp = (pid_t*) S_realloc( (char*) v->stor_begin, size, alloc_size, sizeof(pid_t));
^
processx-vector.c(24): error: expected a ";"
tmp = (pid_t*) S_realloc( (char*) v->stor_begin, size, alloc_size, sizeof(pid_t));
^
processx-vector.c(34): error: identifier "pid_t" is undefined
void processx_vector_push_back(processx_vector_t *v, pid_t e) {
^
processx-vector.c(57): error: identifier "pid_t" is undefined
int processx_vector_find(const processx_vector_t *v, pid_t e, size_t from, size_t *idx) {
^
processx-vector.c(82): error: identifier "pid_t" is undefined
void processx_vector_rooted_tree(pid_t root, const processx_vector_t *nodes,
^
processx-vector.c(95): error: identifier "pid_t" is undefined
pid_t parent = VECTOR(*parents)[i];
^
compilation aborted for processx-vector.c (code 2)
make: *** [processx-vector.o] Error 2
ERROR: compilation failed for package ‘processx’