Hi there! I am trying to install Bioconductor on a self-compiled version of R on a ia64 machine, using the icc 11.1. However I get a very weird compilation error (I removed uninformative lines from the output): > biocLite("preprocessCore") Using R version 2.11.1, biocinstall version 2.6.7. Installing Bioconductor version 2.6 packages: [1] "preprocessCore" [... snip ... ] * installing *source* package 'preprocessCore' ... checking for gcc... /opt/intel/Compiler/11.1/059/bin/ia64/icc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /opt/intel/Compiler/11.1/059/bin/ia64/icc accepts -g... yes checking for /opt/intel/Compiler/11.1/059/bin/ia64/icc option to accept ISO C89... none needed checking for pthread_create in -lpthread... yes checking if we can use pthreads... yes checking if PTHREAD_STACK_MIN is defined... yes configure: creating ./config.status config.status: creating src/Makevars [... snip ...] /opt/intel/Compiler/11.1/059/bin/ia64/icc -std=c99 -I/bioinf_ag/work/unterthiner/R-2.11.1/include -I/usr/local/include -mp -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -std=c99 -c R_subColSummarize.c -o R_subColSummarize.o icc: command line remark #10010: option '-mp' is deprecated and will be removed in a future release. See '-help deprecated' R_subColSummarize.c(83): warning #1011: missing return statement at end of non-void function "subColSummarize_avg_log_group" } ^ R_subColSummarize.c(113): error: identifier "PTHREAD_STACK_MIN" is undefined size_t stacksize = PTHREAD_STACK_MIN + 0x4000; [... snip ... ] I found this really puzzling, since the following piece of code compiles without problems: #include <pthread.h> #include <limits.h> #include <stdio.h> int main() { printf("%d\n", PTHREAD_STACK_MIN); return 0; } (I later noticed that a similar minimal-code example was used in the ./configure-script for the package to check for PTHREAD_STACK_MIN-functionality) Does anyone have any pointers as to why this behavior occurs or more importantly what can be done about it? cheers Thomas