Hello, I hope this is an appropriate mailing list for my question. If not, please excuse me and point me towards another forum if possible.
I'm trying to install a microarray analysis software package called EDGE which relies on R. The package is available as binaries or source code from http://www.genomine.org/edge/ . I'm using R from R-2.13.2.pkg, and tcltk-8.5.5-x11.dmg. I am running OSX Lion and when I tried to install the binaries from edge_intel_1.1.290.tar.tar.gz, I had several failures. After working through some trivial problems I found out that knnimpute.so, one of the two precompiled binaries in this package, is for PPC not intel. Next, I decided to try and compile the package myself. I installed Xcode Version 4.1 (4B103), MacTeX-2011.mpkg and gfortran-lion-5666-3.pkg. After cd to the src/ directory I run make and get the following error. ********************************** g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -DMAC_OS_X -Dassert\(expr\)= -fPIC -I/Library/Frameworks/R.framework/Resources -I./threads -I./cluster -I/Library/Frameworks/R.framework/Resources/include -I. -DEDGE_LIBRARY_VERSION=\"1.0.\" -D__STDC_LIMIT_MACROS -Wall -fPIC -g -O2 -c Rintf_threads.cpp -o Rintf_threads.o Rintf_threads.cpp: In function SEXPREC* GetProgressValues(SEXPREC*): Rintf_threads.cpp:66: error: cast from _opaque_pthread_t* to int loses precision make[2]: *** [Rintf_threads.o] Error 1 build failed make[1]: *** [edge.so] Error 1 make: *** [all] Error 2 ********************************** The relevant section of code in Rintf_threads.ccp is: ********************************** PROTECT(sval=NEW_INTEGER(1)); INTEGER_POINTER(sval)[0] = (int)ppt->GetThreadId(); // This line is the problem SET_STRING_ELT(snames, i, CREATE_STRING_VECTOR("threadid")); SET_VECTOR_ELT(slist, i, sval); i++; ********************************** This same construction, converting THREAD_ID_T to int, is also used at line 525 of RInterfaces.cpp and line 179 of Rintf_cluster.cpp. My guess is that the problem is caused by compiling as x86_64, but I can't figure out how to edit the Makefile to force compilation as i386. I've contacted one of the authors of the software, but they haven't gotten back to me yet. I will greatly appreciate any help you can provide. Best and Thank You, Morri Feldman [[alternative HTML version deleted]]
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