Installing or Compiling EDGE
On Oct 11, 2011, at 6:49 AM, Morri Feldman wrote:
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,
You, you can't store 64-bit pointer into a 32-bit integer so that code won't work in 64-bit mode.
but I can't figure out how to edit the Makefile to force compilation as i386.
The package is a bit of a mess - for several reasons. In has no global CC definition (and always overrides the system one), so you'll need to edit src/Makevars as well as all other Makefiles and add -arch i386 to the compiler lines. Also you'll need to edit src/Makevars and replace the RCMD=R line for Darwin with RCMD=R --arch i386
Once you have done that, you're almost there - you can compile it, but you'll also need to edit edge.r and fix the version check (it is so old that it considers only one digit of the minor number so 2.14 < 2.4 in that logic).
That's it. Below is the diff of all needed changes.
Cheers,
Simon
diff -ru edge_1.1.290/edge.r edge_1.1.290-i386/edge.r
--- edge_1.1.290/edge.r 2007-07-06 15:12:38.000000000 -0400
+++ edge_1.1.290-i386/edge.r 2011-10-11 10:43:40.000000000 -0400
@@ -8,7 +8,7 @@
## this or any files in this software package.
#########################################################
Rversion <- R.Version()
-if(Rversion$major < "2" || as.numeric(substring(Rversion$minor, 0, 1)) < 4)
+if(Rversion$major < "2" || as.numeric(gsub("\\..*","",Rversion$minor)) < 4)
{
stop("R version greater than or equal to 2.4.0 required")
}
diff -ru edge_1.1.290/src/Makevars edge_1.1.290-i386/src/Makevars
--- edge_1.1.290/src/Makevars 2006-03-07 12:50:29.000000000 -0500
+++ edge_1.1.290-i386/src/Makevars 2011-10-11 10:24:48.000000000 -0400
@@ -28,7 +28,7 @@
OS_FLAGS=-DMAC_OS_X -Dassert\(expr\)= -fPIC
PKG_KNNLIBS=-L/sw/lib
SOEXT=.so
-RCMD=R
+RCMD=R --arch i386
RCMD_CMD=CMD
endif
@@ -58,8 +58,8 @@
PKG_CXXFLAGS=$(OS_FLAGS) $(INCLUDEDIRS) $(EDGELIBVERSION) $(DEBUG) -D__STDC_LIMIT_MACROS -Wall
PKG_CFLAGS=$(OS_FLAGS) $(INCLUDEDIRS) $(EDGELIBVERSION) $(DEBUG) -D__STDC_LIMIT_MACROS -Wall
-CC=gcc
+CC=gcc -arch i386
CCOPTS=-c -g
-CXX=g++
+CXX=g++ -arch i386
CXXOPTS=-c -g
diff -ru edge_1.1.290/src/cluster/TestFramework/Makefile edge_1.1.290-i386/src/cluster/TestFramework/Makefile
--- edge_1.1.290/src/cluster/TestFramework/Makefile 2005-09-23 18:22:56.000000000 -0400
+++ edge_1.1.290-i386/src/cluster/TestFramework/Makefile 2011-10-11 10:27:13.000000000 -0400
@@ -1,5 +1,5 @@
SRCBASE=../..
-CC=g++
+CC=g++ -arch i386
CCOPTS=-c -g
LIBOBJECTS=UnitTestRunner.o UnitTestClass.o
diff -ru edge_1.1.290/src/cluster/Tests/Makefile edge_1.1.290-i386/src/cluster/Tests/Makefile
--- edge_1.1.290/src/cluster/Tests/Makefile 2006-03-02 14:50:12.000000000 -0500
+++ edge_1.1.290-i386/src/cluster/Tests/Makefile 2011-10-11 10:26:12.000000000 -0400
@@ -1,7 +1,7 @@
SRCBASE=../..
include ../../Makevars
-CC=g++
+CC=g++ -arch i386
CCOPTS=-I.. -I../TestFramework -I../../threads -D__STDC_LIMIT_MACROS -ftrapv
LINKOPTS=-L../TestFramework -L.. -L../../threads
diff -ru edge_1.1.290/src/threads/Tests/Makefile edge_1.1.290-i386/src/threads/Tests/Makefile
--- edge_1.1.290/src/threads/Tests/Makefile 2005-09-23 18:22:56.000000000 -0400
+++ edge_1.1.290-i386/src/threads/Tests/Makefile 2011-10-11 10:27:38.000000000 -0400
@@ -1,7 +1,7 @@
SRCBASE=../..
include ../../Makevars
-CC=g++
+CC=g++ -arch i386
CCOPTS=-c -g
OBJECTS=main.o
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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