[Rd] Problem building R 2.10 release

From: dshih <david.shih_at_utoronto.ca>
Date: Thu, 12 Nov 2009 22:57:46 -0800 (PST)

Hi,

I am having problem building R 2.10, and it does not seem anyone else is having a similar problem...

My system information:

uname -m = x86_64
uname -r = 2.6.31-ARCH
uname -s = Linux

gcc (GCC) 4.4.1
icc (ICC) 11.0 20081105

The first problem I encounter seems to be with icc and wctype.h during ./configure.

export CC="icc -std=c99"
export CXX=icpc
export OBJC="icc -std=c99"
export FC=ifort
export CFLAGS="-mssse3 -g -O3 -wd188 -ip" export CXXFLAGS="-mssse3 -g -O3 -no-gcc" export OBJCFLAGS=-"-mssse3 -g -O3"
export FCFLAGS="-mssse3 -g -O3 -mp"

./configure --with-system-zlib --with-system-bzlib --with-system-pcre
--with-blas=/usr/local/lib/libgoto_penrynp-r1.26.so
--with-lapack=/usr/local/lib/liblapack.so
--with-readline=/usr/lib/libreadline.so --with-jpeglib=/usr/lib/libjpeg.so.7

The error:
checking wchar.h usability... yes
checking wchar.h presence... yes
checking for wchar.h... yes
checking wctype.h usability... no

checking wctype.h presence... yes
configure: WARNING: wctype.h: present but cannot be compiled
configure: WARNING: wctype.h:     check for missing prerequisite headers?
configure: WARNING: wctype.h: see the Autoconf documentation
configure: WARNING: wctype.h:     section "Present But Cannot Be Compiled"
configure: WARNING: wctype.h: proceeding with the preprocessor's result
configure: WARNING: wctype.h: in the future, the compiler will take
precedence
configure: WARNING:     ## ----------------------------------- ##
configure: WARNING:     ## Report this to r-bugs_at_R-project.org ##
configure: WARNING:     ## ----------------------------------- ##
checking for wctype.h... yes
checking whether mbrtowc exists and is declared... yes
checking whether wcrtomb exists and is declared... yes
checking whether wcscoll exists and is declared... yes
checking whether wcsftime exists and is declared... yes
checking whether wcstod exists and is declared... yes
checking whether mbstowcs exists and is declared... yes
checking whether wcstombs exists and is declared... yes
checking whether wctrans exists and is declared... no
checking whether iswblank exists and is declared... no
checking whether wctype exists and is declared... no checking whether iswctype exists and is declared... no configure: error: Support for MBCS locales is required.

wctype.h appears to be usable when I declare export CC=gcc

However, I encountered another problem during make. I think it is because I built the lapack libraries using intel compilers.

sparseQR.o: In function `sparseQR_coef':                                           
sparseQR.c:(.text+0x52a): undefined reference to `Rf_protect'                      
sparseQR.c:(.text+0x53a): undefined reference to `Rf_install'                      
sparseQR.c:(.text+0x54f): undefined reference to `R_do_slot'                       
sparseQR.c:(.text+0x55f): undefined reference to `Rf_install'                      
sparseQR.c:(.text+0x574): undefined reference to `R_do_slot'                       
sparseQR.c:(.text+0x5aa): undefined reference to `Rf_install'                      
sparseQR.c:(.text+0x5bf): undefined reference to `R_do_slot'                       
sparseQR.c:(.text+0x602): undefined reference to `R_do_slot'                       
sparseQR.c:(.text+0x60a): undefined reference to `INTEGER'                         
sparseQR.c:(.text+0x61a): undefined reference to `INTEGER'                         
sparseQR.c:(.text+0x62a): undefined reference to `LENGTH'
sparseQR.c:(.text+0x65a): undefined reference to `R_do_slot'
sparseQR.c:(.text+0x662): undefined reference to `REAL'
sparseQR.c:(.text+0x69a): undefined reference to `R_CheckStack'
sparseQR.c:(.text+0x69f): undefined reference to `R_CheckStack'
sparseQR.c:(.text+0x6b8): undefined reference to `R_do_slot'
sparseQR.c:(.text+0x6c0): undefined reference to `REAL'
sparseQR.c:(.text+0x6df): undefined reference to `R_do_slot'
sparseQR.c:(.text+0x6e7): undefined reference to `INTEGER'
sparseQR.c:(.text+0x6f6): undefined reference to `Rf_install'
sparseQR.c:(.text+0x70b): undefined reference to `R_do_slot'
sparseQR.c:(.text+0x713): undefined reference to `REAL'
sparseQR.c:(.text+0x7c5): undefined reference to `Rf_unprotect'
sparseQR.o: In function `sparseQR_resid_fitted':
sparseQR.c:(.text+0x801): undefined reference to `Rf_protect'
sparseQR.c:(.text+0x811): undefined reference to `Rf_install'
sparseQR.c:(.text+0x823): undefined reference to `R_do_slot'
sparseQR.c:(.text+0x866): undefined reference to `R_do_slot'
sparseQR.c:(.text+0x86e): undefined reference to `INTEGER'
sparseQR.c:(.text+0x88b): undefined reference to `R_do_slot'
sparseQR.c:(.text+0x893): undefined reference to `INTEGER'
sparseQR.c:(.text+0x8b7): undefined reference to `Rf_asLogical'
sparseQR.c:(.text+0x8d3): undefined reference to `R_do_slot'
sparseQR.c:(.text+0x8db): undefined reference to `REAL'
sparseQR.c:(.text+0x8eb): undefined reference to `Rf_install'
sparseQR.c:(.text+0x8fd): undefined reference to `R_do_slot'
sparseQR.c:(.text+0x905): undefined reference to `REAL'
sparseQR.c:(.text+0x90e): undefined reference to `R_CheckStack'
sparseQR.c:(.text+0x9f1): undefined reference to `Rf_unprotect'
/home/katana/builds/R-2.10.0/lib/libRlapack.so: undefined reference to `xerbla_'
make[3]: *** [Matrix.so] Error 1
make[3]: Leaving directory `/tmp/Rtmp0FGSqu/R.INSTALL327b23c6/Matrix/src' ERROR: compilation failed for package 'Matrix'

I had been able to compile R 2.9.1 using icc. There did not appear to be an issue with wctype.h back then.

Is there any way for me to compile R 2.10 using icc? There are other programs on the lapack libraries I built with icc.

Thanks,
--

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