[R] problems installing R on Linux

[Rebecca]

Hi everyone,

I am having installation problems, but this is how it all started:
I had some errors running the bioconductor package affyPLM that uses
LAPACK/Blas

	> Pset <- fitPLM(Data)
	Background correcting PM
	Normalizing PM
	Fitting models
	/usr/local/lib/R/bin/exec/R: relocation error:
/usr/local/lib/R/lib/libRlapack.so: undefined symbol: s_copy
	# thrown out of R ....

I was using R version 2.4.0, so I decided to upgrade to 2.4.1 (on
i686-pc-linux-gnu) and to try various configuration options : default,
'--with -lapack' and '--with-blas="lacml"', as described in "appendix A of
the Installation and Admin" manual.

Everytime I configure and make, the message streams seem clean. But the
'make check' is always a disaster (see below), and if I make install
regardless of the make check errors, I get the same "relocation error" from
fitPLM as above (of course the appropriate BioC packages were installed
too).

I believe my problems are dealt with in Appendix A of the Installation and
Administration Guide, but I can't seem to resolve them. Indeed, I have never
been able to use png() for graphics because of some unresolved issues
concerning access to the X11 graphics device, which I suspected had to do
with the libpng and zlib programs (also mentioned in Appendix A).

Some of the postings that I have read on this forum seem to imply that
installation problems are sometimes due to old versions of zlib. I don't
understand this since the recent zlib (1.2.3) is in
"/usr/local/lib/R-2.4.1/src/extra/zlib". Appendix A says, referring to zlib,
that "the versions in the R sources will be compiled in".
But just to be sure, I verified that my system's version is old :
 rpm -q zlib
zlib-1.1.3-25.7
I downloaded and tried to install zlib-1.2.3 using tar, configure, make,
make test, and make install. But when I type "rpm -q zlib", I am still
informed that my version is "zlib-1.1.3-25.7". So, still hopeful, I thought
that I instead would use rpm to install zlib; I found an intermediate rpm
zlib version 1.2.1.2-1.2 and tried "rpm -Uhv zlib-1.2.1.2-1.2.src.rpm". No
diagnostics appear, but when I type "rpm -q zlib", my version is still
"zlib-1.1.3-25.7". I tried to uninstall the old zlib using "rpm -e zlib",
but rpm refuses, saying that there are too many dependencies...

Does anyone have any suggestions?
Thanks!



The 'make check' disaster : 
	make[1]: Entering directory `/usr/local/lib/R-2.4.1/tests'
	make[2]: Entering directory `/usr/local/lib/R-2.4.1/tests'
	make[3]: Entering directory `/usr/local/lib/R-2.4.1/tests/Examples'
	make[4]: Entering directory `/usr/local/lib/R-2.4.1/tests/Examples'
	make[4]: Leaving directory `/usr/local/lib/R-2.4.1/tests/Examples'
	make[4]: Entering directory `/usr/local/lib/R-2.4.1/tests/Examples'
	collecting examples for package 'base' ...
	make[5]: Entering directory `/usr/local/lib/R-2.4.1/src/library'
	 >>> Building/Updating help pages for package 'base'
	     Formats: text html latex example
	make[5]: Leaving directory `/usr/local/lib/R-2.4.1/src/library'
	running code in 'base-Ex.R' ...make[4]: *** [base-Ex.Rout] Error 1
	make[4]: Leaving directory `/usr/local/lib/R-2.4.1/tests/Examples'
	make[3]: *** [test-Examples-Base] Error 2
	make[3]: Leaving directory `/usr/local/lib/R-2.4.1/tests/Examples'
	make[2]: *** [test-Examples] Error 2
	make[2]: Leaving directory `/usr/local/lib/R-2.4.1/tests'
	make[1]: *** [test-all-basics] Error 1
	make[1]: Leaving directory `/usr/local/lib/R-2.4.1/tests'
	make: *** [check] Error 2


I don't really *know* if the configure results are "clean". Here is a subset
of the configure results (that may be suspect) :

	checking build system type... i686-pc-linux-gnu	
	checking host system type... i686-pc-linux-gnu 
	. . . 
	checking for cblas_cdotu_sub in vecLib framework... no
	checking iconv.h usability... yes
	checking iconv.h presence... yes
	checking for iconv.h... yes
	checking for iconv... yes
	checking whether iconv() accepts "UTF-8", "latin1" and "UCS-*"...
yes
	checking for iconvlist... no
	. . .
	checking for g77... g77
	checking whether we are using the GNU Fortran 77 compiler... yes
	checking whether g77 accepts -g... yes
	checking for g++... g++
	checking whether we are using the GNU C++ compiler... yes
	checking whether g++ accepts -g... yes
	checking how to run the C++ preprocessor... g++ -E
	checking whether __attribute__((visibility())) is supported... no
	checking whether gcc accepts -fvisibility... no
	checking whether g77 accepts -fvisibility... no
	. . .
	checking if libtool supports shared libraries... yes
	checking whether to build shared libraries... yes
	checking whether to build static libraries... no
	. . .
	checking floatingpoint.h usability... no
	checking floatingpoint.h presence... no
	checking for floatingpoint.h... no
	. . .
	checking ieee754.h usability... yes
	checking ieee754.h presence... yes
	checking for ieee754.h... yes
	checking ieeefp.h usability... no
	checking ieeefp.h presence... no
	checking for ieeefp.h... no
	. . .
	checking for dummy main to link with Fortran libraries... none
	. . .
	checking whether isfinite is declared... no
	. . .
	checking for mkdtemp... no
	. . .
	checking whether mkdtemp is declared... no
	. . .
	checking for special C compiler options needed for large files... no
	checking for _FILE_OFFSET_BITS value needed for large files... 64
	checking for _LARGE_FILES value needed for large files... no
	checking for _LARGEFILE_SOURCE value needed for large files... no
	checking for fseeko... (cached) yes
	checking whether KERN_USRSTACK sysctl is supported... no
	checking for visible __lib_stack_end... yes
	. . .
	
	checking for g77... g77
	checking whether we are using the GNU Fortran compiler... yes
	checking whether g77 accepts -g... yes
	. . .
	checking for bison... no
	checking for CFPreferencesCopyAppValue... (cached) no
	checking for CFLocaleCopyCurrent... (cached) no
	checking whether NLS is requested... yes
	checking whether included gettext is requested... no
	checking for GNU gettext in libc... no
	checking for GNU gettext in libintl... no
	. . .
	R is now configured for i686-pc-linux-gnu
  	Source directory:          .
  	Installation directory:    /usr/local
  	C compiler:                gcc  -g -O2
  	Fortran 77 compiler:       g77  -g -O2
  	C++ compiler:              g++  -g -O2
  	Fortran 90/95 compiler:    g77 -g -O2
  	Interfaces supported:      X11, tcltk
  	External libraries:        readline
  	Additional capabilities:   PNG, JPEG, iconv, MBCS, NLS
  	Options enabled:           shared BLAS, R profiling
  	Recommended packages:      yes