[R] problems installing R on Linux

Prof Brian Ripley ripley at stats.ox.ac.uk
Wed Feb 7 10:07:24 CET 2007 

We don't know what 'Linux' is here.  What Linux distribution, what are 
your C and Fortran compilers (in detail, e.g. from gcc --version and g77 
--version)?

We need to see the tail of tests/Examples/base-Ex.Rout.fail to know what 
went wrong.

If you can supply those pieces of information we can begin to help.
(But zlib is a red herring: at most it affects the png() device.)


On Wed, 7 Feb 2007, Rebecca wrote:

> 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
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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