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 > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > 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, [EMAIL PROTECTED] 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 ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
