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
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 > > ______________________________________________ > R-help at stat.math.ethz.ch 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, 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
Hi, in general Prof. Ripley is right that more information is needed, but here's a hint that you might try first.> /usr/local/lib/R/bin/exec/R: relocation error: > /usr/local/lib/R/lib/libRlapack.so: undefined symbol: s_copy > # thrown out of R ....Could simply mean that the /usr/local/lib/R/lib/libRlapack.so is not found, and considering that you say make was alright, then maybe it was make install that did not copy it. But what you can try, try running R from the directory where you compiled it in: get a fresh R tarball, untar it. configure it with "./configure --prefix=`pwd`" and do make. Do not do make install, simply run it from the bin dir here. You might need to install the packages though if they are not in R_LIBS. This will ensure that all files are there, nothing was left behind by make install.> rpm -q zlib > zlib-1.1.3-25.7After you installed zlib with ./configure && make && make install, your rpm request will not give you the just installed zlib version because it refers to a different source. If by doing make install you overwrite the files from zlib*.rpm, it will still report the version written in the rpm database. And you cannot uninstall this rpm without braking half of your system dependencies. Best, Oleg -- Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466