Hi everyone This is my first post to the list. I had experience installing and using Bioconductor on Linux and Windows systems but I am encountering problems installing Biobase on Solaris running on Sparc. The package compilation works fine, with only a warning warning: implicit declaration of function `__builtin_isnan' the help files are generated but in the end it fails with an error also related __builtin_isnan ** building package indices ... Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/local/lib/R/library/Biobase/libs/Biobase.so': ld.so.1: R: fatal: relocation error: file /usr/local/lib/R/library/Biobase/libs/Biobase.so: symbol __builtin_isnan: referenced symbol not found Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted ERROR: installing package indices failed The machine I am using is a Sun SPARC Victoria Falls SunOS 5.10 Generic_127111-11 sun4v sparc SUNW,T5140 I posted this message to the BioC list and it was suggested that I tried installing any R package that needed compilation. I installed the XML package with no problems. Any help is appreciated. Thanks in advance Paulo
Problem installing Biobase on Solaris
6 messages · Brian Ripley, Paulo Nuin
What compiler is this? This is a compiler issue, not an R one. My guess is that you are mixing gcc (which has __builtin_isnan) and cc (which does not).
On Fri, 5 Sep 2008, Paulo Nuin wrote:
Hi everyone This is my first post to the list. I had experience installing and using Bioconductor on Linux and Windows systems but I am encountering problems installing Biobase on Solaris running on Sparc. The package compilation works fine, with only a warning warning: implicit declaration of function `__builtin_isnan' the help files are generated but in the end it fails with an error also related __builtin_isnan ** building package indices ... Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/local/lib/R/library/Biobase/libs/Biobase.so': ld.so.1: R: fatal: relocation error: file /usr/local/lib/R/library/Biobase/libs/Biobase.so: symbol __builtin_isnan: referenced symbol not found Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted ERROR: installing package indices failed The machine I am using is a Sun SPARC Victoria Falls SunOS 5.10 Generic_127111-11 sun4v sparc SUNW,T5140 I posted this message to the BioC list and it was suggested that I tried installing any R package that needed compilation. I installed the XML package with no problems. Any help is appreciated. Thanks in advance Paulo
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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 I thought of that. We have gcc 3.4.3 installed /gates/sfw10/builds/sfw10-gate/usr/src/cmd/gcc/gcc-3.4.3/configure --prefix=/usr/sfw --with-as=/usr/sfw/bin/gas --with-gnu-as --with-ld=/usr/ccs/bin/ld --without-gnu-ld --enable-languages=c,c++ --enable-shared How to make sure which compiler R is using? Thanks in advance Paulo
Prof Brian Ripley wrote:
What compiler is this? This is a compiler issue, not an R one. My guess is that you are mixing gcc (which has __builtin_isnan) and cc (which does not). On Fri, 5 Sep 2008, Paulo Nuin wrote:
Hi everyone This is my first post to the list. I had experience installing and using Bioconductor on Linux and Windows systems but I am encountering problems installing Biobase on Solaris running on Sparc. The package compilation works fine, with only a warning warning: implicit declaration of function `__builtin_isnan' the help files are generated but in the end it fails with an error also related __builtin_isnan ** building package indices ... Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/local/lib/R/library/Biobase/libs/Biobase.so': ld.so.1: R: fatal: relocation error: file /usr/local/lib/R/library/Biobase/libs/Biobase.so: symbol __builtin_isnan: referenced symbol not found Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted ERROR: installing package indices failed The machine I am using is a Sun SPARC Victoria Falls SunOS 5.10 Generic_127111-11 sun4v sparc SUNW,T5140 I posted this message to the BioC list and it was suggested that I tried installing any R package that needed compilation. I installed the XML package with no problems. Any help is appreciated. Thanks in advance Paulo
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Hi I forgot to paste the compiler output: gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I/usr/local/ssl/include -I/usr/local/pgsql/include -I/usr/local/include/ncurses -I/usr/local/BerkeleyDB.4.2/include -I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include -fPIC -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib -I/usr/local/rrdtool-1.2.19/include -c anyMissing.c -o anyMissing.o anyMissing.c: In function `anyMissing': anyMissing.c:33: warning: implicit declaration of function `__builtin_isnan' gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I/usr/local/ssl/include -I/usr/local/pgsql/include -I/usr/local/include/ncurses -I/usr/local/BerkeleyDB.4.2/include -I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include -fPIC -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib -I/usr/local/rrdtool-1.2.19/include -c envir.c -o envir.o gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I/usr/local/ssl/include -I/usr/local/pgsql/include -I/usr/local/include/ncurses -I/usr/local/BerkeleyDB.4.2/include -I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include -fPIC -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib -I/usr/local/rrdtool-1.2.19/include -c matchpt.c -o matchpt.o gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I/usr/local/ssl/include -I/usr/local/pgsql/include -I/usr/local/include/ncurses -I/usr/local/BerkeleyDB.4.2/include -I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include -fPIC -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib -I/usr/local/rrdtool-1.2.19/include -c Rinit.c -o Rinit.o gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I/usr/local/ssl/include -I/usr/local/pgsql/include -I/usr/local/include/ncurses -I/usr/local/BerkeleyDB.4.2/include -I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include -fPIC -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib -I/usr/local/rrdtool-1.2.19/include -c rowMedians.c -o rowMedians.o gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I/usr/local/ssl/include -I/usr/local/pgsql/include -I/usr/local/include/ncurses -I/usr/local/BerkeleyDB.4.2/include -I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include -fPIC -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib -I/usr/local/rrdtool-1.2.19/include -c sublist_extract.c -o sublist_extract.o gcc -std=gnu99 -G -L/usr/local/lib -R/usr/local/lib -R/usr/lib -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/lib -R/usr/openwin/lib -L/usr/openwin/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/local/BerkeleyDB.4.2/lib -R/usr/local/BerkeleyDB.4.2/lib -L/usr/X11R6/lib -R/usr/X11R6/lib -o Biobase.so anyMissing.o envir.o matchpt.o Rinit.o rowMedians.o sublist_extract.o Thanks Paulo
Prof Brian Ripley wrote:
What compiler is this? This is a compiler issue, not an R one. My guess is that you are mixing gcc (which has __builtin_isnan) and cc (which does not). On Fri, 5 Sep 2008, Paulo Nuin wrote:
Hi everyone This is my first post to the list. I had experience installing and using Bioconductor on Linux and Windows systems but I am encountering problems installing Biobase on Solaris running on Sparc. The package compilation works fine, with only a warning warning: implicit declaration of function `__builtin_isnan' the help files are generated but in the end it fails with an error also related __builtin_isnan ** building package indices ... Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/local/lib/R/library/Biobase/libs/Biobase.so': ld.so.1: R: fatal: relocation error: file /usr/local/lib/R/library/Biobase/libs/Biobase.so: symbol __builtin_isnan: referenced symbol not found Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted ERROR: installing package indices failed The machine I am using is a Sun SPARC Victoria Falls SunOS 5.10 Generic_127111-11 sun4v sparc SUNW,T5140 I posted this message to the BioC list and it was suggested that I tried installing any R package that needed compilation. I installed the XML package with no problems. Any help is appreciated. Thanks in advance Paulo
______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Is this a pre-compiled R? If so, please do compile from the sources on your own machine. The compiler output you show is rather unusually complex and quite likely you are picking up some spurious headers or libraries. gcc 3.4.3 is a very old compiler: sunfreeware (which is what you appear to be using) has 3.4.6. I don't currently have R built on a Solaris 10 Sparc system (I do on amd64), but we have in the past and will again when we have a box back in production use. We did find the Sun Studio compiler (which is a free download) worked much more smoothly than gcc and gave better performance.
On Fri, 5 Sep 2008, Paulo Nuin wrote:
Hi I thought of that. We have gcc 3.4.3 installed /gates/sfw10/builds/sfw10-gate/usr/src/cmd/gcc/gcc-3.4.3/configure --prefix=/usr/sfw --with-as=/usr/sfw/bin/gas --with-gnu-as --with-ld=/usr/ccs/bin/ld --without-gnu-ld --enable-languages=c,c++ --enable-shared How to make sure which compiler R is using?
Look in R_HOME/etc/Makeconf for CC.
Thanks in advance Paulo Prof Brian Ripley wrote:
What compiler is this? This is a compiler issue, not an R one. My guess is that you are mixing gcc (which has __builtin_isnan) and cc (which does not). On Fri, 5 Sep 2008, Paulo Nuin wrote:
Hi everyone This is my first post to the list. I had experience installing and using Bioconductor on Linux and Windows systems but I am encountering problems installing Biobase on Solaris running on Sparc. The package compilation works fine, with only a warning warning: implicit declaration of function `__builtin_isnan' the help files are generated but in the end it fails with an error also related __builtin_isnan ** building package indices ... Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/local/lib/R/library/Biobase/libs/Biobase.so': ld.so.1: R: fatal: relocation error: file /usr/local/lib/R/library/Biobase/libs/Biobase.so: symbol __builtin_isnan: referenced symbol not found Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted ERROR: installing package indices failed The machine I am using is a Sun SPARC Victoria Falls SunOS 5.10 Generic_127111-11 sun4v sparc SUNW,T5140 I posted this message to the BioC list and it was suggested that I tried installing any R package that needed compilation. I installed the XML package with no problems. Any help is appreciated. Thanks in advance Paulo
______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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 Thanks a lot for your suggestions. I had problems compiling R with gcc on Solaris, that's why I decided to install the pre-compiled version. I am in the process of compiling now using the Sun Studio compiler and it is, so far, working wonderfully. I will continue installing it and if I have any other errors I will reply to the list. Sorry if my questions sounded naive, but I don't have a lot of experience with Solaris, I am more a Linux person. Thanks again Paulo
Prof Brian Ripley wrote:
Is this a pre-compiled R? If so, please do compile from the sources on your own machine. The compiler output you show is rather unusually complex and quite likely you are picking up some spurious headers or libraries. gcc 3.4.3 is a very old compiler: sunfreeware (which is what you appear to be using) has 3.4.6. I don't currently have R built on a Solaris 10 Sparc system (I do on amd64), but we have in the past and will again when we have a box back in production use. We did find the Sun Studio compiler (which is a free download) worked much more smoothly than gcc and gave better performance. On Fri, 5 Sep 2008, Paulo Nuin wrote:
Hi I thought of that. We have gcc 3.4.3 installed /gates/sfw10/builds/sfw10-gate/usr/src/cmd/gcc/gcc-3.4.3/configure --prefix=/usr/sfw --with-as=/usr/sfw/bin/gas --with-gnu-as --with-ld=/usr/ccs/bin/ld --without-gnu-ld --enable-languages=c,c++ --enable-shared How to make sure which compiler R is using?
Look in R_HOME/etc/Makeconf for CC.
Thanks in advance Paulo Prof Brian Ripley wrote:
What compiler is this? This is a compiler issue, not an R one. My guess is that you are mixing gcc (which has __builtin_isnan) and cc (which does not). On Fri, 5 Sep 2008, Paulo Nuin wrote:
Hi everyone This is my first post to the list. I had experience installing and using Bioconductor on Linux and Windows systems but I am encountering problems installing Biobase on Solaris running on Sparc. The package compilation works fine, with only a warning warning: implicit declaration of function `__builtin_isnan' the help files are generated but in the end it fails with an error also related __builtin_isnan ** building package indices ... Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/local/lib/R/library/Biobase/libs/Biobase.so': ld.so.1: R: fatal: relocation error: file /usr/local/lib/R/library/Biobase/libs/Biobase.so: symbol __builtin_isnan: referenced symbol not found Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted ERROR: installing package indices failed The machine I am using is a Sun SPARC Victoria Falls SunOS 5.10 Generic_127111-11 sun4v sparc SUNW,T5140 I posted this message to the BioC list and it was suggested that I tried installing any R package that needed compilation. I installed the XML package with no problems. Any help is appreciated. Thanks in advance Paulo
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