Hi, after the installation of BioConductor, running > biocLite("xps") produces compilation error (see full log at the end of email): g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c XPSUtils.cxx XPSUtils.cxx: In function ?void READ_WSTRING(std::ifstream&, char*&, Bool_t)?: XPSUtils.cxx:4611: error: ?wcstombs? was not declared in this scope make: *** [XPSUtils.o] Error 1 ERROR: compilation failed for package ?xps? * Removing ?/home/bogdan/R/i486-pc-linux-gnu-library/2.9/xps? I'm running Debian testing (squeeze) on i386, and have gcc-4.3 installed. Resolving: - adding #include <stdlib.h> to XPSUtils.cxx caused "'atoi' was not declared in XPSSchemes.cxx" - adding #include <stdlib.h> to XPSSchemes.cxx caused "XPSData.cxx:2029: error: ?wcstombs? was not declared in this scope" - adding #include <stdlib.h> to XPSData.cxx caused "XPSSelector.cxx:502: error: call of overloaded ?abs(Int_t&)? is ambiguous" - adding #include <stdlib.h> to XPSSelector.cxx caused "XPSPreProcessing.cxx:5693: error: call of overloaded ?abs(Int_t&)? is ambiguous" - same include in XPSPreProcessing caused "XPSFilter.cxx:739: error: ?atof? was not declared in this scope" - finally, adding that same include to XPSFilter.cxx allowed successful compilation, installation, and loading of xps package; I haven't yet tested any further, though. My 'solution' looks ugly, and might have introduced errors into XPS. Any other suggestions on proper installation are welcome (please CC me on reply, I am not subscribed to this list). Regards, Bogdan === full log of xps installation follows === >biocLite("xps") Using R version 2.9.1, biocinstall version 2.4.12. Installing Bioconductor version 2.4 packages: [1] "xps" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/bogdan/R/i486-pc-linux-gnu-library/2.9' trying URL 'http://bioconductor.org/packages/2.4/bioc/src/contrib/xps_1.4.8.tar.g z' Content type 'application/x-gzip' length 5021629 bytes (4.8 Mb) opened URL ================================================== downloaded 4.8 Mb * Installing *source* package ?xps? ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for gcc... (cached) gcc -std=gnu99 checking whether we are using the GNU C compiler... (cached) yes checking whether gcc -std=gnu99 accepts -g... (cached) yes checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed checking for root-config... yes found ROOT version 5.18/00b in directory /usr ** libs ** arch - g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c TMLMath.cxx TMLMath.cxx:1109:1: warning: "xmax" redefined TMLMath.cxx:1060:1: warning: this is the location of the previous definition g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c TStat.cxx g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c StatUtils.cxx g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c XPSBase.cxx g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c XPSUtils.cxx XPSUtils.cxx: In function ?void READ_WSTRING(std::ifstream&, char*&, Bool_t)?: XPSUtils.cxx:4611: error: ?wcstombs? was not declared in this scope make: *** [XPSUtils.o] Error 1 ERROR: compilation failed for package ?xps? * Removing ?/home/bogdan/R/i486-pc-linux-gnu-library/2.9/xps? The downloaded packages are in ?/tmp/RtmpbYQURP/downloaded_packages? Warning message: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'xps' had non-zero exit status

Dear Bogdan, Since I do not have Debian and have no experience with Debian it is hard for me to comment on your compilation problems. However, looking at the web-site I realize that Debian "squeeze" is a development version, which may account for the problems. One issue may be that you are using gcc-4.3 for compilation. From my experience with openSUSE I can say that I did have some problems with openSUSE 11.0 which used a beta version of gcc-4.3.1 in the release version of openSUSE. Some users including me have reported these problems in RootTalk, see: http://root.cern.ch/phpBB2/viewtopic.php?t=6932&highlight=gcc4&sid=ab7 bb0ad75fec896c4d9d013bd74675b Luckily these problems have been solved in openSUSE 11.1 which uses the release version gcc-4.3.1. Maybe, you could try this version of gcc. Another issue may be that you are using a very old version of ROOT, i.e. root_v5.18/00b. In your case I would suggest to install and compile the newest version root_v5.24.00.source.tar.gz. It would be great if you could use gcc-4.3.1 and root_v5.24.00, and let me know if you still get the compiler errors. Best regards Christian Bogdan wrote: > Hi, > > after the installation of BioConductor, running > > >> biocLite("xps") >> > > produces compilation error (see full log at the end of email): > > g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c XPSUtils.cxx > XPSUtils.cxx: In function ?void READ_WSTRING(std::ifstream&, char*&, > Bool_t)?: > XPSUtils.cxx:4611: error: ?wcstombs? was not declared in this scope > make: *** [XPSUtils.o] Error 1 > ERROR: compilation failed for package ?xps? > * Removing ?/home/bogdan/R/i486-pc-linux-gnu-library/2.9/xps? > > I'm running Debian testing (squeeze) on i386, and have gcc-4.3 > installed. > > Resolving: > - adding #include <stdlib.h> to XPSUtils.cxx caused "'atoi' was not > declared in XPSSchemes.cxx" > - adding #include <stdlib.h> to XPSSchemes.cxx caused "XPSData.cxx:2029: > error: ?wcstombs? was not declared in this scope" > - adding #include <stdlib.h> to XPSData.cxx caused "XPSSelector.cxx:502: > error: call of overloaded ?abs(Int_t&)? is ambiguous" > - adding #include <stdlib.h> to XPSSelector.cxx caused > "XPSPreProcessing.cxx:5693: error: call of overloaded ?abs(Int_t&)? is > ambiguous" > - same include in XPSPreProcessing caused "XPSFilter.cxx:739: error: > ?atof? was not declared in this scope" > - finally, adding that same include to XPSFilter.cxx allowed successful > compilation, installation, and loading of xps package; I haven't yet > tested any further, though. > > My 'solution' looks ugly, and might have introduced errors into XPS. Any > other suggestions on proper installation are welcome (please CC me on > reply, I am not subscribed to this list). > > > Regards, > Bogdan > > > === > full log of xps installation follows > === > > > >> biocLite("xps") >> > Using R version 2.9.1, biocinstall version > 2.4.12. > Installing Bioconductor version 2.4 > packages: > [1] > "xps" > Please > wait... > > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > argument 'lib' is missing: using > '/home/bogdan/R/i486-pc-linux-gnu-library/2.9' > trying URL > 'http://bioconductor.org/packages/2.4/bioc/src/contrib/xps_1.4.8.tar .gz' > Content type 'application/x-gzip' length 5021629 bytes (4.8 > Mb) > opened > URL > ================================================== > downloaded 4.8 > Mb > > * Installing *source* package ?xps? ... > checking for gcc... gcc -std=gnu99 > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc -std=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ANSI C... none needed > checking how to run the C preprocessor... gcc -std=gnu99 -E > checking for gcc... (cached) gcc -std=gnu99 > checking whether we are using the GNU C compiler... (cached) yes > checking whether gcc -std=gnu99 accepts -g... (cached) yes > checking for gcc -std=gnu99 option to accept ANSI C... (cached) none > needed > checking for root-config... yes > found ROOT version 5.18/00b in directory /usr > ** libs > ** arch - > g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c TMLMath.cxx > TMLMath.cxx:1109:1: warning: "xmax" redefined > TMLMath.cxx:1060:1: warning: this is the location of the previous > definition > g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c TStat.cxx > g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c StatUtils.cxx > g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c XPSBase.cxx > g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c XPSUtils.cxx > XPSUtils.cxx: In function ?void READ_WSTRING(std::ifstream&, char*&, > Bool_t)?: > XPSUtils.cxx:4611: error: ?wcstombs? was not declared in this scope > make: *** [XPSUtils.o] Error 1 > ERROR: compilation failed for package ?xps? > * Removing ?/home/bogdan/R/i486-pc-linux-gnu-library/2.9/xps? > > The downloaded packages are in > ?/tmp/RtmpbYQURP/downloaded_packages? > Warning message: > In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'xps' had non-zero exit status > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Dear Bogdan, I forgot to mention that root_v5.24.00 works only with the development version of xps, thus if you download the official version of xps you need to use root_v5.22.00. One more issue: Since you had to "#include <stdlib.h>" in so many files I suspect that you may be missing an essential development package, may be for make? However, since I am no expert, maybe a Debian expert has a hint what might be the problem. Best regards Christian Bogdan wrote: > Hi, > > after the installation of BioConductor, running > > >> biocLite("xps") >> > > produces compilation error (see full log at the end of email): > > g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c XPSUtils.cxx > XPSUtils.cxx: In function ?void READ_WSTRING(std::ifstream&, char*&, > Bool_t)?: > XPSUtils.cxx:4611: error: ?wcstombs? was not declared in this scope > make: *** [XPSUtils.o] Error 1 > ERROR: compilation failed for package ?xps? > * Removing ?/home/bogdan/R/i486-pc-linux-gnu-library/2.9/xps? > > I'm running Debian testing (squeeze) on i386, and have gcc-4.3 > installed. > > Resolving: > - adding #include <stdlib.h> to XPSUtils.cxx caused "'atoi' was not > declared in XPSSchemes.cxx" > - adding #include <stdlib.h> to XPSSchemes.cxx caused "XPSData.cxx:2029: > error: ?wcstombs? was not declared in this scope" > - adding #include <stdlib.h> to XPSData.cxx caused "XPSSelector.cxx:502: > error: call of overloaded ?abs(Int_t&)? is ambiguous" > - adding #include <stdlib.h> to XPSSelector.cxx caused > "XPSPreProcessing.cxx:5693: error: call of overloaded ?abs(Int_t&)? is > ambiguous" > - same include in XPSPreProcessing caused "XPSFilter.cxx:739: error: > ?atof? was not declared in this scope" > - finally, adding that same include to XPSFilter.cxx allowed successful > compilation, installation, and loading of xps package; I haven't yet > tested any further, though. > > My 'solution' looks ugly, and might have introduced errors into XPS. Any > other suggestions on proper installation are welcome (please CC me on > reply, I am not subscribed to this list). > > > Regards, > Bogdan > > > === > full log of xps installation follows > === > > > >> biocLite("xps") >> > Using R version 2.9.1, biocinstall version > 2.4.12. > Installing Bioconductor version 2.4 > packages: > [1] > "xps" > Please > wait... > > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > argument 'lib' is missing: using > '/home/bogdan/R/i486-pc-linux-gnu-library/2.9' > trying URL > 'http://bioconductor.org/packages/2.4/bioc/src/contrib/xps_1.4.8.tar .gz' > Content type 'application/x-gzip' length 5021629 bytes (4.8 > Mb) > opened > URL > ================================================== > downloaded 4.8 > Mb > > * Installing *source* package ?xps? ... > checking for gcc... gcc -std=gnu99 > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc -std=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ANSI C... none needed > checking how to run the C preprocessor... gcc -std=gnu99 -E > checking for gcc... (cached) gcc -std=gnu99 > checking whether we are using the GNU C compiler... (cached) yes > checking whether gcc -std=gnu99 accepts -g... (cached) yes > checking for gcc -std=gnu99 option to accept ANSI C... (cached) none > needed > checking for root-config... yes > found ROOT version 5.18/00b in directory /usr > ** libs > ** arch - > g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c TMLMath.cxx > TMLMath.cxx:1109:1: warning: "xmax" redefined > TMLMath.cxx:1060:1: warning: this is the location of the previous > definition > g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c TStat.cxx > g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c StatUtils.cxx > g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c XPSBase.cxx > g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/include/root -c XPSUtils.cxx > XPSUtils.cxx: In function ?void READ_WSTRING(std::ifstream&, char*&, > Bool_t)?: > XPSUtils.cxx:4611: error: ?wcstombs? was not declared in this scope > make: *** [XPSUtils.o] Error 1 > ERROR: compilation failed for package ?xps? > * Removing ?/home/bogdan/R/i486-pc-linux-gnu-library/2.9/xps? > > The downloaded packages are in > ?/tmp/RtmpbYQURP/downloaded_packages? > Warning message: > In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'xps' had non-zero exit status > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor