cannot install rsbml
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@richard-birnie-3056
Last seen 10.3 years ago
Dear list, I'm trying to install the package rsbml from bioconductor. I followed the instructions on http://bioconductor.org/packages/2.2/bioc/html/rsbml.html i.e. ran the commands source("http://bioconductor.org/biocLite.R") biocLite("rsbml"). The installation consistently fails with this error: #################### make: *** [check.o] Error 1 chmod: cannot access `/usr/local/lib/R/site-library/rsbml/libs/*': No such file or directory ERROR: compilation failed for package 'rsbml' ** Removing '/usr/local/lib/R/site-library/rsbml' #################### It is true that the directory does not exist but I have no idea why or what I need to do about it. My session info is ################### sessionInfo() R version 2.6.2 (2008-02-08) i486-pc-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB .UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.2 ################### I have libsbml installed which was done by running the following commands: ./configure --with-python --with-bzip2=no make sudo make install Can anybody suggest what I need to do. thanks, Richard -- Dr Richard Birnie Research Scientist Pro-Cure Therapeutics Limited Biocentre Innovation Way, Heslington, York, YO10 5NY, UK Registered in England : Reg No. 421 6368 telephone +44 (0)1904 435125 Email richard.birnie at pro-cure.uk.com www.pro-cure.uk.com CONFIDENTIAL AND PRIVILEGED. This email and any attachment(s) are confidential and may contain privileged information. It is intended solely for the addressee(s). If you have received this message in error, please notify the sender immediately and remove it from your system.
rsbml rsbml • 1.9k views
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@sean-davis-490
Last seen 4 months ago
United States
On Fri, Oct 3, 2008 at 3:32 AM, Richard Birnie <richard.birnie at="" pro-cure.uk.com=""> wrote: > Dear list, > > I'm trying to install the package rsbml from bioconductor. I followed the > instructions on http://bioconductor.org/packages/2.2/bioc/html/rsbml.html > i.e. ran the commands > source("http://bioconductor.org/biocLite.R") > biocLite("rsbml"). > > The installation consistently fails with this error: > #################### > make: *** [check.o] Error 1 > chmod: cannot access `/usr/local/lib/R/site-library/rsbml/libs/*': No such > file or directory > ERROR: compilation failed for package 'rsbml' > ** Removing '/usr/local/lib/R/site-library/rsbml' > #################### > > It is true that the directory does not exist but I have no idea why or what I > need to do about it. My session info is It might help to post the entire output of the installation attempt. The error you show above is a symptom, not a cause. The rest of the output might show the error. Also, you probably want to upgrade your R, as R-2.6.2 is a year old. Sean > ################### > sessionInfo() > R version 2.6.2 (2008-02-08) > i486-pc-linux-gnu > > locale: > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_ GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_G B.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] rcompgen_0.1-17 tools_2.6.2 > ################### > > I have libsbml installed which was done by running the following commands: > ./configure --with-python --with-bzip2=no > make > sudo make install > > Can anybody suggest what I need to do. > > thanks, > Richard > -- > Dr Richard Birnie > Research Scientist > Pro-Cure Therapeutics Limited > Biocentre > Innovation Way, Heslington, York, YO10 5NY, UK > Registered in England : Reg No. 421 6368 > telephone +44 (0)1904 435125 > Email richard.birnie at pro-cure.uk.com > www.pro-cure.uk.com > CONFIDENTIAL AND PRIVILEGED. This email and any attachment(s) are > confidential and may contain privileged information. It is intended solely > for the addressee(s). If you have received this message in error, please > notify the sender immediately and remove it from your system. > > _______________________________________________ > 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 >
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On Friday 03 October 2008 12:48:15 Sean Davis wrote: > On Fri, Oct 3, 2008 at 3:32 AM, Richard Birnie > > <richard.birnie at="" pro-cure.uk.com=""> wrote: > > Dear list, > > > > I'm trying to install the package rsbml from bioconductor. I followed the > > instructions on http://bioconductor.org/packages/2.2/bioc/html/rsbml.html > > i.e. ran the commands > > source("http://bioconductor.org/biocLite.R") > > biocLite("rsbml"). > > > > The installation consistently fails with this error: > > #################### > > make: *** [check.o] Error 1 > > chmod: cannot access `/usr/local/lib/R/site-library/rsbml/libs/*': No > > such file or directory > > ERROR: compilation failed for package 'rsbml' > > ** Removing '/usr/local/lib/R/site-library/rsbml' > > #################### > > > > It is true that the directory does not exist but I have no idea why or > > what I need to do about it. My session info is > > It might help to post the entire output of the installation attempt. > The error you show above is a symptom, not a cause. The rest of the > output might show the error. Also, you probably want to upgrade your > R, as R-2.6.2 is a year old. > > Sean As requested the complete output of the installation attempt is below. I'm still using 2.6.2 because that is what is packaged for my distribution. If it's essential to upgrade then I can try that when I get some time. The last time I tried to compile R from source it was a bit of a trial. Thanks for the help Richard biocLite("rsbml") Running biocinstall version 2.1.11 with R version 2.6.2 Your version of R requires version 2.1 of BioConductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/usr/local/lib/R/site-library' trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/rsbml_1.4.0 .tar.gz' Content type 'application/x-gzip' length 161149 bytes (157 Kb) opened URL ================================================== downloaded 157 Kb * Installing *source* package 'rsbml' ... checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking SBMLDocument.h usability... yes checking SBMLDocument.h presence... yes checking for SBMLDocument.h... yes checking for SBMLDocument_create in -lsbml... yes configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -I/usr/include/sbml -I/usr/local/include/sbml -fpic -g -O2 -c check.c -o check.o check.c:2:30: error: xml/ParseMessage.h: No such file or directory check.c:5: error: expected ?)? before ?*? token check.c: In function ?rsbml_problems?: check.c:31: warning: implicit declaration of function ?SBMLDocument_getNumWarnings? check.c:35: warning: implicit declaration of function ?SBMLDocument_getNumFatals? check.c:46: warning: implicit declaration of function ?rsbml_problem? check.c:46: warning: implicit declaration of function ?SBMLDocument_getWarning? check.c:46: warning: passing argument 3 of ?SET_VECTOR_ELT? makes pointer from integer without a cast check.c:48: warning: passing argument 3 of ?SET_VECTOR_ELT? makes pointer from integer without a cast check.c:50: warning: implicit declaration of function ?SBMLDocument_getFatal? check.c:50: warning: passing argument 3 of ?SET_VECTOR_ELT? makes pointer from integer without a cast make: *** [check.o] Error 1 chmod: cannot access `/usr/local/lib/R/site-library/rsbml/libs/*': No such file or directory ERROR: compilation failed for package 'rsbml' ** Removing '/usr/local/lib/R/site-library/rsbml' The downloaded packages are in /tmp/RtmpBB1f0Z/downloaded_packages Warning message: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'rsbml' had non-zero exit status > > > ################### > > sessionInfo() > > R version 2.6.2 (2008-02-08) > > i486-pc-linux-gnu > > > > locale: > > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=e n_GB.UT > >F-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB. UTF-8;L > >C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_ IDENTIF > >ICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > loaded via a namespace (and not attached): > > [1] rcompgen_0.1-17 tools_2.6.2 > > ################### > > > > I have libsbml installed which was done by running the following > > commands: ./configure --with-python --with-bzip2=no > > make > > sudo make install > > > > Can anybody suggest what I need to do. > > > > thanks, > > Richard > > -- > > Dr Richard Birnie > > Research Scientist > > Pro-Cure Therapeutics Limited > > Biocentre > > Innovation Way, Heslington, York, YO10 5NY, UK > > Registered in England : Reg No. 421 6368 > > telephone +44 (0)1904 435125 > > Email richard.birnie at pro-cure.uk.com > > www.pro-cure.uk.com > > CONFIDENTIAL AND PRIVILEGED. This email and any attachment(s) are > > confidential and may contain privileged information. It is intended > > solely for the addressee(s). If you have received this message in error, > > please notify the sender immediately and remove it from your system. > > > > _______________________________________________ > > 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 -- Dr Richard Birnie Research Scientist Pro-Cure Therapeutics Limited Biocentre Innovation Way, Heslington, York, YO10 5NY, UK Registered in England : Reg No. 421 6368 telephone +44 (0)1904 435125 Email richard.birnie at pro-cure.uk.com www.pro-cure.uk.com CONFIDENTIAL AND PRIVILEGED. This email and any attachment(s) are confidential and may contain privileged information. It is intended solely for the addressee(s). If you have received this message in error, please notify the sender immediately and remove it from your system.
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On Fri, Oct 3, 2008 at 8:07 AM, Richard Birnie <richard.birnie at="" pro-cure.uk.com=""> wrote: > On Friday 03 October 2008 12:48:15 Sean Davis wrote: >> On Fri, Oct 3, 2008 at 3:32 AM, Richard Birnie >> >> <richard.birnie at="" pro-cure.uk.com=""> wrote: >> > Dear list, >> > >> > I'm trying to install the package rsbml from bioconductor. I followed the >> > instructions on http://bioconductor.org/packages/2.2/bioc/html/rsbml.html >> > i.e. ran the commands >> > source("http://bioconductor.org/biocLite.R") >> > biocLite("rsbml"). >> > >> > The installation consistently fails with this error: >> > #################### >> > make: *** [check.o] Error 1 >> > chmod: cannot access `/usr/local/lib/R/site- library/rsbml/libs/*': No >> > such file or directory >> > ERROR: compilation failed for package 'rsbml' >> > ** Removing '/usr/local/lib/R/site-library/rsbml' >> > #################### >> > >> > It is true that the directory does not exist but I have no idea why or >> > what I need to do about it. My session info is >> >> It might help to post the entire output of the installation attempt. >> The error you show above is a symptom, not a cause. The rest of the >> output might show the error. Also, you probably want to upgrade your >> R, as R-2.6.2 is a year old. >> >> Sean > > As requested the complete output of the installation attempt is below. I'm > still using 2.6.2 because that is what is packaged for my distribution. If > it's essential to upgrade then I can try that when I get some time. The last > time I tried to compile R from source it was a bit of a trial. > > Thanks for the help > Richard > > biocLite("rsbml") > Running biocinstall version 2.1.11 with R version 2.6.2 > Your version of R requires version 2.1 of BioConductor. > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > argument 'lib' is missing: using '/usr/local/lib/R/site-library' > trying > URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/rsbml_1.4 .0.tar.gz' > Content type 'application/x-gzip' length 161149 bytes (157 Kb) > opened URL > ================================================== > downloaded 157 Kb > > * Installing *source* package 'rsbml' ... > checking for gcc... gcc > 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 accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -E > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking SBMLDocument.h usability... yes > checking SBMLDocument.h presence... yes > checking for SBMLDocument.h... yes > checking for SBMLDocument_create in -lsbml... yes > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -I/usr/include/sbml -I/usr/local/include/sbml -fpic -g -O2 -c > check.c -o check.o > check.c:2:30: error: xml/ParseMessage.h: No such file or directory So, xml/ParseMessage.h is not being found. Do you have either: /usr/include/sbml/xml/ParseMessage.h OR /usr/local/include/sbml/xml/ParseMessage.h on your computer? Sean > check.c:5: error: expected ')' before '*' token > check.c: In function 'rsbml_problems': > check.c:31: warning: implicit declaration of > function 'SBMLDocument_getNumWarnings' > check.c:35: warning: implicit declaration of > function 'SBMLDocument_getNumFatals' > check.c:46: warning: implicit declaration of function 'rsbml_problem' > check.c:46: warning: implicit declaration of > function 'SBMLDocument_getWarning' > check.c:46: warning: passing argument 3 of 'SET_VECTOR_ELT' makes pointer from > integer without a cast > check.c:48: warning: passing argument 3 of 'SET_VECTOR_ELT' makes pointer from > integer without a cast > check.c:50: warning: implicit declaration of function 'SBMLDocument_getFatal' > check.c:50: warning: passing argument 3 of 'SET_VECTOR_ELT' makes pointer from > integer without a cast > make: *** [check.o] Error 1 > chmod: cannot access `/usr/local/lib/R/site-library/rsbml/libs/*': No such > file or directory > ERROR: compilation failed for package 'rsbml' > ** Removing '/usr/local/lib/R/site-library/rsbml' > > The downloaded packages are in > /tmp/RtmpBB1f0Z/downloaded_packages > Warning message: > In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'rsbml' had non-zero exit status > > > >> >> > ################### >> > sessionInfo() >> > R version 2.6.2 (2008-02-08) >> > i486-pc-linux-gnu >> > >> > locale: >> > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE= en_GB.UT >> >F-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB .UTF-8;L >> >C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC _IDENTIF >> >ICATION=C >> > >> > attached base packages: >> > [1] stats graphics grDevices utils datasets methods base >> > >> > loaded via a namespace (and not attached): >> > [1] rcompgen_0.1-17 tools_2.6.2 >> > ################### >> > >> > I have libsbml installed which was done by running the following >> > commands: ./configure --with-python --with-bzip2=no >> > make >> > sudo make install >> > >> > Can anybody suggest what I need to do. >> > >> > thanks, >> > Richard >> > -- >> > Dr Richard Birnie >> > Research Scientist >> > Pro-Cure Therapeutics Limited >> > Biocentre >> > Innovation Way, Heslington, York, YO10 5NY, UK >> > Registered in England : Reg No. 421 6368 >> > telephone +44 (0)1904 435125 >> > Email richard.birnie at pro-cure.uk.com >> > www.pro-cure.uk.com >> > CONFIDENTIAL AND PRIVILEGED. This email and any attachment(s) are >> > confidential and may contain privileged information. It is intended >> > solely for the addressee(s). If you have received this message in error, >> > please notify the sender immediately and remove it from your system. >> > >> > _______________________________________________ >> > 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 > > > > -- > Dr Richard Birnie > Research Scientist > Pro-Cure Therapeutics Limited > Biocentre > Innovation Way, Heslington, York, YO10 5NY, UK > Registered in England : Reg No. 421 6368 > telephone +44 (0)1904 435125 > Email richard.birnie at pro-cure.uk.com > www.pro-cure.uk.com > CONFIDENTIAL AND PRIVILEGED. This email and any attachment(s) are > confidential and may contain privileged information. It is intended solely > for the addressee(s). If you have received this message in error, please > notify the sender immediately and remove it from your system. > > _______________________________________________ > 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
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On Friday 03 October 2008 15:27:56 Sean Davis wrote: > On Fri, Oct 3, 2008 at 8:07 AM, Richard Birnie > > <richard.birnie at="" pro-cure.uk.com=""> wrote: > > On Friday 03 October 2008 12:48:15 Sean Davis wrote: > >> On Fri, Oct 3, 2008 at 3:32 AM, Richard Birnie > >> > >> <richard.birnie at="" pro-cure.uk.com=""> wrote: > >> > Dear list, > >> > > >> > I'm trying to install the package rsbml from bioconductor. I followed > >> > the instructions on > >> > http://bioconductor.org/packages/2.2/bioc/html/rsbml.html i.e. ran the > >> > commands > >> > source("http://bioconductor.org/biocLite.R") > >> > biocLite("rsbml"). > >> > > >> > The installation consistently fails with this error: > >> > #################### > >> > make: *** [check.o] Error 1 > >> > chmod: cannot access `/usr/local/lib/R/site- library/rsbml/libs/*': No > >> > such file or directory > >> > ERROR: compilation failed for package 'rsbml' > >> > ** Removing '/usr/local/lib/R/site-library/rsbml' > >> > #################### > >> > > >> > It is true that the directory does not exist but I have no idea why or > >> > what I need to do about it. My session info is > >> > >> It might help to post the entire output of the installation attempt. > >> The error you show above is a symptom, not a cause. The rest of the > >> output might show the error. Also, you probably want to upgrade your > >> R, as R-2.6.2 is a year old. > >> > >> Sean > > > > As requested the complete output of the installation attempt is below. > > I'm still using 2.6.2 because that is what is packaged for my > > distribution. If it's essential to upgrade then I can try that when I get > > some time. The last time I tried to compile R from source it was a bit of > > a trial. > > > > Thanks for the help > > Richard > > > > biocLite("rsbml") > > Running biocinstall version 2.1.11 with R version 2.6.2 > > Your version of R requires version 2.1 of BioConductor. > > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > > dependencies, : > > argument 'lib' is missing: using '/usr/local/lib/R/site-library' > > trying > > URL > > 'http://bioconductor.org/packages/2.1/bioc/src/contrib/rsbml_1.4.0 .tar.gz > >' Content type 'application/x-gzip' length 161149 bytes (157 Kb) > > opened URL > > ================================================== > > downloaded 157 Kb > > > > * Installing *source* package 'rsbml' ... > > checking for gcc... gcc > > 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 accepts -g... yes > > checking for gcc option to accept ISO C89... none needed > > checking how to run the C preprocessor... gcc -E > > checking for grep that handles long lines and -e... /bin/grep > > checking for egrep... /bin/grep -E > > checking for ANSI C header files... yes > > checking for sys/types.h... yes > > checking for sys/stat.h... yes > > checking for stdlib.h... yes > > checking for string.h... yes > > checking for memory.h... yes > > checking for strings.h... yes > > checking for inttypes.h... yes > > checking for stdint.h... yes > > checking for unistd.h... yes > > checking SBMLDocument.h usability... yes > > checking SBMLDocument.h presence... yes > > checking for SBMLDocument.h... yes > > checking for SBMLDocument_create in -lsbml... yes > > configure: creating ./config.status > > config.status: creating src/Makevars > > ** libs > > gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include > > -I/usr/include/sbml -I/usr/local/include/sbml -fpic -g -O2 -c > > check.c -o check.o > > check.c:2:30: error: xml/ParseMessage.h: No such file or directory > > So, xml/ParseMessage.h is not being found. Do you have either: > > /usr/include/sbml/xml/ParseMessage.h > OR > /usr/local/include/sbml/xml/ParseMessage.h > > on your computer? > > Sean In answer to the immediate question, no I don't have either of those. However, I took the advice to upgrade to R-2.7.2 (which was easier than I remember). I also upgraded all the bioconductor packages I have installed. Now when I attempt to install rsbml it works first time. library(rsbml) shows that the package loads correctly so all seems to be well. It seems that this problem was either specific to version 2.6.2 or something in my distro's packaging thanks for the pointers Sean. regards, Richard
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My guess is that you have libsbml >=3.0 installed, which rsbml 1.4.0 does not support (libsbml 3.0 wasn't around when rsbml 1.4.0 was around). Michael On Fri, Oct 3, 2008 at 8:04 AM, Richard Birnie < richard.birnie@pro-cure.uk.com> wrote: > On Friday 03 October 2008 15:27:56 Sean Davis wrote: > > On Fri, Oct 3, 2008 at 8:07 AM, Richard Birnie > > > > <richard.birnie@pro-cure.uk.com> wrote: > > > On Friday 03 October 2008 12:48:15 Sean Davis wrote: > > >> On Fri, Oct 3, 2008 at 3:32 AM, Richard Birnie > > >> > > >> <richard.birnie@pro-cure.uk.com> wrote: > > >> > Dear list, > > >> > > > >> > I'm trying to install the package rsbml from bioconductor. I > followed > > >> > the instructions on > > >> > http://bioconductor.org/packages/2.2/bioc/html/rsbml.html i.e. ran > the > > >> > commands > > >> > source("http://bioconductor.org/biocLite.R") > > >> > biocLite("rsbml"). > > >> > > > >> > The installation consistently fails with this error: > > >> > #################### > > >> > make: *** [check.o] Error 1 > > >> > chmod: cannot access `/usr/local/lib/R/site- library/rsbml/libs/*': > No > > >> > such file or directory > > >> > ERROR: compilation failed for package 'rsbml' > > >> > ** Removing '/usr/local/lib/R/site-library/rsbml' > > >> > #################### > > >> > > > >> > It is true that the directory does not exist but I have no idea why > or > > >> > what I need to do about it. My session info is > > >> > > >> It might help to post the entire output of the installation attempt. > > >> The error you show above is a symptom, not a cause. The rest of the > > >> output might show the error. Also, you probably want to upgrade your > > >> R, as R-2.6.2 is a year old. > > >> > > >> Sean > > > > > > As requested the complete output of the installation attempt is below. > > > I'm still using 2.6.2 because that is what is packaged for my > > > distribution. If it's essential to upgrade then I can try that when I > get > > > some time. The last time I tried to compile R from source it was a bit > of > > > a trial. > > > > > > Thanks for the help > > > Richard > > > > > > biocLite("rsbml") > > > Running biocinstall version 2.1.11 with R version 2.6.2 > > > Your version of R requires version 2.1 of BioConductor. > > > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > > > dependencies, : > > > argument 'lib' is missing: using '/usr/local/lib/R/site- library' > > > trying > > > URL > > > ' > http://bioconductor.org/packages/2.1/bioc/src/contrib/rsbml_1.4.0.ta r.gz > > >' Content type 'application/x-gzip' length 161149 bytes (157 Kb) > > > opened URL > > > ================================================== > > > downloaded 157 Kb > > > > > > * Installing *source* package 'rsbml' ... > > > checking for gcc... gcc > > > 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 accepts -g... yes > > > checking for gcc option to accept ISO C89... none needed > > > checking how to run the C preprocessor... gcc -E > > > checking for grep that handles long lines and -e... /bin/grep > > > checking for egrep... /bin/grep -E > > > checking for ANSI C header files... yes > > > checking for sys/types.h... yes > > > checking for sys/stat.h... yes > > > checking for stdlib.h... yes > > > checking for string.h... yes > > > checking for memory.h... yes > > > checking for strings.h... yes > > > checking for inttypes.h... yes > > > checking for stdint.h... yes > > > checking for unistd.h... yes > > > checking SBMLDocument.h usability... yes > > > checking SBMLDocument.h presence... yes > > > checking for SBMLDocument.h... yes > > > checking for SBMLDocument_create in -lsbml... yes > > > configure: creating ./config.status > > > config.status: creating src/Makevars > > > ** libs > > > gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include > > > -I/usr/include/sbml -I/usr/local/include/sbml -fpic -g -O2 -c > > > check.c -o check.o > > > check.c:2:30: error: xml/ParseMessage.h: No such file or directory > > > > So, xml/ParseMessage.h is not being found. Do you have either: > > > > /usr/include/sbml/xml/ParseMessage.h > > OR > > /usr/local/include/sbml/xml/ParseMessage.h > > > > on your computer? > > > > Sean > > In answer to the immediate question, no I don't have either of those. > However, > I took the advice to upgrade to R-2.7.2 (which was easier than I remember). > I > also upgraded all the bioconductor packages I have installed. Now when I > attempt to install rsbml it works first time. library(rsbml) shows that the > package loads correctly so all seems to be well. It seems that this problem > was either specific to version 2.6.2 or something in my distro's packaging > > thanks for the pointers Sean. > > regards, > Richard > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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