Hello group, I am working on microarray data analysis using bioconductor, I was able to install some basic packages such as limma , GO, KEGG, etc but some of the other packages such as annotate ,GOstats ,gTools are not getting installed below is the workspace of my installation set up .... > source("http://bioconductor.org/biocLite.R") Warning messages: 1: In safeSource() : Redefining ‘biocinstall’ 2: In safeSource() : Redefining ‘biocinstallPkgGroups’ 3: In safeSource() : Redefining ‘biocinstallRepos’ > biocLite("annotate") 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 '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6' also installing the dependencies ‘RSQLite’, ‘Biobase’, ‘AnnotationDbi’ trying URL 'http://cran.fhcrc.org/src/contrib/RSQLite_0.7-1.tar.gz' Content type 'application/x-gzip' length 1015918 bytes (992 Kb) opened URL ================================================== downloaded 992 Kb trying URL ' http://bioconductor.org/packages/2.1/bioc/src/contrib/Biobase_1.16.3.t ar.gz' Content type 'application/x-gzip' length 1879209 bytes (1.8 Mb) opened URL ================================================== downloaded 1.8 Mb trying URL ' http://bioconductor.org/packages/2.1/bioc/src/contrib/AnnotationDbi_1. 0.6.tar.gz ' Content type 'application/x-gzip' length 228996 bytes (223 Kb) opened URL ================================================== downloaded 223 Kb trying URL ' http://bioconductor.org/packages/2.1/bioc/src/contrib/annotate_1.16.1. tar.gz ' Content type 'application/x-gzip' length 1526767 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 Mb * Installing *source* package 'RSQLite' ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... configure: error: C compiler cannot create executables See `config.log' for more details. ERROR: configuration failed for package 'RSQLite' ** Removing '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6/RSQLite' * Installing *source* package 'Biobase' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -c anyMissing.c -o anyMissing.o In file included from /usr/share/R/include/Rdefines.h:26, from anyMissing.c:11: /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or directory In file included from /usr/share/R/include/Rinternals.h:28, from /usr/share/R/include/Rdefines.h:29, from anyMissing.c:11: /usr/share/R/include/R_ext/Arith.h:35:19: error: math.h: No such file or directory In file included from /usr/share/R/include/Rdefines.h:29, from anyMissing.c:11: /usr/share/R/include/Rinternals.h:36:34: error: stdio.h: No such file or directory In file included from /usr/share/R/include/Rdefines.h:29, from anyMissing.c:11: /usr/share/R/include/Rinternals.h:757: error: expected declaration specifiers or ‘...’ before ‘FILE’ /usr/share/R/include/Rinternals.h:760: error: expected declaration specifiers or ‘...’ before ‘FILE’ anyMissing.c: In function ‘anyMissing’: anyMissing.c:33: warning: implicit declaration of function ‘isnan’ make: *** [anyMissing.o] Error 1 ERROR: compilation failed for package 'Biobase' ** Removing '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6/Biobase' * Installing *source* package 'AnnotationDbi' ... ** R ** inst ** preparing package for lazy loading Error: package 'Biobase' required by 'AnnotationDbi' could not be found Execution halted ERROR: lazy loading failed for package 'AnnotationDbi' ** Removing '/home/mlscub1/R/i486-pc-linux-gnu- library/2.6/AnnotationDbi' * Installing *source* package 'annotate' ... ** R ** data ** inst ** preparing package for lazy loading Loading required package: Biobase Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called 'Biobase' Error: package 'Biobase' could not be loaded Execution halted ERROR: lazy loading failed for package 'annotate' ** Removing '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6/annotate' The downloaded packages are in /tmp/RtmpaoFwjZ/downloaded_packages Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'RSQLite' had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'Biobase' had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'AnnotationDbi' had non-zero exit status 4: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'annotate' had non-zero exit status > library(annotate) Error in library(annotate) : there is no package called 'annotate' If anyone could explain the problem or suggest a suitable solution will be very helpfull.... A.Ashwin Departement of Biotechnology Manipal Life Science Center Manipal University INDIA [[alternative HTML version deleted]]

Hi, you are running an old R version, the actual one is R-2.9 and therfore new Bioc release have to be updated. Cheers Anna Anna Freni Sterrantino Ph.D Student Department of Statistics University of Bologna, Italy via Belle Arti 41, 40124 BO. ________________________________ Da: Ashwin Kumar <ashwin.havoc@gmail.com> A: bioconductor <bioconductor@stat.math.ethz.ch> Inviato: Martedì 12 maggio 2009, 9:01:09 Oggetto: [BioC] Packages not getting installed Hello group, I am working on microarray data analysis using bioconductor, I was able to install some basic packages such as limma , GO, KEGG, etc but some of the other packages such as annotate ,GOstats ,gTools are not getting installed below is the workspace of my installation set up .... > source("http://bioconductor.org/biocLite.R") Warning messages: 1: In safeSource() : Redefining ‘biocinstall’ 2: In safeSource() : Redefining ‘biocinstallPkgGroups’ 3: In safeSource() : Redefining ‘biocinstallRepos’ > biocLite("annotate") 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 '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6' also installing the dependencies ‘RSQLite’, ‘Biobase’, ‘AnnotationDbi’ trying URL 'http://cran.fhcrc.org/src/contrib/RSQLite_0.7-1.tar.gz' Content type 'application/x-gzip' length 1015918 bytes (992 Kb) opened URL ================================================== downloaded 992 Kb trying URL ' http://bioconductor.org/packages/2.1/bioc/src/contrib/Biobase_1.16.3.t ar.gz' Content type 'application/x-gzip' length 1879209 bytes (1.8 Mb) opened URL ================================================== downloaded 1.8 Mb trying URL ' http://bioconductor.org/packages/2.1/bioc/src/contrib/AnnotationDbi_1. 0.6.tar.gz ' Content type 'application/x-gzip' length 228996 bytes (223 Kb) opened URL ================================================== downloaded 223 Kb trying URL ' http://bioconductor.org/packages/2.1/bioc/src/contrib/annotate_1.16.1. tar.gz ' Content type 'application/x-gzip' length 1526767 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 Mb * Installing *source* package 'RSQLite' ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... configure: error: C compiler cannot create executables See `config.log' for more details. ERROR: configuration failed for package 'RSQLite' ** Removing '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6/RSQLite' * Installing *source* package 'Biobase' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -c anyMissing.c -o anyMissing.o In file included from /usr/share/R/include/Rdefines.h:26, from anyMissing.c:11: /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or directory In file included from /usr/share/R/include/Rinternals.h:28, from /usr/share/R/include/Rdefines.h:29, from anyMissing.c:11: /usr/share/R/include/R_ext/Arith.h:35:19: error: math.h: No such file or directory In file included from /usr/share/R/include/Rdefines.h:29, from anyMissing.c:11: /usr/share/R/include/Rinternals.h:36:34: error: stdio.h: No such file or directory In file included from /usr/share/R/include/Rdefines.h:29, from anyMissing.c:11: /usr/share/R/include/Rinternals.h:757: error: expected declaration specifiers or ‘...’ before ‘FILE’ /usr/share/R/include/Rinternals.h:760: error: expected declaration specifiers or ‘...’ before ‘FILE’ anyMissing.c: In function ‘anyMissing’: anyMissing.c:33: warning: implicit declaration of function ‘isnan’ make: *** [anyMissing.o] Error 1 ERROR: compilation failed for package 'Biobase' ** Removing '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6/Biobase' * Installing *source* package 'AnnotationDbi' ... ** R ** inst ** preparing package for lazy loading Error: package 'Biobase' required by 'AnnotationDbi' could not be found Execution halted ERROR: lazy loading failed for package 'AnnotationDbi' ** Removing '/home/mlscub1/R/i486-pc-linux-gnu- library/2.6/AnnotationDbi' * Installing *source* package 'annotate' ... ** R ** data ** inst ** preparing package for lazy loading Loading required package: Biobase Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called 'Biobase' Error: package 'Biobase' could not be loaded Execution halted ERROR: lazy loading failed for package 'annotate' ** Removing '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6/annotate' The downloaded packages are in /tmp/RtmpaoFwjZ/downloaded_packages Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'RSQLite' had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'Biobase' had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'AnnotationDbi' had non-zero exit status 4: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'annotate' had non-zero exit status > library(annotate) Error in library(annotate) : there is no package called 'annotate' If anyone could explain the problem or suggest a suitable solution will be very helpfull.... A.Ashwin Departement of Biotechnology Manipal Life Science Center Manipal University INDIA [[alternative HTML version deleted]] [[alternative HTML version deleted]]

Hi Ashwin, Looks to me like you are missing (at the very least) the C header files. You or your sysadmin need to install glibc-headers and maybe glibc-devel. Not sure exactly what all you need, as I have never used a Linux distro that didn't have these by default (unless you count Mac OSX). Best, Jim Ashwin Kumar wrote: > Hello group, > I am working on microarray data analysis using > bioconductor, I was able to install some basic packages such as limma , GO, > KEGG, etc but some of the other packages such as annotate ,GOstats ,gTools > are not getting installed below is the workspace of my installation set up > .... > >> source("http://bioconductor.org/biocLite.R") > Warning messages: > 1: In safeSource() : Redefining ?biocinstall? > 2: In safeSource() : Redefining ?biocinstallPkgGroups? > 3: In safeSource() : Redefining ?biocinstallRepos? >> biocLite("annotate") > 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 > '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6' > also installing the dependencies ?RSQLite?, ?Biobase?, ?AnnotationDbi? > > trying URL 'http://cran.fhcrc.org/src/contrib/RSQLite_0.7-1.tar.gz' > Content type 'application/x-gzip' length 1015918 bytes (992 Kb) > opened URL > ================================================== > downloaded 992 Kb > > trying URL ' > http://bioconductor.org/packages/2.1/bioc/src/contrib/Biobase_1.16.3 .tar.gz' > Content type 'application/x-gzip' length 1879209 bytes (1.8 Mb) > opened URL > ================================================== > downloaded 1.8 Mb > > trying URL ' > http://bioconductor.org/packages/2.1/bioc/src/contrib/AnnotationDbi_ 1.0.6.tar.gz > ' > Content type 'application/x-gzip' length 228996 bytes (223 Kb) > opened URL > ================================================== > downloaded 223 Kb > > trying URL ' > http://bioconductor.org/packages/2.1/bioc/src/contrib/annotate_1.16. 1.tar.gz > ' > Content type 'application/x-gzip' length 1526767 bytes (1.5 Mb) > opened URL > ================================================== > downloaded 1.5 Mb > > * Installing *source* package 'RSQLite' ... > checking for gcc... gcc -std=gnu99 > checking for C compiler default output file name... > configure: error: C compiler cannot create executables > See `config.log' for more details. > ERROR: configuration failed for package 'RSQLite' > ** Removing '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6/RSQLite' > * Installing *source* package 'Biobase' ... > ** libs > gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g > -O2 -c anyMissing.c -o anyMissing.o > In file included from /usr/share/R/include/Rdefines.h:26, > from anyMissing.c:11: > /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or > directory > In file included from /usr/share/R/include/Rinternals.h:28, > from /usr/share/R/include/Rdefines.h:29, > from anyMissing.c:11: > /usr/share/R/include/R_ext/Arith.h:35:19: error: math.h: No such file or > directory > In file included from /usr/share/R/include/Rdefines.h:29, > from anyMissing.c:11: > /usr/share/R/include/Rinternals.h:36:34: error: stdio.h: No such file or > directory > In file included from /usr/share/R/include/Rdefines.h:29, > from anyMissing.c:11: > /usr/share/R/include/Rinternals.h:757: error: expected declaration > specifiers or ?...? before ?FILE? > /usr/share/R/include/Rinternals.h:760: error: expected declaration > specifiers or ?...? before ?FILE? > anyMissing.c: In function ?anyMissing?: > anyMissing.c:33: warning: implicit declaration of function ?isnan? > make: *** [anyMissing.o] Error 1 > ERROR: compilation failed for package 'Biobase' > ** Removing '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6/Biobase' > * Installing *source* package 'AnnotationDbi' ... > ** R > ** inst > ** preparing package for lazy loading > Error: package 'Biobase' required by 'AnnotationDbi' could not be found > Execution halted > ERROR: lazy loading failed for package 'AnnotationDbi' > ** Removing '/home/mlscub1/R/i486-pc-linux-gnu- library/2.6/AnnotationDbi' > * Installing *source* package 'annotate' ... > ** R > ** data > ** inst > ** preparing package for lazy loading > Loading required package: Biobase > Warning in library(pkg, character.only = TRUE, logical.return = TRUE, > lib.loc = lib.loc) : > there is no package called 'Biobase' > Error: package 'Biobase' could not be loaded > Execution halted > ERROR: lazy loading failed for package 'annotate' > ** Removing '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6/annotate' > > The downloaded packages are in > /tmp/RtmpaoFwjZ/downloaded_packages > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'RSQLite' had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'Biobase' had non-zero exit status > 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'AnnotationDbi' had non-zero exit status > 4: In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'annotate' had non-zero exit status >> library(annotate) > Error in library(annotate) : there is no package called 'annotate' > > If anyone could explain the problem or suggest a suitable solution will be > very helpfull.... > > A.Ashwin > Departement of Biotechnology > Manipal Life Science Center > Manipal University > INDIA > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826