Packages not getting installed
2
0
Entering edit mode
Ashwin Kumar ▴ 90
@ashwin-kumar-3410
Last seen 10.3 years ago
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]]
Microarray GO annotate Microarray GO annotate • 5.3k views
ADD COMMENT
0
Entering edit mode
@anna-freni-sterrantino-2847
Last seen 10.3 years ago
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]]
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 2 days ago
United States
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
ADD COMMENT

Login before adding your answer.

Traffic: 640 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6