Hi, I am working on "Microarray Data analysis" using R programming. I need to do some Gene Ontology and Pathway analysis of the extracted genelist. For the same i am trying to download some Packages like - > goTools, topGO for Gene Ontology. > sigPathway for Pathway analysis. But unfortunately i am not able to download them successfully, All the time i am trying, I am getting a "lazy loading failed error!". And this is the error same for all the packages which i am trying to download. Every time am down loading, some portion of the package is getting downloaded but after some time the downloaded packages gets stored in to a temp. file and the downloading is terminated with a lazy loading error! > source("http://bioconductor.org/biocLite.R") > biocLite("sigPathway", dependencies=TRUE) Running biocinstall version 2.3.14 with R version 2.8.1 Your version of R requires version 2.3 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/veerendra/R/i486-pc-linux-gnu-library/2.8' also installing the dependencies ‘hgu95av2.db’, ‘GO.db’, ‘hgu133a.db’, ‘XML’, ‘AnnotationDbi’ trying URL ' http://bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu95 av2.db_2.2.5.tar.gz ' Content type 'application/x-gzip' length 14191802 bytes (13.5 Mb) opened URL ================================================== downloaded 13.5 Mb trying URL ' http://bioconductor.org/packages/2.3/data/annotation/src/contrib/GO.db _2.2.5.tar.gz ' Content type 'application/x-gzip' length 12812568 bytes (12.2 Mb) opened URL ================================================== downloaded 12.2 Mb trying URL ' http://bioconductor.org/packages/2.3/data/annotation/src/contrib/hgu13 3a.db_2.2.5.tar.gz ' Content type 'application/x-gzip' length 17991647 bytes (17.2 Mb) opened URL ====================================== downloaded 761 Kb trying URL ' http://bioconductor.org/packages/2.3/bioc/src/contrib/AnnotationDbi_1. 4.3.tar.gz ' Content type 'application/x-gzip' length 625680 bytes (611 Kb) opened URL ================================================== downloaded 611 Kb trying URL ' http://bioconductor.org/packages/2.3/bioc/src/contrib/sigPathway_1.10. 0.tar.gz ' Content type 'application/x-gzip' length 968137 bytes (945 Kb) opened URL ================================================== downloaded 945 Kb * Installing *source* package 'XML' ... 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 sed... /bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package 'XML' ** Removing '/home/veerendra/R/i486-pc-linux-gnu-library/2.8/XML' * Installing *source* package 'AnnotationDbi' ... ** R ** inst ** preparing package for lazy loading Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Error in loadNamespace(i, c(lib.loc, .libPaths())) : there is no package called 'RSQLite' Calls: <anonymous> ... code2LazyLoadDB -> loadNamespace -> namespaceImport -> loadNamespace Execution halted ERROR: lazy loading failed for package 'AnnotationDbi' ** Removing '/home/veerendra/R/i486-pc-linux-gnu- library/2.8/AnnotationDbi' * Installing *source* package 'sigPathway' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c calc_gene_set_internal.c -o calc_gene_set_internal.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c calc_gene_set_stat.c -o calc_gene_set_stat.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c calc_probe_stat.c -o calc_probe_stat.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c calc_weights.c -o calc_weights.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c matrix_fn.c -o matrix_fn.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c permute.c -o permute.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c shuffle.c -o shuffle.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c sigPathway.c -o sigPathway.o gcc -std=gnu99 -shared -o sigPathway.so calc_gene_set_internal.o calc_gene_set_stat.o calc_probe_stat.o calc_weights.o matrix_fn.o permute.o shuffle.o sigPathway.o -llapack -lblas -lgfortran -lm -L/usr/lib/R/lib -lR ** R ** data ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'sigPathway' Formats: text html latex example MuscleExample text html latex calcTNullFast text html latex calcTStatFast text html latex example calculate.GSEA text html latex calculate.NGSk text html latex example calculatePathwayStatistics text html latex example estimateNumPerm text html latex example getPathwayStatistics.NGSk text html latex getPathwayStatistics text html latex importGeneSets text html latex rankPathways.NGSk text html latex rankPathways text html latex runSigPathway text html latex example selectGeneSets text html latex writeSigPathway text html latex ** building package indices ... * DONE (sigPathway) * Installing *source* package 'hgu95av2.db' ... ** R ** inst ** preparing package for lazy loading Error: package 'AnnotationDbi' required by 'hgu95av2.db' could not be found Execution halted ERROR: lazy loading failed for package 'hgu95av2.db' ** Removing '/home/veerendra/R/i486-pc-linux-gnu- library/2.8/hgu95av2.db' * Installing *source* package 'GO.db' ... ** R ** inst ** preparing package for lazy loading Error: package 'AnnotationDbi' required by 'GO.db' could not be found Execution halted ERROR: lazy loading failed for package 'GO.db' ** Removing '/home/veerendra/R/i486-pc-linux-gnu-library/2.8/GO.db' * Installing *source* package 'hgu133a.db' ... ** R ** inst ** preparing package for lazy loading Error: package 'AnnotationDbi' required by 'hgu133a.db' could not be found Execution halted ERROR: lazy loading failed for package 'hgu133a.db' ** Removing '/home/veerendra/R/i486-pc-linux-gnu- library/2.8/hgu133a.db' The downloaded packages are in /tmp/Rtmpnf0fC4/downloaded_packages Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : dependency ‘RSQLite’ is not available 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'XML' 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 'hgu95av2.db' had non-zero exit status 5: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'GO.db' had non-zero exit status 6: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'hgu133a.db' had non-zero exit status Is there any solution for this problem. if its there then please help me out, As i am facing this problem from last two weeks!. thank you! -- Veerendra. 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[snip] > * Installing *source* package 'XML' ... > 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 sed... /bin/sed > checking for pkg-config... /usr/bin/pkg-config > checking for xml2-config... no > Cannot find xml2-config > ERROR: configuration failed for package 'XML' > ** Removing '/home/veerendra/R/i486-pc-linux-gnu-library/2.8/XML' > * Installing *source* package 'AnnotationDbi' ... ^this you cannot install package XML which is a dependency of other packages, because you need libxml2 I guess you are using red-hat, centos or smth, you didn't give the sessionInfo(). Install libxml2 and libxml2-devel using your package manager, aka.: # yum install libxml2 libxml2-devel or apt-get install ^^ on debian

Hi, let's keep it on the list. you can use apt-get install. Not sure about the package names there, try apt-cache search libxml2 to find out. Also these dependencies on XML affect other package installation, try to get XML installed first, then continue with biobase. Of course, *in principle* these dependencies to external libraries should be listed in the package documentation/README file somewhere (and i guess for XML they are...) Cheers Michael Am Oct 7, 2010 um 2:44 PM schrieb Veerendra GP: > I am using ubuntu 9.04- Tha jaunty jackalop. so, can i use the same command to download it? > > On Thu, Oct 7, 2010 at 6:00 PM, Michael Dondrup <michael.dondrup at="" uni.no=""> wrote: > [snip] > > * Installing *source* package 'XML' ... > > 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 sed... /bin/sed > > checking for pkg-config... /usr/bin/pkg-config > > checking for xml2-config... no > > Cannot find xml2-config > > ERROR: configuration failed for package 'XML' > > ** Removing '/home/veerendra/R/i486-pc-linux-gnu-library/2.8/XML' > > * Installing *source* package 'AnnotationDbi' ... > > ^this > you cannot install package XML which is a dependency of other packages, because you need libxml2 > I guess you are using red-hat, centos or smth, you didn't give the sessionInfo(). > Install libxml2 and libxml2-devel using your package manager, aka.: > # yum install libxml2 libxml2-devel > or apt-get install ^^ on debian > > > > -- > Veerendra.