On 04/30/2014 01:38 PM, Julian Gehring wrote: > Hi Huma, > > Can you install a single package successfully (e.g. > 'biocLite("GenomicFeatures")')? What does 'biocValid()' tell you? The problem turned out to be a corrupt installation of the 'BatchJobs' package. We found this out by trying to use biocLite("BiocParallel") -- the first package that had problems. When that did not work we tried to install each of the BiocParallel dependencies, e.g., listed on the page 'Depends' and 'Imports' field of http://bioconductor.org/packages/release/bioc/html/BiocParallel.html When BatchJobs failed, we re-installed it with biocLite("BatchJobs"), and then had success with biocLite("SomaticSignatures") Martin > > Best wishes > Julian > > > On 30.04.2014 16:15, Huma Asif wrote: >> Dear All, >> I followed all instructions given step by step and tried to reinstall and got >> these errors? >>> source('http://bioconductor.org/biocLite.R') >> Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite >> for help >>> library(tools) >>> library(utils) >>> library(BiocInstaller) >>> biocLite("SomaticSignatures") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R >> version >> ? 3.1.0. >> Installing package(s) 'SomaticSignatures' >> also installing the dependencies ???BiocParallel???, >> ???GenomicFeatures???, ???rtracklayer???, ???biovizBase???, >> ???GenomicAlignments???, >> ???VariantAnnotation???, ???ggbio??? >> ? >> trying URL >> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/BiocParalle l_0.6.0.tar.gz' >> >> Content type 'application/x-gzip' length 296665 bytes (289 >> Kb) >> opened URL >> ================================================== >> downloaded 289 Kb >> ? >> trying URL >> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicFeat ures_1.16.0.tar.gz' >> >> Content type 'application/x-gzip' length 765601 bytes (747 >> Kb) >> opened URL >> ================================================== >> downloaded 747 Kb >> ? >> trying URL >> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/rtracklayer _1.24.0.tar.gz' >> >> Content type 'application/x-gzip' length 1337513 bytes (1.3 >> Mb) >> opened URL >> ================================================== >> downloaded 1.3 Mb >> ? >> trying URL >> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/biovizBase_ 1.12.1.tar.gz' >> Content type 'application/x-gzip' length 2429449 bytes (2.3 >> Mb) >> opened URL >> ================================================== >> downloaded 2.3 Mb >> ? >> trying URL >> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicAlig nments_1.0.0.tar.gz' >> >> Content type 'application/x-gzip' length 1935667 bytes (1.8 >> Mb) >> opened URL >> ================================================== >> downloaded 1.8 Mb >> ? >> trying URL >> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/VariantAnno tation_1.10.0.tar.gz' >> >> Content type 'application/x-gzip' length 1300072 bytes (1.2 >> Mb) >> opened URL >> ================================================== >> downloaded 1.2 Mb >> ? >> trying URL >> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/ggbio_1.12. 3.tar.gz' >> Content type 'application/x-gzip' length 2471353 bytes (2.4 >> Mb) >> opened URL >> ================================================== >> downloaded 2.4 Mb >> ? >> trying URL >> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/SomaticSign atures_1.0.0.tar.gz' >> >> Content type 'application/x-gzip' length 1007992 bytes (984 >> Kb) >> opened URL >> ================================================== >> downloaded 984 Kb >> ? >> * installing *source* package ???BiocParallel??? ... >> ** R >> ** inst >> ** preparing package for lazy loading >> Error in readRDS(nsInfoFilePath) : error reading from >> connection >> ERROR: lazy loading failed for package ???BiocParallel??? >> * removing >> ???/home/asif/R/i686-pc-linux-gnu-library/3.1/BiocParallel??? >> ERROR: dependency ???BiocParallel??? is not available for >> package ???GenomicAlignments??? >> * removing >> ???/home/asif/R/i686-pc-linux-gnu-library/3.1/GenomicAlignments??? >> ERROR: dependency ???GenomicAlignments??? is not available for >> package ???rtracklayer??? >> * removing ???/home/asif/R/i686-pc-linux-gnu- library/3.1/rtracklayer??? >> ERROR: dependency ???rtracklayer??? is not available for package >> ???GenomicFeatures??? >> * removing >> ???/home/asif/R/i686-pc-linux-gnu-library/3.1/GenomicFeatures??? >> ERROR: dependencies ???GenomicFeatures???, ???rtracklayer??? are not >> available for package ???VariantAnnotation??? >> * removing >> ???/home/asif/R/i686-pc-linux-gnu-library/3.1/VariantAnnotation??? >> ERROR: dependencies ???GenomicAlignments???, ???GenomicFeatures???, >> ???VariantAnnotation??? are not available for package ???biovizBase??? >> * removing ???/home/asif/R/i686-pc-linux-gnu- library/3.1/biovizBase??? >> ERROR: dependencies ???biovizBase???, ???GenomicFeatures???, >> ???GenomicAlignments???, ???VariantAnnotation???, ???rtracklayer??? are not >> available for >> package ???ggbio??? >> * removing >> ???/home/asif/R/i686-pc-linux-gnu-library/3.1/ggbio??? >> ERROR: dependencies ???VariantAnnotation???, ???ggbio??? are not >> available for package ???SomaticSignatures??? >> * removing >> ???/home/asif/R/i686-pc-linux-gnu-library/3.1/SomaticSignatures??? >> ? >> The downloaded source packages are in >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???/tmp/RtmpoYsGgy/downloaded_packages??? >> Warning messages: >> 1: In install.packages(pkgs = pkgs, lib = lib, repos = >> repos, ...) : >> ? installation of >> package ???BiocParallel??? had non-zero exit status >> 2: In install.packages(pkgs = pkgs, lib = lib, repos = >> repos, ...) : >> ? installation of >> package ???GenomicAlignments??? had non-zero exit status >> 3: In install.packages(pkgs = pkgs, lib = lib, repos = >> repos, ...) : >> ? installation of >> package ???rtracklayer??? had non-zero exit status >> 4: In install.packages(pkgs = pkgs, lib = lib, repos = >> repos, ...) : >> ? installation of >> package ???GenomicFeatures??? had non-zero exit status >> 5: In install.packages(pkgs = pkgs, lib = lib, repos = >> repos, ...) : >> ? installation of >> package ???VariantAnnotation??? had non-zero exit status >> 6: In install.packages(pkgs = pkgs, lib = lib, repos = >> repos, ...) : >> ? installation of >> package ???biovizBase??? had non-zero exit status >> 7: In install.packages(pkgs = pkgs, lib = lib, repos = >> repos, ...) : >> ? installation of >> package ???ggbio??? had non-zero exit status >> 8: In install.packages(pkgs = pkgs, lib = lib, repos = >> repos, ...) : >> ? installation of >> package ???SomaticSignatures??? had non-zero exit status >> 9: installed directory not writable, cannot update packages >> 'boot', >> ? 'class', 'cluster', >> 'foreign', 'KernSmooth', 'lattice', 'MASS', >> ? 'Matrix', 'mgcv', >> 'nlme', 'nnet', 'rpart', 'spatial' >> >> Regards >>> Huma >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793