[BioC] SomaticSignatures

[Julian Gehring]

Hi Huma,

Can you install a single package successfully (e.g. 
'biocLite("GenomicFeatures")')?  What does 'biocValid()' tell you?

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 errorsÂ
>> 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
> Â  3.1.0.
> Installing package(s) 'SomaticSignatures'
> also installing the dependencies ‘BiocParallel’,
> ‘GenomicFeatures’, ‘rtracklayer’, ‘biovizBase’, ‘GenomicAlignments’,
> ‘VariantAnnotation’, ‘ggbio’
> Â
> trying URL
> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/BiocParallel_0.6.0.tar.gz'
> Content type 'application/x-gzip' length 296665 bytes (289
> Kb)
> opened URL
> ==================================================
> downloaded 289 Kb
> Â
> trying URL
> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicFeatures_1.16.0.tar.gz'
> Content type 'application/x-gzip' length 765601 bytes (747
> Kb)
> opened URL
> ==================================================
> downloaded 747 Kb
> Â
> 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
> Â
> 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
> Â
> trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicAlignments_1.0.0.tar.gz'
> Content type 'application/x-gzip' length 1935667 bytes (1.8
> Mb)
> opened URL
> ==================================================
> downloaded 1.8 Mb
> Â
> trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/VariantAnnotation_1.10.0.tar.gz'
> Content type 'application/x-gzip' length 1300072 bytes (1.2
> Mb)
> opened URL
> ==================================================
> downloaded 1.2 Mb
> Â
> 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
> Â
> trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/SomaticSignatures_1.0.0.tar.gz'
> Content type 'application/x-gzip' length 1007992 bytes (984
> Kb)
> opened URL
> ==================================================
> downloaded 984 Kb
> Â
> * 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’
> Â
> The downloaded source packages are in
>                 ‘/tmp/RtmpoYsGgy/downloaded_packages’
> Warning messages:
> 1: In install.packages(pkgs = pkgs, lib = lib, repos =
> repos, ...) :
> Â  installation of
> package ‘BiocParallel’ had non-zero exit status
> 2: In install.packages(pkgs = pkgs, lib = lib, repos =
> repos, ...) :
> Â  installation of
> package ‘GenomicAlignments’ had non-zero exit status
> 3: In install.packages(pkgs = pkgs, lib = lib, repos =
> repos, ...) :
> Â  installation of
> package ‘rtracklayer’ had non-zero exit status
> 4: In install.packages(pkgs = pkgs, lib = lib, repos =
> repos, ...) :
> Â  installation of
> package ‘GenomicFeatures’ had non-zero exit status
> 5: In install.packages(pkgs = pkgs, lib = lib, repos =
> repos, ...) :
> Â  installation of
> package ‘VariantAnnotation’ had non-zero exit status
> 6: In install.packages(pkgs = pkgs, lib = lib, repos =
> repos, ...) :
> Â  installation of
> package ‘biovizBase’ had non-zero exit status
> 7: In install.packages(pkgs = pkgs, lib = lib, repos =
> repos, ...) :
> Â  installation of
> package ‘ggbio’ had non-zero exit status
> 8: In install.packages(pkgs = pkgs, lib = lib, repos =
> repos, ...) :
> Â  installation of
> package ‘SomaticSignatures’ had non-zero exit status
> 9: installed directory not writable, cannot update packages
> 'boot',
> Â  'class', 'cluster',
> 'foreign', 'KernSmooth', 'lattice', 'MASS',
> Â  'Matrix', 'mgcv',
> 'nlme', 'nnet', 'rpart', 'spatial'
>
> Regards
>> Huma
> 	[[alternative HTML version deleted]]
>
>
>
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