[BioC] SomaticSignatures

[Martin Morgan]

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 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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>
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