[BioC] SomaticSignatures
Huma Asif
humaasif79 at yahoo.com
Mon Mar 31 21:16:16 CEST 2014
Hi every one,
here is the new summary of what i did. sorry in advance for if it bothers u much.
first
R
R version 3.1.0 alpha (2014-03-25 r65283)
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: i686-pc-linux-gnu (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Then > source("http://bioconductor.org/biocLite.R")
Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) :
'lib = "/usr/local/lib/R/library"' is not writable
Would you like to use a personal library instead? (y/n) y
Would you like to create a personal library
~/R/i686-pc-linux-gnu-library/3.1
to install packages into? (y/n) y
trying URL 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInstaller_1.13.3.tar.gz'
Content type 'application/x-gzip' length 14183 bytes (13 Kb)
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* installing *source* package ‘BiocInstaller’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help
* DONE (BiocInstaller)
The downloaded source packages are in
‘/tmp/RtmpM1d0B0/downloaded_packages’
Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help
> library(tools)
> library(utils)
> library(BiocInstaller)
> pdb <- available.packages(contrib.url(biocinstallRepos()))
> pkgs <- unlist(unname(package_dependencies("SomaticSignatures",
+ db=pdb, recursive=TRUE)))
> pkgs <- c("SomaticSignatures", pkgs)
> download.packages(pkgs, '.', repos=biocinstallRepos(), type="source")
trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/SomaticSignatures_0.99.0.tar.gz'
Content type 'application/x-gzip' length 1270216 bytes (1.2 Mb)
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicRanges_1.15.41.tar.gz'
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/IRanges_1.21.38.tar.gz'
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/VariantAnnotation_1.9.48.tar.gz'
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Biostrings_2.31.20.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/reshape2_1.2.2.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/NMF_0.20.5.tar.gz'
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no package ‘methods’ at the repositories
trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/pcaMethods_1.53.4.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/gtools_3.3.1.tar.gz'
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/BiocGenerics_0.9.3.tar.gz'
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/XVector_0.3.7.tar.gz'
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Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") :
no package ‘graphics’ at the repositories
Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") :
no package ‘stats’ at the repositories
Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") :
no package ‘utils’ at the repositories
trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/zlibbioc_1.9.0.tar.gz'
Content type 'application/x-gzip' length 257656 bytes (251 Kb)
opened URL
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomeInfoDb_0.99.26.tar.gz'
Content type 'application/x-gzip' length 190989 bytes (186 Kb)
opened URL
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Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") :
no package ‘grid’ at the repositories
Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") :
no package ‘grDevices’ at the repositories
trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/biovizBase_1.11.13.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/gtable_0.1.2.tar.gz'
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opened URL
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Biobase_2.23.6.tar.gz'
Content type 'application/x-gzip' length 1865270 bytes (1.8 Mb)
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicFeatures_1.15.13.tar.gz'
Content type 'application/x-gzip' length 765992 bytes (748 Kb)
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Rsamtools_1.15.37.tar.gz'
Content type 'application/x-gzip' length 2935389 bytes (2.8 Mb)
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicAlignments_0.99.32.tar.gz'
Content type 'application/x-gzip' length 1936773 bytes (1.8 Mb)
opened URL
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/BSgenome_1.31.12.tar.gz'
Content type 'application/x-gzip' length 540283 bytes (527 Kb)
opened URL
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trying URL 'http://cran.fhcrc.org/src/contrib/gridExtra_0.9.1.tar.gz'
Content type 'application/x-gzip' length 29183 bytes (28 Kb)
opened URL
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trying URL 'http://cran.fhcrc.org/src/contrib/scales_0.2.3.tar.gz'
Content type 'application/x-gzip' length 39429 bytes (38 Kb)
opened URL
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trying URL 'http://cran.fhcrc.org/src/contrib/Hmisc_3.14-3.tar.gz'
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/rtracklayer_1.23.20.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/plyr_1.8.1.tar.gz'
Content type 'application/x-gzip' length 393233 bytes (384 Kb)
opened URL
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trying URL 'http://cran.fhcrc.org/src/contrib/digest_0.6.4.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/proto_0.3-10.tar.gz'
Content type 'application/x-gzip' length 530758 bytes (518 Kb)
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trying URL 'http://cran.fhcrc.org/src/contrib/MASS_7.3-31.tar.gz'
Content type 'application/x-gzip' length 486427 bytes (475 Kb)
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Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") :
no package ‘stats4’ at the repositories
trying URL 'http://cran.fhcrc.org/src/contrib/pkgmaker_0.20.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/registry_0.2.tar.gz'
Content type 'application/x-gzip' length 196136 bytes (191 Kb)
opened URL
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trying URL 'http://cran.fhcrc.org/src/contrib/rngtools_1.2.4.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/cluster_1.15.2.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/gridBase_0.4-7.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/colorspace_1.2-4.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/RColorBrewer_1.0-5.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/foreach_1.4.1.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/doParallel_1.0.8.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/Rcpp_0.11.1.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/lattice_0.20-27.tar.gz'
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opened URL
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/AnnotationDbi_1.25.17.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/DBI_0.2-7.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/RSQLite_0.11.4.tar.gz'
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opened URL
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downloaded 1.5 Mb
Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") :
no package ‘parallel’ at the repositories
trying URL 'http://cran.fhcrc.org/src/contrib/dichromat_2.0-0.tar.gz'
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opened URL
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trying URL 'http://cran.fhcrc.org/src/contrib/iterators_1.0.6.tar.gz'
Content type 'application/x-gzip' length 287154 bytes (280 Kb)
opened URL
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trying URL 'http://cran.fhcrc.org/src/contrib/codetools_0.2-8.tar.gz'
Content type 'application/x-gzip' length 12392 bytes (12 Kb)
opened URL
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/BiocParallel_0.5.18.tar.gz'
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trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/biomaRt_2.19.3.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-4.1.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/survival_2.37-7.tar.gz'
Content type 'application/x-gzip' length 4132583 bytes (3.9 Mb)
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trying URL 'http://cran.fhcrc.org/src/contrib/Formula_1.1-1.tar.gz'
Content type 'application/x-gzip' length 148430 bytes (144 Kb)
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trying URL 'http://cran.fhcrc.org/src/contrib/latticeExtra_0.6-26.tar.gz'
Content type 'application/x-gzip' length 1295154 bytes (1.2 Mb)
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Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") :
no package ‘tools’ at the repositories
trying URL 'http://cran.fhcrc.org/src/contrib/xtable_1.7-3.tar.gz'
Content type 'application/x-gzip' length 357303 bytes (348 Kb)
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trying URL 'http://cran.fhcrc.org/src/contrib/bitops_1.0-6.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.98-1.1.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/munsell_0.4.2.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/labeling_0.2.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/BatchJobs_1.2.tar.gz'
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opened URL
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trying URL 'http://cran.fhcrc.org/src/contrib/BBmisc_1.5.tar.gz'
Content type 'application/x-gzip' length 54602 bytes (53 Kb)
opened URL
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Warning in download.packages(pkgs, ".", repos = biocinstallRepos(), type = "source") :
no package ‘splines’ at the repositories
trying URL 'http://cran.fhcrc.org/src/contrib/sendmailR_1.1-2.tar.gz'
Content type 'application/x-gzip' length 7071 bytes
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trying URL 'http://cran.fhcrc.org/src/contrib/brew_1.0-6.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/fail_1.2.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/base64enc_0.1-1.tar.gz'
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[,1] [,2]
[1,] "SomaticSignatures" "./SomaticSignatures_0.99.0.tar.gz"
[2,] "GenomicRanges" "./GenomicRanges_1.15.41.tar.gz"
[3,] "IRanges" "./IRanges_1.21.38.tar.gz"
[4,] "VariantAnnotation" "./VariantAnnotation_1.9.48.tar.gz"
[5,] "Biostrings" "./Biostrings_2.31.20.tar.gz"
[6,] "ggplot2" "./ggplot2_0.9.3.1.tar.gz"
[7,] "ggbio" "./ggbio_1.11.15.tar.gz"
[8,] "stringr" "./stringr_0.6.2.tar.gz"
[9,] "reshape2" "./reshape2_1.2.2.tar.gz"
[10,] "NMF" "./NMF_0.20.5.tar.gz"
[11,] "pcaMethods" "./pcaMethods_1.53.4.tar.gz"
[12,] "gtools" "./gtools_3.3.1.tar.gz"
[13,] "BiocGenerics" "./BiocGenerics_0.9.3.tar.gz"
[14,] "XVector" "./XVector_0.3.7.tar.gz"
[15,] "zlibbioc" "./zlibbioc_1.9.0.tar.gz"
[16,] "GenomeInfoDb" "./GenomeInfoDb_0.99.26.tar.gz"
[17,] "biovizBase" "./biovizBase_1.11.13.tar.gz"
[18,] "gtable" "./gtable_0.1.2.tar.gz"
[19,] "Biobase" "./Biobase_2.23.6.tar.gz"
[20,] "GenomicFeatures" "./GenomicFeatures_1.15.13.tar.gz"
[21,] "Rsamtools" "./Rsamtools_1.15.37.tar.gz"
[22,] "GenomicAlignments" "./GenomicAlignments_0.99.32.tar.gz"
[23,] "BSgenome" "./BSgenome_1.31.12.tar.gz"
[24,] "gridExtra" "./gridExtra_0.9.1.tar.gz"
[25,] "scales" "./scales_0.2.3.tar.gz"
[26,] "Hmisc" "./Hmisc_3.14-3.tar.gz"
[27,] "rtracklayer" "./rtracklayer_1.23.20.tar.gz"
[28,] "plyr" "./plyr_1.8.1.tar.gz"
[29,] "digest" "./digest_0.6.4.tar.gz"
[30,] "proto" "./proto_0.3-10.tar.gz"
[31,] "MASS" "./MASS_7.3-31.tar.gz"
[32,] "pkgmaker" "./pkgmaker_0.20.tar.gz"
[33,] "registry" "./registry_0.2.tar.gz"
[34,] "rngtools" "./rngtools_1.2.4.tar.gz"
[35,] "cluster" "./cluster_1.15.2.tar.gz"
[36,] "gridBase" "./gridBase_0.4-7.tar.gz"
[37,] "colorspace" "./colorspace_1.2-4.tar.gz"
[38,] "RColorBrewer" "./RColorBrewer_1.0-5.tar.gz"
[39,] "foreach" "./foreach_1.4.1.tar.gz"
[40,] "doParallel" "./doParallel_1.0.8.tar.gz"
[41,] "Rcpp" "./Rcpp_0.11.1.tar.gz"
[42,] "lattice" "./lattice_0.20-27.tar.gz"
[43,] "AnnotationDbi" "./AnnotationDbi_1.25.17.tar.gz"
[44,] "DBI" "./DBI_0.2-7.tar.gz"
[45,] "RSQLite" "./RSQLite_0.11.4.tar.gz"
[46,] "dichromat" "./dichromat_2.0-0.tar.gz"
[47,] "iterators" "./iterators_1.0.6.tar.gz"
[48,] "codetools" "./codetools_0.2-8.tar.gz"
[49,] "BiocParallel" "./BiocParallel_0.5.18.tar.gz"
[50,] "biomaRt" "./biomaRt_2.19.3.tar.gz"
[51,] "RCurl" "./RCurl_1.95-4.1.tar.gz"
[52,] "survival" "./survival_2.37-7.tar.gz"
[53,] "Formula" "./Formula_1.1-1.tar.gz"
[54,] "latticeExtra" "./latticeExtra_0.6-26.tar.gz"
[55,] "xtable" "./xtable_1.7-3.tar.gz"
[56,] "bitops" "./bitops_1.0-6.tar.gz"
[57,] "XML" "./XML_3.98-1.1.tar.gz"
[58,] "munsell" "./munsell_0.4.2.tar.gz"
[59,] "labeling" "./labeling_0.2.tar.gz"
[60,] "BatchJobs" "./BatchJobs_1.2.tar.gz"
[61,] "BBmisc" "./BBmisc_1.5.tar.gz"
[62,] "sendmailR" "./sendmailR_1.1-2.tar.gz"
[63,] "brew" "./brew_1.0-6.tar.gz"
[64,] "fail" "./fail_1.2.tar.gz"
[65,] "base64enc" "./base64enc_0.1-1.tar.gz"
install.packages(dir('.', pattern=".tar.gz$"),
repos=NULL, type="source")
now the summary of warning after this command i attached please see
Regards
Huma
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