[BioC] SomaticSignatures
Dan Tenenbaum
dtenenba at fhcrc.org
Tue Apr 1 21:57:51 CEST 2014
Buried in all that output is the line:
Try removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/00LOCK-scales’
So try that:
rm -rf /home/asif/R/i686-pc-linux-gnu-library/3.1/00LOCK-scales
Then try the biocLite command again.
Dan
----- Original Message -----
> From: "Huma Asif" <humaasif79 at yahoo.com>
> To: "Martin Morgan" <mtmorgan at fhcrc.org>, "Steve Lianoglou" <lianoglou.steve at gene.com>, "Dan Tenenbaum"
> <dtenenba at fhcrc.org>
> Cc: "bioconductor at r-project.org list" <bioconductor at r-project.org>
> Sent: Tuesday, April 1, 2014 12:37:34 PM
> Subject: Re: [BioC] SomaticSignatures
>
>
>
> hi this is what i get now. please help with these new problems
> library(tools)
> > library(utils)
> > library(BiocInstaller)
> Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help
> > biocLite("SomaticSignatures")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.14 (BiocInstaller 1.13.3), R version
> 3.1.0.
> Installing package(s) 'SomaticSignatures'
> Error in readRDS(file) : error reading from connection
> Error in readRDS(file) : error reading from connection
> also installing the dependencies ‘biomaRt’, ‘BiocParallel’,
> ‘Rsamtools’, ‘BSgenome’, ‘GenomicFeatures’,
>
>
> ‘rtracklayer’, ‘scales’, ‘biovizBase’, ‘GenomicAlignments’,
> ‘rngtools’, ‘GenomicRanges’, ‘VariantAnnotation’,
>
>
> ‘Biostrings’, ‘ggplot2’, ‘ggbio’, ‘reshape2’, ‘NMF’
>
>
> trying URL
> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/biomaRt_2.19.3.tar.gz'
> Content type 'application/x-gzip' length 276803 bytes (270 Kb)
> opened URL
> ==================================================
> downloaded 270 Kb
>
>
> trying URL
> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/BiocParallel_0.5.18.tar.gz'
> Content type 'application/x-gzip' length 296586 bytes (289 Kb)
> opened URL
> ==================================================
> downloaded 289 Kb
>
>
> 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)
> opened URL
> ==================================================
> downloaded 2.8 Mb
>
>
> 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
> ==================================================
> downloaded 527 Kb
>
>
> 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)
> opened URL
> ==================================================
> downloaded 748 Kb
>
>
> trying URL
> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/rtracklayer_1.23.20.tar.gz'
> Content type 'application/x-gzip' length 1337394 bytes (1.3 Mb)
> opened URL
> ==================================================
> downloaded 1.3 Mb
>
>
> 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
> ==================================================
> downloaded 38 Kb
>
>
> trying URL
> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/biovizBase_1.11.13.tar.gz'
> Content type 'application/x-gzip' length 1050572 bytes (1.0 Mb)
> opened URL
> ==================================================
> downloaded 1.0 Mb
>
>
> 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
> ==================================================
> downloaded 1.8 Mb
>
>
> trying URL 'http://cran.fhcrc.org/src/contrib/rngtools_1.2.4.tar.gz'
> Content type 'application/x-gzip' length 120986 bytes (118 Kb)
> opened URL
> ==================================================
> downloaded 118 Kb
>
>
> trying URL
> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicRanges_1.15.41.tar.gz'
> Content type 'application/x-gzip' length 550470 bytes (537 Kb)
> opened URL
> ==================================================
> downloaded 537 Kb
>
>
> trying URL
> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/VariantAnnotation_1.9.48.tar.gz'
> Content type 'application/x-gzip' length 1297449 bytes (1.2 Mb)
> opened URL
> ==================================================
> downloaded 1.2 Mb
>
>
> trying URL
> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Biostrings_2.31.20.tar.gz'
> Content type 'application/x-gzip' length 1514126 bytes (1.4 Mb)
> opened URL
> ==================================================
> downloaded 1.4 Mb
>
>
> trying URL 'http://cran.fhcrc.org/src/contrib/ggplot2_0.9.3.1.tar.gz'
> Content type 'application/x-gzip' length 2330942 bytes (2.2 Mb)
> opened URL
> ==================================================
> downloaded 2.2 Mb
>
>
> trying URL
> 'http://bioconductor.org/packages/2.14/bioc/src/contrib/ggbio_1.11.15.tar.gz'
> Content type 'application/x-gzip' length 3151730 bytes (3.0 Mb)
> opened URL
> ==================================================
> downloaded 3.0 Mb
>
>
> trying URL 'http://cran.fhcrc.org/src/contrib/reshape2_1.2.2.tar.gz'
> Content type 'application/x-gzip' length 27220 bytes (26 Kb)
> opened URL
> ==================================================
> downloaded 26 Kb
>
>
> trying URL 'http://cran.fhcrc.org/src/contrib/NMF_0.20.5.tar.gz'
> Content type 'application/x-gzip' length 1763782 bytes (1.7 Mb)
> opened URL
> ==================================================
> downloaded 1.7 Mb
>
>
> 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)
> opened URL
> ==================================================
> downloaded 1.2 Mb
>
>
> * installing *source* package ‘biomaRt’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (biomaRt)
> * 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: failed to lock directory
> ‘/home/asif/R/i686-pc-linux-gnu-library/3.1’ for modifying
> Try removing
> ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/00LOCK-scales’
> * installing *source* package ‘rngtools’ ...
> ** package ‘rngtools’ successfully unpacked and MD5 sums checked
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (rngtools)
> * installing *source* package ‘GenomicRanges’ ...
> ** libs
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> IRanges_stubs.c -o IRanges_stubs.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> R_init_GenomicRanges.c -o R_init_GenomicRanges.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> XVector_stubs.c -o XVector_stubs.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> transcript_utils.c -o transcript_utils.o
> gcc -std=gnu99 -shared -L/usr/local/lib -o GenomicRanges.so
> IRanges_stubs.o R_init_GenomicRanges.o XVector_stubs.o
>
>
> transcript_utils.o
> installing to
> /home/asif/R/i686-pc-linux-gnu-library/3.1/GenomicRanges/libs
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (GenomicRanges)
> * installing *source* package ‘Biostrings’ ...
> ** libs
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> BAB_class.c -o BAB_class.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> BitMatrix.c -o BitMatrix.o
> BitMatrix.c: In function ‘debug_BitMatrix’:
> BitMatrix.c:382:3: warning: left shift count >= width of type
> [enabled by default]
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> IRanges_stubs.c -o IRanges_stubs.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> MIndex_class.c -o MIndex_class.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> PreprocessedTB_class.c -o PreprocessedTB_class.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> R_init_Biostrings.c -o R_init_Biostrings.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> RoSeqs_utils.c -o RoSeqs_utils.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> SparseList_utils.c -o SparseList_utils.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> XStringSetList_class.c -o XStringSetList_class.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> XStringSet_class.c -o XStringSet_class.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> XStringSet_io.c -o XStringSet_io.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> XString_class.c -o XString_class.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> XVector_stubs.c -o XVector_stubs.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> align_needwunsQS.c -o align_needwunsQS.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> align_pairwiseAlignment.c -o align_pairwiseAlignment.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> align_utils.c -o align_utils.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> find_palindromes.c -o find_palindromes.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> gtestsim.c -o gtestsim.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> inject_code.c -o inject_code.o
> gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG
> -I/usr/local/include -I"/home/asif/R/i686-pc-linux-gnu-
>
>
> library/3.1/IRanges/include"
> -I"/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector/include" -fpic
> -g -O2 -c
>
>
> io_utils.c -o io_utils.o
> io_utils.c:18:19: fatal error: bzlib.h: No such file or directory
> compilation terminated.
> gmake: *** [io_utils.o] Error 1
> ERROR: compilation failed for package ‘Biostrings’
> * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/Biostrings’
> * installing *source* package ‘reshape2’ ...
> ** package ‘reshape2’ successfully unpacked and MD5 sums checked
> ** R
> ** data
> *** moving datasets to lazyload DB
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> * DONE (reshape2)
> ERROR: dependency ‘Biostrings’ is not available for package
> ‘Rsamtools’
> * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/Rsamtools’
> Error in readRDS(pfile) : error reading from connection
> * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/ggplot2’
> ERROR: dependencies ‘Biostrings’, ‘Rsamtools’ are not available for
> package ‘BSgenome’
> * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/BSgenome’
> ERROR: dependency ‘ggplot2’ is not available for package ‘NMF’
> * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/NMF’
> ERROR: dependencies ‘Biostrings’, ‘Rsamtools’, ‘BSgenome’,
> ‘BiocParallel’ are not available for package
>
>
> ‘GenomicAlignments’
> * removing
> ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/GenomicAlignments’
> ERROR: dependencies ‘Biostrings’, ‘BSgenome’, ‘Rsamtools’,
> ‘GenomicAlignments’ are not available for package
>
>
> ‘rtracklayer’
> * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/rtracklayer’
> ERROR: dependencies ‘Biostrings’, ‘rtracklayer’ are not available for
> package ‘GenomicFeatures’
> * removing
> ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/GenomicFeatures’
> ERROR: dependencies ‘Rsamtools’, ‘Biostrings’, ‘BSgenome’,
> ‘GenomicFeatures’, ‘rtracklayer’ are not available for
>
>
> package ‘VariantAnnotation’
> * removing
> ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/VariantAnnotation’
> Error in readRDS(pfile) : error reading from connection
> * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/biovizBase’
> Error in readRDS(pfile) : error reading from connection
> * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/ggbio’
> ERROR: dependencies ‘VariantAnnotation’, ‘Biostrings’, ‘ggplot2’,
> ‘ggbio’, ‘NMF’ 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/Rtmprkls3c/downloaded_packages’
> Error in readRDS(file) : error reading from connection
> In addition: There were 14 warnings (use warnings() to see them)
> Warning message:
> installed directory not writable, cannot update packages 'boot',
> 'class',
> 'cluster', 'foreign', 'KernSmooth', 'MASS', 'Matrix', 'mgcv', 'nlme',
> 'nnet',
>
> 'rpart', 'spatial'
>
>
> Regards Huma
>
>
>
>
>
>
>
>
>
> From: Martin Morgan <mtmorgan at fhcrc.org>
> To: Huma Asif <humaasif79 at yahoo.com>; Steve Lianoglou
> <lianoglou.steve at gene.com>; Dan Tenenbaum <dtenenba at fhcrc.org>
> Cc: "bioconductor at r-project.org list" <bioconductor at r-project.org>
> Sent: Monday, March 31, 2014 6:43 PM
> Subject: Re: [BioC] SomaticSignatures
>
>
> On 03/31/2014 12:16 PM, Huma Asif wrote:
> > 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.
> > You are welcome to redistribute it under certain conditions.
> > Type 'license()' or 'licence()' for distribution details.
> >
> > Natural language support but running in an English locale
> >
> > R is a collaborative project with many contributors.
> > Type 'contributors()' for more information and
> > 'citation()' on how to cite R or R packages in publications.
> >
> > 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)
> > opened URL
> > ==================================================
> > downloaded 13 Kb
> >
> > * 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)
>
> At this point, to install SomaticSignatures with internet access, you
> just want to
>
> biocLite("SomaticSignatures")
>
> If that accomplishes what you want, then stop reading. If this is
> what you want
> to do, but there is an error, then please copy and paste the commands
> you used
> and the error that occurred.
>
> If you want to install SomaticSignatures from your own repository,
> then continue
> to read below
>
>
> >> 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)
> > opened URL
>
> SNIP! This info WAS useful in the original email
>
> > ==================================================
> > downloaded 10 Kb
> >
> > trying URL '
> > http://cran.fhcrc.org/src/contrib/base64enc_0.1-1.tar.gz'
> > Content type 'application/x-gzip' length 6296 bytes
> > opened URL
> > ==================================================
> > downloaded 6296 bytes
> >
> > [,1] [,2]
> > [1,] "SomaticSignatures" "./SomaticSignatures_0.99.0.tar.gz"
> > [2,] "GenomicRanges" "./GenomicRanges_1.15.41.tar.gz"
>
> SNIP
>
> > [64,] "fail" "./fail_1.2.tar.gz"
> > [65,] "base64enc" "./base64enc_0.1-1.tar.gz"
> >
> >
> > install.packages(dir('.', pattern=".tar.gz$"),
> > repos=NULL, type="source")
>
> Your command says to install the packages as given, with no
> information about
> relation between packages. It fails on the first one (AnnotationDbi)
> because it
> has not yet installed dependencies.
>
> If you want a one-time, off-line installation, then
>
> 1. create a directory, e.g., /tmp/R3.1_Bioc2.14/src/contrib/
>
> 2. download files into that directory
>
> 3. create a PACKAGES file to index the repository
>
> 4. install packages from your repository
>
> Here's what I did, entirely in R:
>
> ## 1. create repository
> repos <- "file:///tmp/R3.1_Bioc2.14"
> dest <- "/tmp/R3.1_Bioc2.14/src/contrib/"
> dir.create(dest, recursive=TRUE)
>
> ## 2. populate with relevant packages
> pdb <- available.packages(contrib.url(biocinstallRepos()))
> deps <- tools::package_dependencies("SomaticSignatures", db=pdb,
> recursive=TRUE)
> pkgs <- c("SomaticSignatures", deps$SomaticSignatures)
> download.packages(pkgs, dest, repos=biocinstallRepos(),
> type="source")
>
> ## 3. create a PACKAGES file
> tools::write_PACKAGES(dest)
>
> ## 4. install from repository
> install.packages("SomaticSignatures", repos=repos)
>
> However, it will usually be better to maintain a proper mirror of the
> Bioconductor repository, as outlined at
>
> http://bioconductor.org/about/mirrors/mirror-how-to/
>
> For instance, to mirror the software only portion of the Bioconductor
> devel branch
>
> /tmp$ mkdir -p 2.14/bioc/src/contrib
> /tmp$ rsync -zrtlv --delete
> master.bioconductor.org::2.14/bioc/src/contrib
> /tmp/2.14/bioc/src/
>
> Likely you would also mirror CRAN
> http://cran.r-project.org/mirror-howto.html
> following a similar scenario. You'd update these repositories
> regularly using
> the rsync linux command (which just downloads the changes, not the
> entire
> repository), and would install packages from them using
>
> install.packages("SomaticSignatures", repos="file:///tmp/2.14/bioc")
>
> Perhaps you would make your repositories available via a local http
> server.
> There are instructions in the 'R-admin' document
>
> http://cran.r-project.org/doc/manuals/R-admin.html#Setting-up-a-package-repository
>
>
>
> >
> > now the summary of warning after this command i attached please see
> > Regards
> > Huma
> >
> >
> >
> > _______________________________________________
> > 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
>
>
>
>
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