hi i tried as you said. error reduced from 14 to 12 but still there:(
> 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
also installing the dependencies ‘BiocParallel’, ‘Rsamtools’, ‘BSgenome’, ‘GenomicFeatures’, ‘rtracklayer’, ‘scales’, ‘biovizBase’, ‘GenomicAlignments’, 

‘VariantAnnotation’, ‘Biostrings’, ‘ggplot2’, ‘ggbio’, ‘NMF’

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://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/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 ‘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’
* installing *source* package ‘scales’ ...
** package ‘scales’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (scales)
* 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’
ERROR: dependency ‘Biostrings’ is not available for package ‘Rsamtools’
* removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/Rsamtools’
* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ 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 (ggplot2)
ERROR: dependencies ‘Biostrings’, ‘Rsamtools’ are not available for package ‘BSgenome’
* removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/BSgenome’
* installing *source* package ‘NMF’ ...
** package ‘NMF’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c distance.cpp -o distance.o
g++ -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c divergence.cpp -o divergence.o
g++ -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c euclidean.cpp -o euclidean.o
g++ -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c utils.cpp -o utils.o
g++ -shared -L/usr/local/lib -o NMF.so distance.o divergence.o euclidean.o utils.o
installing to /home/asif/R/i686-pc-linux-gnu-library/3.1/NMF/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Setting package specific options: package:NMF (10 default option(s))
Registering extra action 'Biobase' for handler 'install.packages' ... OK
Creating meta registry in package 'NMF' ... OK
Creating registry 'pkgmaker::extra_action' in package 'NMF' ... OK
Adding entry 'Biobase' in registry 'pkgmaker::extra_action' ... OK
Creating registry 'algorithm' in package 'NMF' ... OK
Registering NMF algorithm '.R#brunet' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'brunet' [NMFStrategyIterative] based on template '.R#brunet' ... OK
Registering NMF algorithm 'KL' [NMFStrategyIterative] ... OK
Registering NMF algorithm '.R#lee' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'lee' [NMFStrategyIterative] based on template '.R#lee' ... OK
Registering NMF algorithm 'Frobenius' [NMFStrategyIterative] ... OK
Registering NMF algorithm '.R#offset' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'offset' [NMFStrategyIterative] based on template '.R#offset' ... OK
Registering NMF algorithm '.R#nsNMF' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'nsNMF' [NMFStrategyIterative] based on template '.R#nsNMF' ... OK
Registering NMF algorithm '.M#brunet' [NMFStrategyOctave] ... OK
Registering NMF algorithm 'ls-nmf' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'pe-nmf' [NMFStrategyIterative] ... OK
Registering NMF algorithm '.siNMF' [NMFStrategyIterative] based on template 'lee' ... OK
Registering NMF algorithm 'siNMF' [NMFStrategyIterative] based on template 'lee' ... OK
Registering NMF algorithm 'snmf/r' [NMFStrategyFunction] ... OK
Registering NMF algorithm 'snmf/l' [NMFStrategyFunction] ... OK
Creating registry 'seed' in package 'NMF' ... OK
Registering extra action 'bigmemory' for handler 'install.packages' ... OK
Adding entry 'bigmemory' in registry 'pkgmaker::extra_action' ... OK
Registering extra action 'synchronicity' for handler 'install.packages' ... OK
Adding entry 'synchronicity' in registry 'pkgmaker::extra_action' ... OK
Registering NMF seeding method 'none' [NMFSeed] ... OK
Registering NMF seeding method 'random' [NMFSeed] ... OK
Registering NMF seeding method 'ica' [NMFSeed] ... OK
Registering NMF seeding method 'nndsvd' [NMFSeed] ... OK
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (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: dependencies ‘Biostrings’, ‘Rsamtools’, ‘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’, ‘Rsamtools’, ‘GenomicAlignments’, ‘BSgenome’, ‘VariantAnnotation’, ‘rtracklayer’, ‘Biostrings’ are not 

available for package ‘ggbio’
* removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/ggbio’
ERROR: dependencies ‘VariantAnnotation’, ‘Biostrings’, ‘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/Rtmp8lYN7H/downloaded_packages’
There were 12 warnings (use warnings() to see them)
> 



>________________________________
> From: Dan Tenenbaum <dtenenba@fhcrc.org>
>To: Huma Asif <humaasif79@yahoo.com> 
>Cc: "bioconductor@r-project.org list" <bioconductor@r-project.org>; Martin Morgan <mtmorgan@fhcrc.org>; Steve Lianoglou <lianoglou.steve@gene.com> 
>Sent: Tuesday, April 1, 2014 4:57 PM
>Subject: Re: [BioC] SomaticSignatures
> 
>
>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@yahoo.com>
>> To: "Martin Morgan" <mtmorgan@fhcrc.org>, "Steve Lianoglou" <lianoglou.steve@gene.com>, "Dan Tenenbaum"
>> <dtenenba@fhcrc.org>
>> Cc: "bioconductor@r-project.org list" <bioconductor@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@fhcrc.org>
>> To: Huma Asif <humaasif79@yahoo.com>; Steve Lianoglou
>> <lianoglou.steve@gene.com>; Dan Tenenbaum <dtenenba@fhcrc.org>
>> Cc: "bioconductor@r-project.org list" <bioconductor@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@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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