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/Bio cParallel_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/Rsa mtools_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/BSg enome_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/Gen omicFeatures_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/rtr acklayer_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/bio vizBase_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/Gen omicAlignments_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/Var iantAnnotation_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/Bio strings_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/ggb io_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/Som aticSignatures_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_2.1 9.3.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/BiocParalle l_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/GenomicFeat ures_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/GenomicAlig nments_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/GenomicRang es_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/VariantAnno tation_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/SomaticSign atures_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/BiocIn staller_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/SomaticSig natures_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 >> >> >> >> > > [[alternative HTML version deleted]]