SomaticSignatures
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 8 months ago
United States
In addition to what Martin says, you'll need to "install" gmake, which on most linux systems is just a matter of creating a symbolic link called 'gmake' which points to make. sudo ln -s /usr/bin/make /usr/bin/gmake Dan ----- Original Message ----- > 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 2:43:18 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 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 >
Cancer SomaticSignatures Cancer SomaticSignatures • 1.5k views
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Huma Asif ▴ 90
@huma-asif-6466
Last seen 7.1 years ago
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/bio maRt_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/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://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/Gen omicRanges_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/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/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/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 ‘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/cont rib/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 > > > [[alternative HTML version deleted]]
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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_1.3 1.12.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/GenomicFeatu res_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/GenomicAlign ments_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/GenomicRange s_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/VariantAnnot ation_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_1.11.1 5.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/SomaticSigna tures_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/BiocIns taller_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/SomaticSign atures_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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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]]
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I think the errors related to Biostrings On 04/01/2014 01:13 PM, Huma Asif wrote: > * 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? I really don't know what is causing this, but can only guess that it is a corrupt file from a previous installation attempt. You might try rm -rf /home/asif/R/i686-pc-linux-gnu-library/3.1/BiocParallel > * installing *source* package ?Biostrings? ... > ** libs ... > -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 Address this (and perhaps subsequent errors relating to unavailability of Biostrings) by installing the system dependency sudo apt-get install libbz2-dev (my understanding is that a revision to the devel version of Biostrings will not require this dependency). Martin -- 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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Dear All, I followed all instructions given step by step and tried to reinstall and got these errors > source('http://bioconductor.org/biocLite.R') Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help > library(tools) > library(utils) > library(BiocInstaller) > biocLite("SomaticSignatures") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version   3.1.0. Installing package(s) 'SomaticSignatures' also installing the dependencies ‘BiocParallel’, ‘GenomicFeatures’, ‘rtracklayer’, ‘biovizBase’, ‘GenomicAlignments’, ‘VariantAnnotation’, ‘ggbio’  trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/BiocParallel_0 .6.0.tar.gz' Content type 'application/x-gzip' length 296665 bytes (289 Kb) opened URL ================================================== downloaded 289 Kb  trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicFeature s_1.16.0.tar.gz' Content type 'application/x-gzip' length 765601 bytes (747 Kb) opened URL ================================================== downloaded 747 Kb  trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/rtracklayer_1. 24.0.tar.gz' Content type 'application/x-gzip' length 1337513 bytes (1.3 Mb) opened URL ================================================== downloaded 1.3 Mb  trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/biovizBase_1.1 2.1.tar.gz' Content type 'application/x-gzip' length 2429449 bytes (2.3 Mb) opened URL ================================================== downloaded 2.3 Mb  trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Gen omicAlignments_1.0.0.tar.gz' Content type 'application/x-gzip' length 1935667 bytes (1.8 Mb) opened URL ================================================== downloaded 1.8 Mb  trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Var iantAnnotation_1.10.0.tar.gz' Content type 'application/x-gzip' length 1300072 bytes (1.2 Mb) opened URL ================================================== downloaded 1.2 Mb  trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/ggbio_1.12.3.t ar.gz' Content type 'application/x-gzip' length 2471353 bytes (2.4 Mb) opened URL ================================================== downloaded 2.4 Mb  trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Som aticSignatures_1.0.0.tar.gz' Content type 'application/x-gzip' length 1007992 bytes (984 Kb) opened URL ================================================== downloaded 984 Kb  * installing *source* package ‘BiocParallel’ ... ** R ** inst ** preparing package for lazy loading Error in readRDS(nsInfoFilePath) : error reading from connection ERROR: lazy loading failed for package ‘BiocParallel’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/BiocParallel’ ERROR: dependency ‘BiocParallel’ is not available for package ‘GenomicAlignments’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/GenomicAlignments’ ERROR: dependency ‘GenomicAlignments’ is not available for package ‘rtracklayer’ * removing ‘/home/asif/R/i686-pc-linux-gnu- library/3.1/rtracklayer’ ERROR: dependency ‘rtracklayer’ is not available for package ‘GenomicFeatures’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/GenomicFeatures’ ERROR: dependencies ‘GenomicFeatures’, ‘rtracklayer’ are not available for package ‘VariantAnnotation’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/VariantAnnotation’ ERROR: dependencies ‘GenomicAlignments’, ‘GenomicFeatures’, ‘VariantAnnotation’ are not available for package ‘biovizBase’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/biovizBase’ ERROR: dependencies ‘biovizBase’, ‘GenomicFeatures’, ‘GenomicAlignments’, ‘VariantAnnotation’, ‘rtracklayer’ are not available for package ‘ggbio’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/ggbio’ ERROR: dependencies ‘VariantAnnotation’, ‘ggbio’ are not available for package ‘SomaticSignatures’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/SomaticSignatures’  The downloaded source packages are in                ‘/tmp/RtmpoYsGgy/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘BiocParallel’ had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘GenomicAlignments’ had non-zero exit status 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘rtracklayer’ had non-zero exit status 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘GenomicFeatures’ had non-zero exit status 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘VariantAnnotation’ had non-zero exit status 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘biovizBase’ had non-zero exit status 7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘ggbio’ had non-zero exit status 8: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :   installation of package ‘SomaticSignatures’ had non-zero exit status 9: installed directory not writable, cannot update packages 'boot',   'class', 'cluster', 'foreign', 'KernSmooth', 'lattice', 'MASS',   'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial' Regards >Huma [[alternative HTML version deleted]]
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Hi Huma, Can you install a single package successfully (e.g. 'biocLite("GenomicFeatures")')? What does 'biocValid()' tell you? Best wishes Julian On 30.04.2014 16:15, Huma Asif wrote: > Dear All, > I followed all instructions given step by step and tried to reinstall and got these errors? >> source('http://bioconductor.org/biocLite.R') > Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite > for help >> library(tools) >> library(utils) >> library(BiocInstaller) >> biocLite("SomaticSignatures") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R > version > ? 3.1.0. > Installing package(s) 'SomaticSignatures' > also installing the dependencies ???BiocParallel???, > ???GenomicFeatures???, ???rtracklayer???, ???biovizBase???, ???GenomicAlignments???, > ???VariantAnnotation???, ???ggbio??? > ? > trying URL > 'http://bioconductor.org/packages/2.14/bioc/src/contrib/BiocParallel _0.6.0.tar.gz' > Content type 'application/x-gzip' length 296665 bytes (289 > Kb) > opened URL > ================================================== > downloaded 289 Kb > ? > trying URL > 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicFeatu res_1.16.0.tar.gz' > Content type 'application/x-gzip' length 765601 bytes (747 > Kb) > opened URL > ================================================== > downloaded 747 Kb > ? > trying URL > 'http://bioconductor.org/packages/2.14/bioc/src/contrib/rtracklayer_ 1.24.0.tar.gz' > Content type 'application/x-gzip' length 1337513 bytes (1.3 > Mb) > opened URL > ================================================== > downloaded 1.3 Mb > ? > trying URL > 'http://bioconductor.org/packages/2.14/bioc/src/contrib/biovizBase_1 .12.1.tar.gz' > Content type 'application/x-gzip' length 2429449 bytes (2.3 > Mb) > opened URL > ================================================== > downloaded 2.3 Mb > ? > trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/G enomicAlignments_1.0.0.tar.gz' > Content type 'application/x-gzip' length 1935667 bytes (1.8 > Mb) > opened URL > ================================================== > downloaded 1.8 Mb > ? > trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/V ariantAnnotation_1.10.0.tar.gz' > Content type 'application/x-gzip' length 1300072 bytes (1.2 > Mb) > opened URL > ================================================== > downloaded 1.2 Mb > ? > trying URL > 'http://bioconductor.org/packages/2.14/bioc/src/contrib/ggbio_1.12.3 .tar.gz' > Content type 'application/x-gzip' length 2471353 bytes (2.4 > Mb) > opened URL > ================================================== > downloaded 2.4 Mb > ? > trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/S omaticSignatures_1.0.0.tar.gz' > Content type 'application/x-gzip' length 1007992 bytes (984 > Kb) > opened URL > ================================================== > downloaded 984 Kb > ? > * installing *source* package ???BiocParallel??? ... > ** R > ** inst > ** preparing package for lazy loading > Error in readRDS(nsInfoFilePath) : error reading from > connection > ERROR: lazy loading failed for package ???BiocParallel??? > * removing > ???/home/asif/R/i686-pc-linux-gnu-library/3.1/BiocParallel??? > ERROR: dependency ???BiocParallel??? is not available for > package ???GenomicAlignments??? > * removing > ???/home/asif/R/i686-pc-linux-gnu-library/3.1/GenomicAlignments??? > ERROR: dependency ???GenomicAlignments??? is not available for > package ???rtracklayer??? > * removing ???/home/asif/R/i686-pc-linux-gnu- library/3.1/rtracklayer??? > ERROR: dependency ???rtracklayer??? is not available for package > ???GenomicFeatures??? > * removing > ???/home/asif/R/i686-pc-linux-gnu-library/3.1/GenomicFeatures??? > ERROR: dependencies ???GenomicFeatures???, ???rtracklayer??? are not > available for package ???VariantAnnotation??? > * removing > ???/home/asif/R/i686-pc-linux-gnu-library/3.1/VariantAnnotation??? > ERROR: dependencies ???GenomicAlignments???, ???GenomicFeatures???, > ???VariantAnnotation??? are not available for package ???biovizBase??? > * removing ???/home/asif/R/i686-pc-linux-gnu- library/3.1/biovizBase??? > ERROR: dependencies ???biovizBase???, ???GenomicFeatures???, > ???GenomicAlignments???, ???VariantAnnotation???, ???rtracklayer??? are not available for > package ???ggbio??? > * removing > ???/home/asif/R/i686-pc-linux-gnu-library/3.1/ggbio??? > ERROR: dependencies ???VariantAnnotation???, ???ggbio??? are not > available for package ???SomaticSignatures??? > * removing > ???/home/asif/R/i686-pc-linux-gnu-library/3.1/SomaticSignatures??? > ? > The downloaded source packages are in > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ???/tmp/RtmpoYsGgy/downloaded_packages??? > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = > repos, ...) : > ? installation of > package ???BiocParallel??? had non-zero exit status > 2: In install.packages(pkgs = pkgs, lib = lib, repos = > repos, ...) : > ? installation of > package ???GenomicAlignments??? had non-zero exit status > 3: In install.packages(pkgs = pkgs, lib = lib, repos = > repos, ...) : > ? installation of > package ???rtracklayer??? had non-zero exit status > 4: In install.packages(pkgs = pkgs, lib = lib, repos = > repos, ...) : > ? installation of > package ???GenomicFeatures??? had non-zero exit status > 5: In install.packages(pkgs = pkgs, lib = lib, repos = > repos, ...) : > ? installation of > package ???VariantAnnotation??? had non-zero exit status > 6: In install.packages(pkgs = pkgs, lib = lib, repos = > repos, ...) : > ? installation of > package ???biovizBase??? had non-zero exit status > 7: In install.packages(pkgs = pkgs, lib = lib, repos = > repos, ...) : > ? installation of > package ???ggbio??? had non-zero exit status > 8: In install.packages(pkgs = pkgs, lib = lib, repos = > repos, ...) : > ? installation of > package ???SomaticSignatures??? had non-zero exit status > 9: installed directory not writable, cannot update packages > 'boot', > ? 'class', 'cluster', > 'foreign', 'KernSmooth', 'lattice', 'MASS', > ? 'Matrix', 'mgcv', > 'nlme', 'nnet', 'rpart', 'spatial' > > Regards >> Huma > [[alternative HTML version deleted]] > > > > _______________________________________________ > 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 >
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Julian Gehring ★ 1.3k
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Hi Huma, If you haven't installed the developer version of 'SomaticSignatures' so far, it should be easy now with the bioconductor 2.14 release: biocLite("SomaticSignatures") Best wishes Julian On 24/03/14 20:02, Huma Asif wrote: > Hi > Is there any other way to install Somatic signature if not via biocLite > Do you means i have to wait till April to use this Package. > Though i have downloaded and unzip the package but dont know how to proceed next. > in document it says > The starting point of the analysis is a VRanges object which describes the somatic variants in terms of their genomic locations as well as reference and alternative alleles > > > > so do i need to install VariantAnnotation also > Sorry if it sounds stupid > Huma >
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Julian Gehring ★ 1.3k
@julian-gehring-5818
Last seen 2.4 years ago
Hi Huma, If you haven't installed the developer version of 'SomaticSignatures' so far, it should be easy now with the bioconductor 2.14 release: biocLite("SomaticSignatures") Best wishes Julian On 24/03/14 20:02, Huma Asif wrote: > Hi > Is there any other way to install Somatic signature if not via biocLite > Do you means i have to wait till April to use this Package. > Though i have downloaded and unzip the package but dont know how to proceed next. > in document it says > The starting point of the analysis is a VRanges object which describes the somatic variants in terms of their genomic locations as well as reference and alternative alleles > > > > so do i need to install VariantAnnotation also > Sorry if it sounds stupid > Huma >
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