Hi I purged R from the system and installed a fresh. Then opened R, issued these commands and got the same error as before... > source("http://www.bioconductor.org/biocLite.R") > biocLite("ArrayExpressHTS") > biocLite("ShortRead") > biocLite("Rsamtools") ** preparing package for lazy loading Error : object ‘normalizePath’ is not exported by 'namespace:utils' ERROR: lazy loading failed for package ‘Rsamtools’ * removing ‘/usr/local/lib/R/site-library/Rsamtools’ Please, where am I going wrong? Full R output below Thanks John jn42@bioinf4:/home/jn42# R R version 2.14.0 (2011-10-31) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-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. [Previously saved workspace restored] > source("http://www.bioconductor.org/biocLite.R") Installing package(s) into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/ BiocInstaller_1.2.1.tar.gz' Content type 'application/x-gzip' length 9097 bytes opened URL ================================================== downloaded 9097 bytes * 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 BiocInstaller version 1.2.1, ?biocLite for help * DONE (BiocInstaller) The downloaded packages are in ‘/tmp/Rtmp0hLYYZ/downloaded_packages’ BiocInstaller version 1.2.1, ?biocLite for help Attaching package: ‘BiocInstaller’ The following object(s) are masked _by_ ‘.GlobalEnv’: biocinstallRepos, biocLite > biocLite("ArrayExpressHTS") Using R version 2.14.0, biocinstall version 2.6.8. Installing Bioconductor version 2.6 packages: [1] "ArrayExpressHTS" Please wait... Installing package(s) into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘ArrayExpressHTS’ is not available (for R version 2.14.0) > biocLite("ShortRead") Using R version 2.14.0, biocinstall version 2.6.8. Installing Bioconductor version 2.6 packages: [1] "ShortRead" Please wait... Installing package(s) into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) also installing the dependencies ‘IRanges’, ‘GenomicRanges’, ‘Biostrings’, ‘Rsamtools’, ‘Biobase’, ‘hwriter’ trying URL 'http://www.bioconductor.org/packages/2.6/bioc/src/contrib/ IRanges_1.6.17.tar.gz' Content type 'application/x-gzip' length 532086 bytes (519 Kb) opened URL ================================================== downloaded 519 Kb trying URL 'http://www.bioconductor.org/packages/2.6/bioc/src/contrib/ GenomicRanges_1.0.9.tar.gz' Content type 'application/x-gzip' length 773023 bytes (754 Kb) opened URL ================================================== downloaded 754 Kb trying URL 'http://www.bioconductor.org/packages/2.6/bioc/src/contrib/ Biostrings_2.16.9.tar.gz' Content type 'application/x-gzip' length 1023015 bytes (999 Kb) opened URL ================================================== downloaded 999 Kb trying URL 'http://www.bioconductor.org/packages/2.6/bioc/src/contrib/ Rsamtools_1.0.8.tar.gz' Content type 'application/x-gzip' length 1451209 bytes (1.4 Mb) opened URL ================================================== downloaded 1.4 Mb trying URL 'http://www.bioconductor.org/packages/2.6/bioc/src/contrib/ Biobase_2.8.0.tar.gz' Content type 'application/x-gzip' length 1971622 bytes (1.9 Mb) opened URL ================================================== downloaded 1.9 Mb trying URL 'http://cran.fhcrc.org/src/contrib/hwriter_1.3.tar.gz' Content type 'application/x-gzip' length 112608 bytes (109 Kb) opened URL ================================================== downloaded 109 Kb trying URL 'http://www.bioconductor.org/packages/2.6/bioc/src/contrib/ ShortRead_1.6.2.tar.gz' Content type 'application/x-gzip' length 1977572 bytes (1.9 Mb) opened URL ================================================== downloaded 1.9 Mb * installing *source* package ‘IRanges’ ... ** libs gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c AEbufs.c -o AEbufs.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c DataFrame_class.c -o DataFrame_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c GappedRanges_class.c -o GappedRanges_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c Grouping_class.c -o Grouping_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c IRanges_class.c -o IRanges_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c IRanges_constructor.c -o IRanges_constructor.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c IRanges_utils.c -o IRanges_utils.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c IntervalTree.c -o IntervalTree.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c R_init_IRanges.c -o R_init_IRanges.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c RangedData_class.c -o RangedData_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c RleViews_utils.c -o RleViews_utils.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c Rle_class.c -o Rle_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c Rle_utils.c -o Rle_utils.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c SEXP_utils.c -o SEXP_utils.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c Sequence_class.c -o Sequence_class.o Sequence_class.c: In function ‘vector_seqselect’: Sequence_class.c:95:4: warning: implicit declaration of function ‘UNIMPLEMENTED_TYPE’ [-Wimplicit-function-declaration] gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c SharedDouble_utils.c -o SharedDouble_utils.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c SharedInteger_utils.c -o SharedInteger_utils.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c SharedRaw_utils.c -o SharedRaw_utils.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c SharedVector_class.c -o SharedVector_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c SimpleList_class.c -o SimpleList_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c SimpleRangesList_class.c -o SimpleRangesList_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c XDoubleViews_class.c -o XDoubleViews_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c XIntegerViews_class.c -o XIntegerViews_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c XIntegerViews_utils.c -o XIntegerViews_utils.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c XVectorList_class.c -o XVectorList_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c XVector_class.c -o XVector_class.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c anyMissing.c -o anyMissing.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c chain_io.c -o chain_io.o chain_io.c: In function ‘read_chain_file’: chain_io.c:113:14: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c common.c -o common.o common.c: In function ‘firstWordInFile’: common.c:1787:6: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c compact_bitvector.c -o compact_bitvector.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c coverage.c -o coverage.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c dlist.c -o dlist.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c errabort.c -o errabort.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c hash.c -o hash.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c localmem.c -o localmem.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c memalloc.c -o memalloc.o memalloc.c: In function ‘carefulAlloc’: memalloc.c:293:2: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ [-Wformat] memalloc.c:293:2: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ [-Wformat] gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c rbTree.c -o rbTree.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c sort_utils.c -o sort_utils.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c strutils.c -o strutils.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c vector_copy.c -o vector_copy.o gcc -std=gnu99 -shared -o IRanges.so AEbufs.o CompressedIRangesList_class.o DataFrame_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o IRanges_utils.o IntervalTree.o Ocopy_byteblocks.o R_init_IRanges.o RangedData_class.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o Sequence_class.o SharedDouble_utils.o SharedInteger_utils.o SharedRaw_utils.o SharedVector_class.o SimpleList_class.o SimpleRangesList_class.o XDoubleViews_class.o XIntegerViews_class.o XIntegerViews_utils.o XVectorList_class.o XVector_class.o anyMissing.o chain_io.o common.o compact_bitvector.o coverage.o dlist.o errabort.o hash.o localmem.o memalloc.o rbTree.o sort_utils.o strutils.o vector_copy.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/IRanges/libs ** R ** inst ** preparing package for lazy loading Creating a generic function for ‘NROW’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘window’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘head’ from package ‘utils’ in package ‘IRanges’ Creating a generic function for ‘tail’ from package ‘utils’ in package ‘IRanges’ Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’ Creating a new generic function for ‘rep.int’ in package ‘IRanges’ Creating a generic function for ‘subset’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘append’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘stack’ from package ‘utils’ in package ‘IRanges’ Creating a generic function for ‘lapply’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘sapply’ from package ‘base’ in package ‘IRanges’ Creating a new generic function for ‘mapply’ in package ‘IRanges’ Creating a generic function for ‘tapply’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘aggregate’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘as.list’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘Reduce’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘Filter’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘Find’ from package ‘base’ in package ‘IRanges’ Creating a new generic function for ‘Map’ in package ‘IRanges’ Creating a generic function for ‘Position’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘eval’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘with’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘NCOL’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘na.omit’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘na.exclude’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘IRanges’ Creating a new generic function for ‘cbind’ in package ‘IRanges’ Creating a new generic function for ‘rbind’ in package ‘IRanges’ Creating a generic function for ‘xtabs’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘start’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘end’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘update’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘as.data.frame’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘unlist’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘duplicated’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘unique’ from package ‘base’ in package ‘IRanges’ Creating a new generic function for ‘order’ in package ‘IRanges’ Creating a generic function for ‘sort’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘rank’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘%in%’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘union’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘intersect’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘setdiff’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘as.vector’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘is.unsorted’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘split’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘summary’ from package ‘base’ in package ‘IRanges’ Creating a new generic function for ‘table’ in package ‘IRanges’ Creating a generic function for ‘which’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘diff’ from package ‘base’ in package ‘IRanges’ Creating a new generic function for ‘pmax’ in package ‘IRanges’ Creating a new generic function for ‘pmin’ in package ‘IRanges’ Creating a new generic function for ‘pmax.int’ in package ‘IRanges’ Creating a new generic function for ‘pmin.int’ in package ‘IRanges’ Creating a generic function for ‘mean’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘var’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘cov’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘cor’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘sd’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘median’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘quantile’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘mad’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘IQR’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘nchar’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘substr’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘substring’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’ Creating a new generic function for ‘paste’ in package ‘IRanges’ Creating a generic function for ‘levels’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘toString’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘nrow’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘ncol’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘rownames’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘colnames’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘rownames<-’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘colnames<-’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘within’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘as.table’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘t’ from package ‘base’ in package ‘IRanges’ ** help *** installing help indices ** building package indices ... *** tangling vignette sources ... ‘IRangesOverview.Rnw’ ‘RleTricks.Rnw’ ** testing if installed package can be loaded * DONE (IRanges) * installing *source* package ‘Biobase’ ... ** libs gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c Rinit.c -o Rinit.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c anyMissing.c -o anyMissing.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c envir.c -o envir.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c matchpt.c -o matchpt.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c rowMedians.c -o rowMedians.o gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c sublist_extract.c -o sublist_extract.o gcc -std=gnu99 -shared -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/Biobase/libs ** R ** data ** inst ** preparing package for lazy loading ** help Warning: /tmp/RtmpQMzB6b/R.INSTALL50b1922e/Biobase/man/cache.Rd: docType ‘function’ is unrecognized Warning: /tmp/RtmpQMzB6b/R.INSTALL50b1922e/Biobase/man/matchpt.Rd: docType ‘function’ is unrecognized *** installing help indices ** building package indices ... *** tangling vignette sources ... ‘BiobaseDevelopment.Rnw’ ‘Bioconductor.Rnw’ ‘ExpressionSetIntroduction.Rnw’ ‘HowTo.Rnw’ ‘Qviews.Rnw’ ‘esApply.Rnw’ ** testing if installed package can be loaded * DONE (Biobase) * installing *source* package ‘hwriter’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... *** tangling vignette sources ... ‘hwriter.Rnw’ ** testing if installed package can be loaded * DONE (hwriter) * installing *source* package ‘GenomicRanges’ ... ** libs gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c cigar_utils.c -o cigar_utils.o gcc -std=gnu99 -shared -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o cigar_utils.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/GenomicRanges/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... *** tangling vignette sources ... ‘GenomicRangesIntroduction.Rnw’ ‘GenomicRangesUseCases.Rnw’ ** testing if installed package can be loaded * DONE (GenomicRanges) * installing *source* package ‘Biostrings’ ... ** libs gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c BAB_class.c -o BAB_class.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c BitMatrix.c -o BitMatrix.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c MIndex_class.c -o MIndex_class.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c SparseList_utils.c -o SparseList_utils.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c XStringSet_class.c -o XStringSet_class.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c XStringSet_io.c -o XStringSet_io.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c XString_class.c -o XString_class.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c align_needwunsQS.c -o align_needwunsQS.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c align_utils.c -o align_utils.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c extract_transcripts.c -o extract_transcripts.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c find_palindromes.c -o find_palindromes.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c gtestsim.c -o gtestsim.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c inject_code.c -o inject_code.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c letter_frequency.c -o letter_frequency.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c lowlevel_matching.c -o lowlevel_matching.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c match_BOC.c -o match_BOC.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c match_BOC2.c -o match_BOC2.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c match_PWM.c -o match_PWM.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c match_WCP.c -o match_WCP.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c match_pattern.c -o match_pattern.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c match_pattern_indels.c -o match_pattern_indels.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c match_pdict.c -o match_pdict.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c match_pdict_Twobit.c -o match_pdict_Twobit.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c match_pdict_utils.c -o match_pdict_utils.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c match_reporting.c -o match_reporting.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c matchprobes.c -o matchprobes.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c pmatchPattern.c -o pmatchPattern.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c replace_letter_at.c -o replace_letter_at.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c strutils.c -o strutils.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c translate.c -o translate.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c utils.c -o utils.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/IRanges/include" -fpic -O3 -pipe -g -c xscat.c -o xscat.o gcc -std=gnu99 -shared -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o SparseList_utils.o XStringSet_class.o XStringSet_io.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o extract_transcripts.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.o match_PWM.o match_WCP.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o translate.o utils.o xscat.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/Biostrings/libs ** R ** data ** inst ** preparing package for lazy loading Creating a generic function for ‘setequal’ from package ‘base’ in package ‘Biostrings’ Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’ Creating a new generic function for ‘offset’ in package ‘Biostrings’ ** help *** installing help indices ** building package indices ... *** tangling vignette sources ... ‘Alignments.Rnw’ ‘Biostrings2Classes.Rnw’ ‘DNAStringVectorization.Rnw’ ‘GenomeSearching.Rnw’ ‘matchprobes.Rnw’ ** testing if installed package can be loaded * DONE (Biostrings) * installing *source* package ‘Rsamtools’ ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gzeof in -lz... yes checking for bzero... yes checking for memset... yes checking for pow... no checking for sqrt... no checking for strcasecmp... yes checking for strdup... yes checking for strstr... yes checking for strtol... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for ptrdiff_t... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for _LARGEFILE_SOURCE value needed for large files... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for off_t... yes checking for size_t... yes configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c io_sam.c -o io_sam.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c utilities.c -o utilities.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c encode.c -o encode.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c R_init_Rsamtools.c -o R_init_Rsamtools.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/bam.c -o samtools/bam.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/bam_import.c -o samtools/bam_import.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/bam_index.c -o samtools/bam_index.o samtools/bam_index.c: In function ‘bam_index_load_core’: samtools/bam_index.c:276:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:283:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:296:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:299:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:303:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:307:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:317:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:321:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/kstring.c -o samtools/kstring.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/bam_aux.c -o samtools/bam_aux.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/sam_header.c -o samtools/sam_header.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/bgzf.c -o samtools/bgzf.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/razf.c -o samtools/razf.o samtools/razf.c: In function ‘razf_close’: samtools/razf.c:804:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:805:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:808:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:810:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c: In function ‘razf_end_flush’: samtools/razf.c:258:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c: In function ‘_razf_write’: samtools/razf.c:201:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c: In function ‘save_zindex’: samtools/razf.c:96:17: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:99:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:106:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:107:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c: In function ‘razf_flush’: samtools/razf.c:221:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:234:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/knetfile.c -o samtools/knetfile.o samtools/knetfile.c: In function ‘khttp_connect_file’: samtools/knetfile.c:416:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/knetfile.c: In function ‘kftp_send_cmd’: samtools/knetfile.c:237:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/sam.c -o samtools/sam.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/bam_pileup.c -o samtools/bam_pileup.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/faidx.c -o samtools/faidx.o gcc -std=gnu99 -shared -o Rsamtools.so io_sam.o utilities.o encode.o Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o samtools/bam.o samtools/bam_import.o samtools/bam_index.o samtools/kstring.o samtools/bam_aux.o samtools/sam_header.o samtools/bgzf.o samtools/razf.o samtools/knetfile.o samtools/sam.o samtools/bam_pileup.o samtools/faidx.o -lz -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/Rsamtools/libs ** R ** inst ** preparing package for lazy loading Error : object ‘normalizePath’ is not exported by 'namespace:utils' ERROR: lazy loading failed for package ‘Rsamtools’ * removing ‘/usr/local/lib/R/site-library/Rsamtools’ ERROR: dependency ‘Rsamtools’ is not available for package ‘ShortRead’ * removing ‘/usr/local/lib/R/site-library/ShortRead’ The downloaded packages are in ‘/tmp/Rtmp0hLYYZ/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ‘Rsamtools’ had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ‘ShortRead’ had non-zero exit status > biocLite("Rsamtools") Using R version 2.14.0, biocinstall version 2.6.8. Installing Bioconductor version 2.6 packages: [1] "Rsamtools" Please wait... Installing package(s) into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) trying URL 'http://www.bioconductor.org/packages/2.6/bioc/src/contrib/ Rsamtools_1.0.8.tar.gz' Content type 'application/x-gzip' length 1451209 bytes (1.4 Mb) opened URL ================================================== downloaded 1.4 Mb * installing *source* package ‘Rsamtools’ ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gzeof in -lz... yes checking for bzero... yes checking for memset... yes checking for pow... no checking for sqrt... no checking for strcasecmp... yes checking for strdup... yes checking for strstr... yes checking for strtol... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for ptrdiff_t... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for _LARGEFILE_SOURCE value needed for large files... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for off_t... yes checking for size_t... yes configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c io_sam.c -o io_sam.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c utilities.c -o utilities.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c encode.c -o encode.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c R_init_Rsamtools.c -o R_init_Rsamtools.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/bam.c -o samtools/bam.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/bam_import.c -o samtools/bam_import.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/bam_index.c -o samtools/bam_index.o samtools/bam_index.c: In function ‘bam_index_load_core’: samtools/bam_index.c:276:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:283:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:296:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:299:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:303:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:307:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:317:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] samtools/bam_index.c:321:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/kstring.c -o samtools/kstring.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/bam_aux.c -o samtools/bam_aux.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/sam_header.c -o samtools/sam_header.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/bgzf.c -o samtools/bgzf.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/razf.c -o samtools/razf.o samtools/razf.c: In function ‘razf_close’: samtools/razf.c:804:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:805:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:808:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:810:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c: In function ‘razf_end_flush’: samtools/razf.c:258:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c: In function ‘_razf_write’: samtools/razf.c:201:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c: In function ‘save_zindex’: samtools/razf.c:96:17: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:99:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:106:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:107:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c: In function ‘razf_flush’: samtools/razf.c:221:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/razf.c:234:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/knetfile.c -o samtools/knetfile.o samtools/knetfile.c: In function ‘khttp_connect_file’: samtools/knetfile.c:416:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] samtools/knetfile.c: In function ‘kftp_send_cmd’: samtools/knetfile.c:237:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/sam.c -o samtools/sam.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/bam_pileup.c -o samtools/bam_pileup.o gcc -std=gnu99 -I/usr/share/R/include -I"/usr/local/lib/R/site- library/Biostrings/include" -I"/usr/local/lib/R/site- library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fpic -O3 -pipe -g -c samtools/faidx.c -o samtools/faidx.o gcc -std=gnu99 -shared -o Rsamtools.so io_sam.o utilities.o encode.o Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o samtools/bam.o samtools/bam_import.o samtools/bam_index.o samtools/kstring.o samtools/bam_aux.o samtools/sam_header.o samtools/bgzf.o samtools/razf.o samtools/knetfile.o samtools/sam.o samtools/bam_pileup.o samtools/faidx.o -lz -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/Rsamtools/libs ** R ** inst ** preparing package for lazy loading Error : object ‘normalizePath’ is not exported by 'namespace:utils' ERROR: lazy loading failed for package ‘Rsamtools’ * removing ‘/usr/local/lib/R/site-library/Rsamtools’ The downloaded packages are in ‘/tmp/Rtmp0hLYYZ/downloaded_packages’ Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ‘Rsamtools’ had non-zero exit status > ?normalizePath > ?namespace:utils Error in genericForPrimitive(f) : methods may not be defined for primitive function ‘:’ in this version of R > ?utils > library(help="utils") > ?namespace No documentation for ‘namespace’ in specified packages and libraries: you could try ‘??namespace’ > ??namespace > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] tools_2.14.0 > q() Save workspace image? [y/n/c]: n jn42@bioinf4:/home/jn42# uname -a Linux bicr-bioinf4 3.0.0-12-generic #20-Ubuntu SMP Fri Oct 7 14:56:25 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux jn42@bioinf4:/home/jn42# > Date: Tue, 8 Nov 2011 10:00:51 -0500 > From: jmacdon@med.umich.edu > To: bahhab@hotmail.com > CC: bioconductor@r-project.org > Subject: Re: [BioC] Rsamtools installation > > Hi John, > > On 11/8/2011 9:33 AM, John Coulthard wrote: > > Hi > > > > I'm trying to install Rsamtools and getting errors! I've tried... > > install.packages("/home/ann/downloads/Rsamtools_1.6.0.tar.gz") > > and > > biocLite("Rsamtools") > > (see below) > > > > > > Why doesn't biocLite() install the current version? > > I'm almost sure the dependencies are all up-to-date using install.packages(). > > So if it's not an out of date dependent what could the problem be? > > If is it an out of date dependent how do I get R to tell me which one? > > You appear to be going rogue here. You should not be using > install.packages() at all, and should not be using an outdated version > of biocLite(). > > You want > > source("http://www.bioconductor.org/biocLite.R") > > which will install the BiocInstaller package (and load it for you this time) > > then in future, you should > > library(BiocInstaller) > biocLite("Rsamtools") > > which will > > > biocLite("Rsamtools") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.0. > Installing package(s) 'Rsamtools' > <snip> > trying URL > 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/Rsamtools _1.6.0.tar.gz' > Content type 'application/x-gzip' length 2088510 bytes (2.0 Mb) > > > Note the message I get compared to what you got. > > Best, > > Jim > > > > > > > Thanks > > John > > > > > >> install.packages("/home/ann/downloads/Rsamtools_1.6.0.tar.gz") > > Installing package(s) into ‘/usr/local/lib/R/site-library’ > > (as ‘lib’ is unspecified) > > inferring 'repos = NULL' from the file name > > * installing *source* package ‘Rsamtools’ ... > > ** libs > > <snip> > > ** R > > ** inst > > ** preparing package for lazy loading > > Error : class "Sequence" is not exported by 'namespace:IRanges' > > ERROR: lazy loading failed for package ‘Rsamtools’ > > * removing ‘/usr/local/lib/R/site-library/Rsamtools’ > > Warning message: > > In install.packages("/home/ann/downloads/Rsamtools_1.6.0.tar.gz") : > > installation of package ‘/home/ann/downloads/Rsamtools_1.6.0.tar.gz’ had non-zero exit status > > > > > >> biocLite("Rsamtools") > > Using R version 2.14.0, biocinstall version 2.7.7. > > Installing Bioconductor version 2.7 packages: > > [1] "Rsamtools" > > Please wait... > > > > Installing package(s) into ‘/usr/local/lib/R/site-library’ > > (as ‘lib’ is unspecified) > > trying URL 'http://bioconductor.org/packages/2.7/bioc/src/contrib/ Rsamtools_1.2.3.tar.gz' > > Content type 'application/x-gzip' length 1618555 bytes (1.5 Mb) > > opened URL > > <snip> > > ** R > > ** inst > > ** preparing package for lazy loading > > Error : object ‘normalizePath’ is not exported by 'namespace:utils' > > ERROR: lazy loading failed for package ‘Rsamtools’ > > * removing ‘/usr/local/lib/R/site-library/Rsamtools’ > > > > The downloaded packages are in > > ‘/tmp/RtmpkLT1S0/downloaded_packages’ > > Warning message: > > In install.packages(pkgs = pkgs, repos = repos, ...) : > > installation of package ‘Rsamtools’ had non-zero exit status > > > > > > Many thanks > > John > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > 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 > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues > [[alternative HTML version deleted]]