
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 
> 
 		 	   		  
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