the first error message is
"configuration failed for package RCurl"
immediately before that it said
"Cannot find curl-config".
It would appear that you don't have curl installed on your computer.
Unfortunately, I cannot help you with that. But you might look at the
documentation for RCurl (available from CRAN) to start trying to find
where to get curl.
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
On 7/15/15, 8:23 PM, "R-help on behalf of Muhammad Sohail Raza"
<r-help-bounces at r-project.org on behalf of muhammadsohailraza at
live.com>
wrote:
>Hi Everyone!
>I am trying to install R Package "VariantAnnotation". I entered
commands:
>
>source("http://bioconductor.org/biocLite.R")
> biocLite("VariantAnnotation")
>
>
>But i am getting the following errors,
>
>ERROR: configuration failed for package ?XML?
>* removing ?/usr/lib64/R/library/XML?
>* installing *source* package ?RCurl? ...
>** package ?RCurl? successfully unpacked and MD5 sums checked
>configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
>checking for curl-config... no
>Cannot find curl-config
>ERROR: configuration failed for package ?RCurl?
>* removing ?/usr/lib64/R/library/RCurl?
>* installing *source* package ?Rsamtools? ...
>** libs
>gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include
>-I"/usr/lib64/R/library/S4Vectors/include"
>-I"/usr/lib64/R/library/IRanges/include"
>-I"/usr/lib64/R/library/XVector/include"
>-I"/usr/lib64/R/library/Biostrings/include" -fopenmp
-D_USE_KNETFILE
>-D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE
>-Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort
>-I./samtools -I./samtools/bcftools -I./tabix -fpic -fmessage-length=0
>-grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector
>-funwind-tables -fasynchronous-unwind-tables -c Biostrings_stubs.c -o
>Biostrings_stubs.o
>gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include
>-I"/usr/lib64/R/library/S4Vectors/include"
>-I"/usr/lib64/R/library/IRanges/include"
>-I"/usr/lib64/R/library/XVector/include"
>-I"/usr/lib64/R/library/Biostrings/include" -fopenmp
-D_USE_KNETFILE
>-D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE
>-Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort
>-I./samtools -I./samtools/bcftools -I./tabix -fpic -fmessage-length=0
>-grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector
>-funwind-tables -fasynchronous-unwind-tables -c IRanges_stubs.c -o
>IRanges_stubs.o
>g++ -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include
>-I"/usr/lib64/R/library/S4Vectors/include"
>-I"/usr/lib64/R/library/IRanges/include"
>-I"/usr/lib64/R/library/XVector/include"
>-I"/usr/lib64/R/library/Biostrings/include" -fpic
-fmessage-length=0
>-grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector
>-funwind-tables -fasynchronous-unwind-tables -c PileupBuffer.cpp -o
>PileupBuffer.o
>/bin/sh: g++: command not found
>/usr/lib64/R/etc/Makeconf:143: recipe for target 'PileupBuffer.o'
failed
>make: *** [PileupBuffer.o] Error 127
>ERROR: compilation failed for package ?Rsamtools?
>* removing ?/usr/lib64/R/library/Rsamtools?
>* installing *source* package ?futile.logger? ...
>** package ?futile.logger? successfully unpacked and MD5 sums checked
>** R
>** preparing package for lazy loading
>** help
>*** installing help indices
>** building package indices
>** testing if installed package can be loaded
>* DONE (futile.logger)
>ERROR: dependencies ?XML?, ?RCurl? are not available for package ?biomaRt?
>* removing ?/usr/lib64/R/library/biomaRt?
>* installing *source* package ?BiocParallel? ...
>** R
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
>** building package indices
>** installing vignettes
>** testing if installed package can be loaded
>* DONE (BiocParallel)
>ERROR: dependency ?Rsamtools? is not available for package
>?GenomicAlignments?
>* removing ?/usr/lib64/R/library/GenomicAlignments?
>ERROR: dependencies ?XML?, ?RCurl?, ?Rsamtools?, ?GenomicAlignments? are
>not available for package ?rtracklayer?
>* removing ?/usr/lib64/R/library/rtracklayer?
>ERROR: dependencies ?rtracklayer?, ?Rsamtools? are not available for
>package ?BSgenome?
>* removing ?/usr/lib64/R/library/BSgenome?
>ERROR: dependencies ?rtracklayer?, ?biomaRt?, ?RCurl? are not available
>for package ?GenomicFeatures?
>* removing ?/usr/lib64/R/library/GenomicFeatures?
>ERROR: dependencies ?Rsamtools?, ?BSgenome?, ?rtracklayer?,
>?GenomicFeatures? are not available for package ?VariantAnnotation?
>* removing ?/usr/lib64/R/library/VariantAnnotation?
>
>The downloaded source packages are in
> ?/tmp/RtmpvpoYjO/downloaded_packages?
>Updating HTML index of packages in '.Library'
>Making 'packages.html' ... done
>Warning messages:
>1: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ?XML? had non-zero exit status
>2: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ?RCurl? had non-zero exit status
>3: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ?Rsamtools? had non-zero exit status
>4: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ?biomaRt? had non-zero exit status
>5: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ?GenomicAlignments? had non-zero exit status
>6: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ?rtracklayer? had non-zero exit status
>7: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ?BSgenome? had non-zero exit status
>8: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ?GenomicFeatures? had non-zero exit status
>9: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ?VariantAnnotation? had non-zero exit status
>
>
>I don't know how to deal with it, can anyone helpo me how to deal with
it?
>
>Thanks!
>
>
>**************************************************************************
>**********
>Muhammad Sohail RazaBeijing Institute of Genomics, CASBeijing,
>China.Phone: +8613552957083
>email: sohail at big.ac.cn muhammadsohailraza at live.com
>
> [[alternative HTML version deleted]]
>