[R] Problem Regarding R Packages installation

[MacQueen, Don]

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 		 	
>		  
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