[R] Problem Regarding R Packages installation

[Muhammad Sohail Raza]

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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