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: soh...@big.ac.cn muhammadsohailr...@live.com
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