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Problem Regarding R Packages installation

2 messages · Muhammad Sohail Raza, MacQueen, Don

Original
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
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.