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-boun...@r-project.org on behalf of muhammadsohailr...@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: soh...@big.ac.cn muhammadsohailr...@live.com > > > [[alternative HTML version deleted]] > ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.