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]]
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