Dear all When I run try to install DESeq it shows this error: > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help > biocLite("DESeq") BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.1 (2016-06-21). Installing package(s) ‘DESeq’ also installing the dependencies ‘XML’, ‘RCurl’, ‘annotate’, ‘genefilter’, ‘geneplotter’ trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.4.tar.gz' Content type 'unknown' length 1599214 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://cran.rstudio.com/src/contrib/RCurl_1.95-4.8.tar.gz' Content type 'unknown' length 916934 bytes (895 KB) ================================================== downloaded 895 KB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/annotate_1.52.0.tar.gz' Content type 'unknown' length 1861023 bytes (1.8 MB) ================================================== downloaded 1.8 MB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/genefilter_1.56.0.tar.gz' Content type 'unknown' length 1407436 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/geneplotter_1.52.0.tar.gz' Content type 'unknown' length 1426298 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/DESeq_1.26.0.tar.gz' Content type 'unknown' length 1698987 bytes (1.6 MB) ================================================== downloaded 1.6 MB * installing *source* package ‘XML’ ... ** package ‘XML’ successfully unpacked and MD5 sums checked checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for sed... /usr/bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package ‘XML’ * removing ‘/usr/lib64/R/library/XML’ * installing *source* package ‘RCurl’ ... ** package ‘RCurl’ successfully unpacked and MD5 sums checked checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ‘RCurl’ * removing ‘/usr/lib64/R/library/RCurl’ ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘annotate’ * removing ‘/usr/lib64/R/library/annotate’ ERROR: dependency ‘annotate’ is not available for package ‘genefilter’ * removing ‘/usr/lib64/R/library/genefilter’ ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’ * removing ‘/usr/lib64/R/library/geneplotter’ ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq’ * removing ‘/usr/lib64/R/library/DESeq’ The downloaded source packages are in ‘/tmp/RtmpsMJs05/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 ‘annotate’ had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘genefilter’ had non-zero exit status 5: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘geneplotter’ had non-zero exit status 6: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘DESeq’ had non-zero exit status Thanks
