"Non Zero Exit Status” R 3.0.1 'XML' and 'RCurl' " in bioconductor while installing packages
Posted on 2015-03-26 20:10 Jimmy_Chen 阅读(1186) 评论(0) 编辑 收藏 举报> install.packages("RCurl") Installing package into ‘/home/steven/R/x86_64-pc-linux-gnu-library/3.0’ (as ‘lib’ is unspecified) trying URL 'http://cran.rstudio.com/src/contrib/RCurl_1.95-4.1.tar.gz' Content type 'application/x-gzip' length 870915 bytes (850 Kb) opened URL ================================================== downloaded 850 Kb * 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 ‘/home/steven/R/x86_64-pc-linux-gnu-library/3.0/RCurl’ Warning in install.packages : installation of package ‘RCurl’ had non-zero exit status The downloaded source packages are in ‘/tmp/RtmpUwBkbS/downloaded_packages’ > install.packages("XML") Installing package into ‘/home/steven/R/x86_64-pc-linux-gnu-library/3.0’ (as ‘lib’ is unspecified) trying URL 'http://cran.rstudio.com/src/contrib/XML_3.98-1.1.tar.gz' Content type 'application/x-gzip' length 1582216 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 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... rm: cannot remove 'a.out.dSYM': Is a directory 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... /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 ‘/home/steven/R/x86_64-pc-linux-gnu-library/3.0/XML’ Warning in install.packages : installation of package ‘XML’ had non-zero exit status The downloaded source packages are in ‘/tmp/RtmpUwBkbS/downloaded_packages’
Solution:
in CentOS 6+
sudo yum -y install curl sudo yum -y install libcurl libcurl-devel sudo yum -y install libxml2 libxml2-devel
in Ubuntu
sudo apt-get install libcurl4-openssl-dev sudo apt-get install libxml2-dev
