快速链接bioconductor,以及安装“XML”
1 options(useHTTPS=FALSE, BioC_mirror="http://bioconductor.org") 2 3 4 source("http://bioconductor.org/biocLite.R")
install.packages("XML") trying URL 'https://cloud.r-project.org/src/contrib/XML_3.98-1.4.tar.gz' Content type 'application/x-gzip' length 1599214 bytes (1.5 MB) ================================================== 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... 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/local/Library/ENV/4.3/sed checking for pkg-config... /usr/local/bin/pkg-config checking for xml2-config... /Users/richiethomas/anaconda/bin/xml2-config USE_XML2 = yes SED_EXTENDED_ARG: -E Minor 9, Patch 2 for 2.9.2 Located parser file -I/Users/richiethomas/anaconda/include/libxml2/parser.h Checking for 1.8: -I/Users/richiethomas/anaconda/include/libxml2 Using libxml2.* checking for gzopen in -lz... yes checking for xmlParseFile in -lxml2... yes You are trying to use a version 2.* edition of libxml but an incompatible library. The header files and library seem to be mismatched. If you have specified LIBXML_INCDIR, make certain to also specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default directories. ERROR: configuration failed for package ‘XML’ * removing ‘/usr/local/lib/R/3.2/site-library/XML’ The downloaded source packages are in ‘/private/var/folders/jy/0cwn40p951xc7f1480z3sxzm0000gn/T/RtmpvWMrkH/downloaded_packages’ Warning message: In install.packages("XML") : installation of package ‘XML’ had non-zero exit status
出现上述报错,的快速解决方法如下
1 conda install -c r r-xml
若继续出现下面错误:
/bin/sh: /root/anaconda2/bin/x86_64-conda_cos6-linux-gnu-gcc: No such file or directory
1 conda install gxx_linux-64 2 3 provides x86_64-conda_cos6-linux-gnu-c++
1 conda install gcc_linux-64 2 conda install gxx_linux-64 3 4 conda install gfortran_linux-64 5 conda install -c tsnyder gfortran_linux-cos6-x86_64