- 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
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