如何指定在安装R软件包时使用哪个R库？

Question

我试图使用一个名为“ XML”的R包 ，但是在安装后无法使用它：

# in R environment
> library("XML")
> XML::parseURI("")
Error in XML::parseURI("") : cannot parse URI 

问题原来是R无法在我的目录中找到安装的“ libxml2”的当前版本：

 echo $LD_LIBRARY_PATH /somewhere/Jun/Programme/libxml2-devel-2.9.1-2.1/usr/lib/:

检索有关链接到的libxml2库“ XML”版本的信息

> path = unclass(getLoadedDLLs()[["XML"]])$path
> path
[1] "/misc/home/Jun/Programme/R-3.3.1/lib64/R/library/XML/libs/XML.so"
> system2("ldd",args=path)
                linux-vdso.so.1 =>  (0x00007fff2a9e8000)
                libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x00002aefc088a000)  # XML is using a common "libxml2.so.2" not the one I installed. 
                libz.so.1 => //home/Jun/Programme/zlib-1.2.11/lib/libz.so.1 (0x00002aefc0bc8000)
                libm.so.6 => /lib64/libm.so.6 (0x00002aefc0de5000)
                libdl.so.2 => /lib64/libdl.so.2 (0x00002aefc1068000)
                ...

有什么建议吗？

为了使“ XML”链接到安装在我的目录中的libxml2，我做了以下努力：

1. 为libxml2设置PATH：

   回声$ LD_LIBRARY_PATH

   /somewhere/Jun/Programme/pcre-8.40/lib/:/somewhere/Jun/Programme/xz-5.2.3/lib/:/somewhere/Jun/Programme/zlib-1.2.11/include/:/somewhere/Jun /Programme/zlib-1.2.11/lib/:/somewhere/Jun/Programme/bzip2-1.0.6/lib/:/somewhere/Jun/Programme/bzip2-1.0.6/include/:/somewhere/Jun/Programme /gcc-6.1.0/lib/:/somewhere/Jun/Programme/gcc-6.1.0/lib64/:/somewhere/Jun/Programme/libxml2-devel-2.9.1-2.1/usr/lib/:/somewhere /Jun/Programme/curl-7.52.1/lib/:/somewhere/Jun/Programme/libtool_CentOS6_64/usr/lib64/:/home/appl/openmpi-1.3.1/lib:/opt22/lsf83_exp/8.3/linux2。 6 glibc2.3-x86_64的/ lib目录中：/ opt / UPS / lib目录

2. 使用“ --enable”参数用指定lib的配置重新编译R

   ./configure --prefix = $ HOME / Programme / R-3.3.1 --enable-R-shlib LDFLAGS =“-L / $ HOME / Programme / zlib-1.2.11 / lib -L ​​/ $ HOME / Programme / bzip2-1.0.6 / lib -L ​​/ $ HOME / Programme / xz-5.2.3 / lib -L ​​/ $ HOME / Programme / pcre-8.40 / lib -L ​​/ $ HOME / Programme / curl-7.52.1 / lib “ CPPFLAGS =“-I / $ HOME / Programme / zlib-1.2.11 / include -I / $ HOME / Programme / bzip2-1.0.6 / include -I / $ HOME / Programme / xz-5.2.3 / include- I / $ HOME / Programme / pcre-8.40 / include -I / $ HOME / Programme / curl-7.52.1 / include“

3. 使用配置参数安装“ XML”：

   biocLite（“ XML”，configure.args ='-with-xml- config =“ / somewhere / Jun / Programme / libxml2-devel-2.9.1-2.1 / usr / bin / xml2-config”'）BioC_mirror： http ：//bioconductor.org使用Bioconductor 3.4（BiocInstaller 1.24.0），R 3.3.1（2016-06-21）。 安装包“ XML”并尝试使用网址“ http://cran.rstudio.com/src/contrib/XML_3.98-1.5.tar.gz ”

   内容类型“应用程序/ x-gzip”长度1599213字节（1.5 MB）

   下载1.5 MB ...

但它们似乎都不起作用：

* 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... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
User defined xml-config: /somewhere/Jun/Programme/libxml2-devel-2.9.1-2.1/usr/bin/xml2-config, XML Version: 2, XML2: yes
USE_XML2 = yes
SED_EXTENDED_ARG: -r
Minor 9, Patch 1 for 2.9.1
Located parser file -I/usr/include/libxml2/parser.h
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... yes
checking for xmlHashSize in -lxml2... yes
Using built-in xmlHashSize
Checking DTD parsing (presence of externalSubset)...
checking for xmlHashSize in -lxml2... yes
Found xmlHashSize
checking for xmlOutputBufferCreateBuffer in -lxml2... yes
have xmlOutputBufferCreateBuffer()
checking for xmlDocDumpFormatMemoryEnc in -lxml2... yes
checking libxml/xmlversion.h usability... yes
checking libxml/xmlversion.h presence... yes
checking for libxml/xmlversion.h... yes
Expat:  FALSE
Checking for return type of xmlHashScan element routine.
No return value for xmlHashScan
xmlNs has a context field
Checking for cetype_t enumeration
Using recent version of R with cetype_t enumeration type for encoding
checking for xmlsec1-config... /usr/bin/xmlsec1-config
nodegc default 
xml-debug default 
No XML_WITH_ZLIB enumeration value.
Version has xmlHasFeature()

****************************************
Configuration information:

Libxml settings

libxml include directory: -I/usr/include/libxml2
libxml library directory: -lxml2 -lz -lm -ldl -lz  -lxml2
libxml 2:                 -DLIBXML2=1

Answer 1

我想我已经找到了解决方案。 与其使用rpm安装“ libxml2”，（我很抱歉在我的帖子中没有提到它；我没有意识到这可能是造成麻烦的原因），我应该从源代码编译“ libxml2”。

对于有类似问题的人：

从http://www.linuxfromscratch.org/blfs/view/svn/general/libxml2.html下载libxml2的当前版本，

请按照上面链接的说明进行操作。

安装两点：

1。

./configure --prefix=$HOME/Programme --disable-static --with-history --with-zlib=/somewhere/Jun/Programme/zlib-1.2.11 && make

您必须指定zlib（--with）; 这也意味着您必须安装zlib。 我必须添加“ --with”以使configure工作。

2. 说明说明您必须以root用户身份调用“ make install”，但没有，您不必这样做。

3. 为您安装的“ libxml2”设置PATH 。

4. 重新安装您的R包“ XML”。