内容类型＆＃39; application / x-gzip＆＃39;长度1599213字节（1.5 MB）

Question

I was trying to use a R package called "XML"，但安装后无法使用它：

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

问题原因是R无法找到当前版本的＆＃34; libxml2＆＃34;安装在我的目录中：

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

检索有关libxml2库的版本的信息＆＃34; XML＆＃34;链接到

> 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)
                ...

有任何建议吗？

为了制作＆＃34; XML＆＃34;链接到我的目录中安装的libxml2，我做了这样的努力：

为libxml2设置PATH：

echo $ LD_LIBRARY_PATH

/somewhere/Jun/Programme/pcre-8.40/lib /：/某处月/ 6 /计划/ XZ-5.2.3 / LIB /：/某处月/ 6 /计划/ zlib的-1.2.11 /包含/：/某处月/ 6 /计划/ zlib的-1.2.11 / lib中/：/某处月/ 6 /计划/ bzip2-1.0.6 / lib中/：/某处月/ 6 /计划/ bzip2-1.0.6 /有/：/地方/君/程序/ GCC-6.1.0 / lib中/：/某处月/ 6 /计划/ GCC-6.1.0 / lib64下/：/某处月/ 6 /计划/的libxml2-devel的-2.9.1-2.1 / usr / lib目录/ ：/somewhere/Jun/Programme/curl-7.52.1/lib /：/某处月/ 6 /计划/ libtool_CentOS6_64在/ usr / lib64下/：/家庭/申请/的openmpi-1.3.1 / lib目录下：/opt22/lsf83_exp/8.3 /linux2.6-glibc2.3-x86_64/lib:/opt/ups/lib
使用＆＃34; - enable＆＃34;使用配置指定lib重新编译R参数

./ configure --prefix = $ HOME / Program / R-3.3.1 --enable-R-shlib LDFLAGS =＆＃34; -L / $ HOME / Program / zlib-1.2.11 / lib -L /$HOME/Programme/bzip2-1.0.6/lib -L / $ HOME / Program / xz-5.2.3 / lib -L / $ HOME / Program / pcre-8.40 / lib -L / $ HOME / Program / curl -7.52.1 / lib＆＃34; CPPFLAGS =＆＃34; -I / $ HOME / Program / zlib-1.2.11 / include -I / $ HOME / Program / bzip2-1.0.6 / include -I / $ HOME / Program / xz-5.2.3 /包括-I / $ HOME / Program / pcre-8.40 / include -I / $ HOME / Program / curl-7.52.1 / include＆＃34;
安装＆＃34; XML＆＃34;使用configure参数：

biocLite（＆＃34; XML＆＃34;，configure.args =＆＃39; - with-xml-config =＆＃34; /somewhere/Jun/Programme/libxml2-devel-2.9.1-2.1的/ usr /斌/ XML2-配置＆＃34;＆＃39;） 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' 尝试访问网址＆＃39; http://cran.rstudio.com/src/contrib/XML_3.98-1.5.tar.gz＆＃39;

内容类型＆＃39; application / x-gzip＆＃39;长度1599213字节（1.5 MB）

下载了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

我想我找到了解决方案。而不是使用rpm来安装＆＃34; libxml2＆＃34; （我很抱歉我没有在我的帖子中提到它;我没有意识到这可能是我麻烦的原因），我应该编译＆＃34; libxml2＆＃34;来源。

对于有类似问题的人：

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

按照上述链接的说明操作。

安装两点：

1

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

你必须指定zlib（--with）;这也意味着您必须安装zlib。我不得不添加＆＃34; - 用＆＃34;使configure工作。

说明中说明您必须致电＆＃34; make install＆＃34;作为root用户，但不是，你不必这样做。
为已安装的＆＃34; libxml2＆＃34;设置PATH。
重新安装R包＆＃34; XML＆＃34;。

如何指定安装R包时使用哪个R lib？

内容类型＆＃39; application / x-gzip＆＃39;长度1599213字节（1.5 MB）

1 个答案: