由于XML依赖性不匹配导致无法安装R包

时间:2016-05-04 18:15:15

标签: python xml r

我在命令行中启动了R并键入以下内容:

install.packages("XML")

选择镜像站点后,我看到了以下输出:

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

我用Google搜索并找到this link,它建议在命令行中运行'which xmllint'命令来查找可能与R依赖的任何XML安装相关的XML安装。我运行时的输出是:

/Users/richiethomas/anaconda/bin/xmllint

如果我错了,请纠正我,但似乎我的Python安装具有XML依赖性,这与R想要下载的冲突相冲突。这是正确的吗?如果是这样,我该如何修复它以便在我的机器上安装Python和R?

编辑:我正在使用OSX。我运行了“brew install libxml2”,但Homebrew表示已经安装了它。

编辑#2:我尝试通过Homebrew卸载并重新安装R,我仍然遇到同样的错误。

编辑#3:我运行了“brew info libxml2”并看到有一个“--with-python”标志,它支持使用Python支持构建。我还注意到以下几点:

Generally there are no consequences of this for you. If you build your
own software and it requires this formula, you'll need to add to your
build variables:

    LDFLAGS:  -L/usr/local/opt/libxml2/lib
    CPPFLAGS: -I/usr/local/opt/libxml2/include

我运行“brew uninstall libxml2”然后“brew install libxml2 --with-python”,然后使用“export”命令设置上述2个环境变量。然后我重新运行R并再次尝试安装XML包。我看到了几十个类型为“将参数传递给参数”的警告(见下文),后面跟一个非零的退出代码:

    * 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
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... no
nodegc default 
xml-debug default 
Version has XML_WITH_ZLIB
Version has xmlHasFeature()

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

Libxml settings

libxml include directory: -I/Users/richiethomas/anaconda/include/libxml2
libxml library directory: -L/Users/richiethomas/anaconda/lib -lxml2 -lz -liconv -lm -lz  -lxml2
libxml 2:                 -DLIBXML2=1

Compilation flags:         -DLIBXML -I/Users/richiethomas/anaconda/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 
Link flags:               -L/Users/richiethomas/anaconda/lib -lxml2 -lz -liconv -lm -lz  -lxml2

****************************************
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/supports.R
config.status: creating inst/scripts/RSXML.csh
config.status: creating inst/scripts/RSXML.bsh
** libs
clang -I/usr/local/Cellar/r/3.2.4_1/R.framework/Resources/include -DNDEBUG -DLIBXML -I/Users/richiethomas/anaconda/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include    -fPIC  -g -O2  -c DocParse.c -o DocParse.o
DocParse.c:375:60: warning: passing 'const char *' to parameter of type 'const xmlChar *' (aka 'const unsigned char *') converts between
      pointers to integer types with different sign [-Wpointer-sign]
    SET_STRING_ELT(VECTOR_ELT(rdoc, FILE_ELEMENT_NAME), 0, ENC_COPY_TO_USER_STRING(doc->name ? XMLCHAR_TO_CHAR(doc->name) : fileName));
                                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./Utils.h:235:74: note: expanded from macro 'ENC_COPY_TO_USER_STRING'
#define ENC_COPY_TO_USER_STRING(x)  CreateCharSexpWithEncoding(encoding, CHAR_TO_XMLCHAR (x)) 
                                                                         ^~~~~~~~~~~~~~~~~~~
./Utils.h:12:31: note: expanded from macro 'CHAR_TO_XMLCHAR'
#define CHAR_TO_XMLCHAR(val)  ((xmlChar *) val)
                              ^~~~~~~~~~~~~~~~~
./Utils.h:220:73: note: passing argument to parameter 'str' here
SEXP CreateCharSexpWithEncoding(const xmlChar *encoding, const xmlChar *str);

.....

/usr/local/Cellar/r/3.2.4_1/R.framework/Resources/include/Rinternals.h:822:28: note: passing argument to parameter here
    SEXP Rf_mkChar(const char *);
                               ^
    schema.c:122:25: warning: passing 'const char *' to parameter of type 'const xmlChar *' (aka 'const unsigned char *') converts between pointers
          to integer types with different sign [-Wpointer-sign]
       p = xmlHashLookup(t, CHAR_DEREF(STRING_ELT(name, 0)));
                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    ./RSCommon.h:140:27: note: expanded from macro 'CHAR_DEREF'
      #define CHAR_DEREF(x)   CHAR((x))
                              ^~~~~~~~~
    /usr/local/Cellar/r/3.2.4_1/R.framework/Resources/include/Rinternals.h:440:18: note: expanded from macro 'CHAR'
    #define CHAR(x)         R_CHAR(x)
                            ^~~~~~~~~
    /Users/richiethomas/anaconda/include/libxml2/libxml/hash.h:171:22: note: passing argument to parameter 'name' here
                                             const xmlChar *name);
                                                            ^
    2 warnings generated.
    clang -I/usr/local/Cellar/r/3.2.4_1/R.framework/Resources/include -DNDEBUG -DLIBXML -I/Users/richiethomas/anaconda/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include    -fPIC  -g -O2  -c xmlsecurity.c -o xmlsecurity.o
    clang -I/usr/local/Cellar/r/3.2.4_1/R.framework/Resources/include -DNDEBUG -DLIBXML -I/Users/richiethomas/anaconda/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include    -fPIC  -g -O2  -c xpath.c -o xpath.o
    xpath.c:36:41: warning: passing 'const xmlChar *' (aka 'const unsigned char *') to parameter of type 'const char *' converts between pointers
          to integer types with different sign [-Wpointer-sign]
              SET_NAMES(ref, ScalarString(mkCharCE(el->name, encoding)));
                                                   ^~~~~~~~
    /usr/local/Cellar/r/3.2.4_1/R.framework/Resources/include/Rdefines.h:135:54: note: expanded from macro 'SET_NAMES'
    #define SET_NAMES(x, n)         setAttrib(x, R_NamesSymbol, n)
                                                                ^
    /usr/local/Cellar/r/3.2.4_1/R.framework/Resources/include/Rinternals.h:889:30: note: passing argument to parameter here
    SEXP Rf_mkCharCE(const char *, cetype_t);
                                 ^
    1 warning generated.
    clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/3.2.4_1/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/openssl/lib -L/usr/local/lib -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o NodeGC.o RSDTD.o RUtils.o Rcatalog.o Utils.o XMLEventParse.o XMLHashTree.o XMLTree.o fixNS.o libxmlFeatures.o schema.o xmlsecurity.o xpath.o -L/Users/richiethomas/anaconda/lib -lxml2 -lz -liconv -lm -lz -lxml2 -F/usr/local/Cellar/r/3.2.4_1/R.framework/.. -framework R -lintl -Wl,-framework -Wl,CoreFoundation
    installing to /usr/local/lib/R/3.2/site-library/XML/libs
    ** R
    ** inst
    ** preparing package for lazy loading
    Creating a generic function for ‘source’ from package ‘base’ in package ‘XML’
    in method for ‘xmlAttrsToDataFrame’ with signature ‘"AsIs"’: no definition for class “AsIs”
    in method for ‘readKeyValueDB’ with signature ‘"AsIs"’: no definition for class “AsIs”
    in method for ‘readSolrDoc’ with signature ‘"AsIs"’: no definition for class “AsIs”
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
    Error : .onLoad failed in loadNamespace() for 'XML', details:
      call: dyn.load(file, DLLpath = DLLpath, ...)
      error: unable to load shared object '/usr/local/lib/R/3.2/site-library/XML/libs/XML.so':
      dlopen(/usr/local/lib/R/3.2/site-library/XML/libs/XML.so, 6): Library not loaded: libxml2.2.dylib
      Referenced from: /usr/local/lib/R/3.2/site-library/XML/libs/XML.so
      Reason: image not found
    Error: loading failed
    Execution halted
    ERROR: loading failed
    * removing ‘/usr/local/lib/R/3.2/site-library/XML’

    The downloaded source packages are in
        ‘/private/var/folders/jy/0cwn40p951xc7f1480z3sxzm0000gn/T/RtmpEi0XEv/downloaded_packages’
    Warning message:
    In install.packages("XML") :
      installation of package ‘XML’ had non-zero exit status

4 个答案:

答案 0 :(得分:4)

我使用anaconda安装XML解决了这个问题:

conda install -c r r-xml=3.98_1.5

答案 1 :(得分:3)

使用conda install -c r r-xml=3.98_1.5conda install -c conda-forge r-xml添加到@Travis的答案是可行的。 但是请确保运行conda update r-essentials并重新打开/重新启动r terminal\notebook(以您的情况为准)。

答案 2 :(得分:3)

Mac OS Catalina的解决方案(即zsh中的版本)。

我是新手,但这对我有用。

  1. 确保在自制软件中安装了libxml2。 (如果知道了,brew list | grep libxml2应该确认;否则请安装brew install libxml2。没有自制软件吗?Install it。)

  2. 创建zsh运行com touch ~/.zshrc,或在主目录cd ~中找到它。 (在终端机中使用ls -a,查看其是否在~中。)

  3. 然后确保:export PATH="/usr/local/opt/libxml2/bin:$PATH"在其中(即~/.zshrc中)。它不应该在那里!使用sudo nano ~/.zshrc添加它。然后将其保存(Ctrl + X,Y,输入)。这应该确保在查找libxml2时首先出现brew的libxml2路径。 (仅供参考,我也将其添加到~/.zprofile中。我不知道哪个是正确的。)

  4. 好,现在重新启动终端。然后使用R在终端中运行R。 R启动后,install.packages("XML"),选择一台服务器进行下载,您应该一切顺利。

答案 3 :(得分:2)

你解释了什么是错的,这有帮助。

此处的XML包文档:https://cran.r-project.org/web/packages/XML/index.html

注意它所在的位置You are trying to use a version 2.* edition of libxml but an incompatible library.

您使用的是什么系统?我使用OSX,当我遇到类似问题时,我确实运行了

brew install libxml2

然后它起作用了

我也看到你使用R 3.0+并且应该非常兼容。