由于 XML 依赖项不匹配，无法安装 R 包答案

【问题标题】：Unable to install R package due to XML dependency mismatch由于 XML 依赖项不匹配，无法安装 R 包
【发布时间】：2016-05-04 18:15:15
【问题描述】：

我在命令行中启动了 R 并输入了以下内容：

install.packages("XML")

选择镜像站点后，看到如下输出：

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

我四处搜索并找到this link，它建议在命令行中运行“which xmllint”命令来查找任何可能与 R 依赖项冲突的 XML 安装。我运行它时的输出是：

/Users/richiethomas/anaconda/bin/xmllint

如果我错了，请纠正我，但我的 Python 安装似乎有一个 XML 依赖项，它与 R 要下载的那个冲突。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 说它已经安装了。

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

编辑#3：我运行“brew info libxml2”并看到有一个“--with-python”标志，它启用了具有 Python 支持的构建。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“将参数传递给参数”类型的警告（见下文），然后是一个非零退出代码：

    * 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

【问题讨论】：

标签： python xml r

【解决方案1】：

我通过使用anaconda安装XML解决了这个问题：

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

【讨论】：

小心这样做 - 上面的命令会安装多个东西，包括 'r-base-3.3.2-1'
对此+1。它对我很有用。我有我的主要 R 作为 conda R，所以这也解决了更新问题。
无论出于何种原因，这对我来说特别不起作用，但如果我取消固定版本 conda install -c r r-xml 它对我有用。有关文档，请参阅 anaconda.org/r/r-xml。

【解决方案2】：

使用conda install -c r r-xml=3.98_1.5 或conda install -c conda-forge r-xml 添加到@Travis 的答案有效。但请确保运行 conda update r-essentials 并重新打开/重新启动 r terminal\notebook（视情况而定）。

【讨论】：

conda install -c conda-forge r-xml 帮助我完成了这项工作。谢谢

【解决方案3】：

Mac OS Catalina 解决方案（即在 zsh 中）。

我是新手，但这对我有用。

确保在 homebrew 中安装了 libxml2。（如果你得到它，brew list | grep libxml2 应该确认它；否则安装它brew install libxml2。没有自制软件？Install it。）
要么创建一个 zsh 运行 com，touch ~/.zshrc，要么在你的主目录 cd ~ 中找到它。（在终端中使用ls -a 来查看它是否在~ 中。）
然后确保：export PATH="/usr/local/opt/libxml2/bin:$PATH" 在其中（即在~/.zshrc 中）。它不应该在那里！使用sudo nano ~/.zshrc 添加它。然后保存（ctrl + x，Y，回车）。这应该确保 brew 的 libxml2 的路径是在寻找 libxml2 时出现的第一件事。（仅供参考，我也添加到~/.zprofile。我不知道哪个是正确的。）
好的，现在重新启动您的终端。然后使用R 在终端中运行 R。一旦 R 启动，install.packages("XML")，选择一个服务器来下载它，你应该很高兴。

【讨论】：

【解决方案4】：

你解释了哪里出了问题，这很有帮助。

XML 包文档在这里：https://cran.r-project.org/web/packages/XML/index.html

注意上面写着You are trying to use a version 2.* edition of libxml but an incompatible library.

你用的是什么系统？我使用 OSX，当我遇到类似问题时，我确实运行了

brew install libxml2

然后就成功了

我还看到您使用 R 3.0+，应该非常兼容。

【讨论】：

我在 OSX 上运行“brew install libxml2”，但 Homebrew 说它已经安装。我将编辑问题以添加此信息。
“brew医生”怎么样，修复所有错误和警告，然后“brew prune”？
pachamaltese：试过了，“brew prune”从 /usr/local 中删除了 16 个符号链接和 4 个目录，但问题仍然存在。
@RichieThomas 你解决了吗？我在安装了 anaconda python 和 R 的 RHEL 6 上遇到了同样的问题
跟进，因为我在 macOS 上遇到了同样的问题。因为我已经通过 brew 安装了libxml2，所以我运行了brew reinstall libxml2，但问题仍然存在。但是 brew 暗示通过echo 'export PATH="/usr/local/opt/libxml2/bin:$PATH"' >> ~/.bash_profile 连接到正确的路径，这解决了我的问题。