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我在命令行推出的R和鍵入以下內容：無法與R包安裝，由於XML的依賴性不匹配
install.packages("XML")
選擇一個鏡像站點之後，我看到了下面的輸出：
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
我搜索了一下，發現this link，它建議在命令行中運行'which xmllint'命令來查找可能與R相沖突的任何XML安裝。當我跑它的輸出是：
/Users/richiethomas/anaconda/bin/xmllint
糾正我，如果我錯了，但現在看來，我的Python安裝具有衝突與一個R要下載一個XML的依賴。這是正確的嗎？如果是這樣，我該如何解決它，以便Python和R都安裝在我的機器上？
編輯：我正在使用OSX。我跑了「brew install libxml2」，但Homebrew說它已經安裝好了。
編輯＃2：我試圖通過自制程序卸載並重新安裝R，我仍然得到相同的錯誤。編輯＃3：我運行了「brew info libxml2」，看到有一個「--with-python」標誌，它可以啓用Python支持的構建。我也注意到以下幾點：
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
我跑了「BREW卸載libxml2的」，然後「釀造安裝的libxml2 --with-蟒蛇」，然後使用「導出」命令設定上述2的環境變量。然後我重新運行R並再次嘗試安裝XML包。只見幾十個「路過的說法在這裏參數」（見下文）類型的警告，接着一個非零退出代碼：
* 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
，我跑了「釀安裝libxml2的」，但家釀說，這是已安裝。我將編輯該問題以添加此信息。 –
如何「釀造醫生」，修復所有的錯誤和警告，然後「釀造修剪」？ – pachamaltese
pachamaltese：試過這個，「brew prune」從/ usr/local刪除了16個符號鏈接和4個目錄，但問題仍然存在。 –