无法在 R/RStudio 中安装 XML 软件包
Cannot install XML package in R/RStudio
[环境：macOS 10.12.6、RStudio 1.1.383、R 3.4.2（通过自制软件）]
请注意，这不是 this question 的副本 - 那里的解决方案对我不起作用。
当我尝试在 RStudio 中安装 XML 包时出现安装错误：
> install.packages("XML")
Installing package into ‘/usr/local/lib/R/3.4/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.9.tar.gz'
Content type 'application/x-gzip' length 1599437 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/bin/sed
checking for pkg-config... /usr/local/bin/pkg-config
checking for xml2-config... /usr/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 9, Patch 4 for 2.9.4
Located parser file -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/libxml2/parser.h
Checking for 1.8: -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/libxml2
Using libxml2.*
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... no
checking for xmlParseFile in -lxml... no
configure: error: "libxml not found"
ERROR: configuration failed for package ‘XML’
* removing ‘/usr/local/lib/R/3.4/site-library/XML’
好的 - 所以我通过自制软件和强制链接安装了 libxml2 (2.9.7)：
>brew install libxml2
>brew link libxml2 --force
我将此代码添加到 ~/.Renviron:
LIBXML_INCDIR=/usr/local/opt/libxml2
LIBXML_LIBDIR=/usr/local/opt/libxml2
PKG_CONFIG_PATH=/usr/local/opt/libxml2/lib/pkgconfig
LDFLAGS=-L/usr/local/opt/libxml2/lib
CPPFLAGS=-I/usr/local/opt/libxml2/include
我退出并重新启动 RStudio；再试一次：
> install.packages("XML")
Installing package into ‘/usr/local/lib/R/3.4/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.9.tar.gz'
Content type 'application/x-gzip' length 1599437 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/bin/sed
checking for pkg-config... /usr/local/bin/pkg-config
Checking directory of LIBXML_INCDIR
You specified LIBXML_INCDIR, but we couldn't find parser.h
Please specify it correctly and re-run the INSTALL'ation.
ERROR: configuration failed for package ‘XML’
* removing ‘/usr/local/lib/R/3.4/site-library/XML’
parser.h 确实存在于 /usr/local/opt/libxml2/include/libxml2/libxml/parser.h（由 brew 放置在那里），我什至将它符号链接到 /usr/local/opt/libxml2/include/parser.h，但无济于事。
所以我几乎不知道如何让 RStudio 识别库 libxml2 和 parser.h。
RStudio 环境：
> Sys.getenv()
__CF_USER_TEXT_ENCODING 0x535:0x0:0x0
Apple_PubSub_Socket_Render
/private/tmp/com.apple.launchd.oqvtmxMkmV/Render
CLICOLOR_FORCE 1
CPPFLAGS -I/usr/local/opt/libxml2/include
DISPLAY /private/tmp/com.apple.launchd.z0UbJdCqkr/org.macosforge.xquartz:0
DYLD_FALLBACK_LIBRARY_PATH
/usr/local/Cellar/r/3.4.2/lib/R/lib:/Users/conrad/lib:/usr/local/lib:/usr/lib:::/lib
EDITOR vi
GIT_ASKPASS rpostback-askpass
HOME /Users/conrad
LANG en_US.UTF-8
LC_CTYPE en_US.UTF-8
LDFLAGS -L/usr/local/opt/libxml2/lib
LIBXML_INCDIR /usr/local/opt/libxml2
LIBXML_LIBDIR /usr/local/opt/libxml2
LN_S ln -s
LOGNAME conrad
MAKE make
PAGER /usr/bin/less
PATH /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/MacGPG2/bin:/Library/Frameworks/Mono.framework/Versions/Current/Commands
PKG_CONFIG_PATH /usr/local/opt/libxml2/lib/pkgconfig
R_BROWSER /usr/bin/open
R_BZIPCMD /usr/bin/bzip2
R_DOC_DIR /usr/local/Cellar/r/3.4.2/lib/R/doc
R_GZIPCMD /usr/bin/gzip
R_HOME /usr/local/Cellar/r/3.4.2/lib/R
R_INCLUDE_DIR /usr/local/Cellar/r/3.4.2/lib/R/include
R_LIBS_SITE
R_LIBS_USER ~/Library/R/3.4/library
R_PAPERSIZE a4
R_PDFVIEWER /usr/bin/open
R_PLATFORM x86_64-apple-darwin16.7.0
R_PRINTCMD lpr
R_RD4PDF times,inconsolata,hyper
R_SESSION_TMPDIR /var/folders/dr/ldgx2z697jv6b0b281qjcsw400019n/T//RtmpvNqwQA
R_SHARE_DIR /usr/local/Cellar/r/3.4.2/lib/R/share
R_SYSTEM_ABI osx,gcc,gxx,gfortran,?
R_TEXI2DVICMD /usr/bin/texi2dvi
R_UNZIPCMD /usr/bin/unzip
R_ZIPCMD /usr/bin/zip
RMARKDOWN_MATHJAX_PATH /Applications/RStudio.app/Contents/Resources/resources/mathjax-26
RS_RPOSTBACK_PATH /Applications/RStudio.app/Contents/MacOS/rpostback
RS_SHARED_SECRET <redacted>
RSTUDIO 1
RSTUDIO_CONSOLE_COLOR 256
RSTUDIO_CONSOLE_WIDTH 91
RSTUDIO_PANDOC /Applications/RStudio.app/Contents/MacOS/pandoc
RSTUDIO_SESSION_PORT 9090
RSTUDIO_USER_IDENTITY conrad
RSTUDIO_WINUTILS bin/winutils
SED /usr/bin/sed
SHELL /bin/tcsh
SSH_ASKPASS rpostback-askpass
SSH_AUTH_SOCK /private/tmp/com.apple.launchd.wBdDUnzsja/Listeners
TAR /usr/bin/tar
TERM xterm-256color
TMPDIR /var/folders/dr/ldgx2z697jv6b0b281qjcsw400019n/T/
USER conrad
XPC_FLAGS 0x0
XPC_SERVICE_NAME 0
(自然是发帖后马上就找到答案了:)
解决方法是删除
LIBXML_INCDIR=/usr/local/opt/libxml2
LIBXML_LIBDIR=/usr/local/opt/libxml2
来自 ~/.Renviron 并添加
XML_CONFIG=/usr/local/bin/xml2-config
这允许 XML 包编译和安装。
这个问题困扰我很久了。仅在 RStudio 中。在 R 上安装包并将其库化。转到 RStudio 并需要包。
请设置PKG_CONFIG_PATH，它应该包含一个libxml-2.0.pc文件。
对我来说，我通过 brew 安装了 libxml2，这段代码有效：
export PKG_CONFIG_PATH="/usr/local/Cellar/libxml2/2.9.8/lib/pkgconfig"
[环境：macOS 10.12.6、RStudio 1.1.383、R 3.4.2（通过自制软件）]
请注意，这不是 this question 的副本 - 那里的解决方案对我不起作用。
当我尝试在 RStudio 中安装 XML 包时出现安装错误：
> install.packages("XML")
Installing package into ‘/usr/local/lib/R/3.4/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.9.tar.gz'
Content type 'application/x-gzip' length 1599437 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/bin/sed
checking for pkg-config... /usr/local/bin/pkg-config
checking for xml2-config... /usr/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 9, Patch 4 for 2.9.4
Located parser file -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/libxml2/parser.h
Checking for 1.8: -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/libxml2
Using libxml2.*
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... no
checking for xmlParseFile in -lxml... no
configure: error: "libxml not found"
ERROR: configuration failed for package ‘XML’
* removing ‘/usr/local/lib/R/3.4/site-library/XML’
好的 - 所以我通过自制软件和强制链接安装了 libxml2 (2.9.7)：
>brew install libxml2
>brew link libxml2 --force
我将此代码添加到 ~/.Renviron:
LIBXML_INCDIR=/usr/local/opt/libxml2
LIBXML_LIBDIR=/usr/local/opt/libxml2
PKG_CONFIG_PATH=/usr/local/opt/libxml2/lib/pkgconfig
LDFLAGS=-L/usr/local/opt/libxml2/lib
CPPFLAGS=-I/usr/local/opt/libxml2/include
我退出并重新启动 RStudio；再试一次：
> install.packages("XML")
Installing package into ‘/usr/local/lib/R/3.4/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.9.tar.gz'
Content type 'application/x-gzip' length 1599437 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/bin/sed
checking for pkg-config... /usr/local/bin/pkg-config
Checking directory of LIBXML_INCDIR
You specified LIBXML_INCDIR, but we couldn't find parser.h
Please specify it correctly and re-run the INSTALL'ation.
ERROR: configuration failed for package ‘XML’
* removing ‘/usr/local/lib/R/3.4/site-library/XML’
parser.h 确实存在于 /usr/local/opt/libxml2/include/libxml2/libxml/parser.h（由 brew 放置在那里），我什至将它符号链接到 /usr/local/opt/libxml2/include/parser.h，但无济于事。
所以我几乎不知道如何让 RStudio 识别库 libxml2 和 parser.h。
RStudio 环境：
> Sys.getenv()
__CF_USER_TEXT_ENCODING 0x535:0x0:0x0
Apple_PubSub_Socket_Render
/private/tmp/com.apple.launchd.oqvtmxMkmV/Render
CLICOLOR_FORCE 1
CPPFLAGS -I/usr/local/opt/libxml2/include
DISPLAY /private/tmp/com.apple.launchd.z0UbJdCqkr/org.macosforge.xquartz:0
DYLD_FALLBACK_LIBRARY_PATH
/usr/local/Cellar/r/3.4.2/lib/R/lib:/Users/conrad/lib:/usr/local/lib:/usr/lib:::/lib
EDITOR vi
GIT_ASKPASS rpostback-askpass
HOME /Users/conrad
LANG en_US.UTF-8
LC_CTYPE en_US.UTF-8
LDFLAGS -L/usr/local/opt/libxml2/lib
LIBXML_INCDIR /usr/local/opt/libxml2
LIBXML_LIBDIR /usr/local/opt/libxml2
LN_S ln -s
LOGNAME conrad
MAKE make
PAGER /usr/bin/less
PATH /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/MacGPG2/bin:/Library/Frameworks/Mono.framework/Versions/Current/Commands
PKG_CONFIG_PATH /usr/local/opt/libxml2/lib/pkgconfig
R_BROWSER /usr/bin/open
R_BZIPCMD /usr/bin/bzip2
R_DOC_DIR /usr/local/Cellar/r/3.4.2/lib/R/doc
R_GZIPCMD /usr/bin/gzip
R_HOME /usr/local/Cellar/r/3.4.2/lib/R
R_INCLUDE_DIR /usr/local/Cellar/r/3.4.2/lib/R/include
R_LIBS_SITE
R_LIBS_USER ~/Library/R/3.4/library
R_PAPERSIZE a4
R_PDFVIEWER /usr/bin/open
R_PLATFORM x86_64-apple-darwin16.7.0
R_PRINTCMD lpr
R_RD4PDF times,inconsolata,hyper
R_SESSION_TMPDIR /var/folders/dr/ldgx2z697jv6b0b281qjcsw400019n/T//RtmpvNqwQA
R_SHARE_DIR /usr/local/Cellar/r/3.4.2/lib/R/share
R_SYSTEM_ABI osx,gcc,gxx,gfortran,?
R_TEXI2DVICMD /usr/bin/texi2dvi
R_UNZIPCMD /usr/bin/unzip
R_ZIPCMD /usr/bin/zip
RMARKDOWN_MATHJAX_PATH /Applications/RStudio.app/Contents/Resources/resources/mathjax-26
RS_RPOSTBACK_PATH /Applications/RStudio.app/Contents/MacOS/rpostback
RS_SHARED_SECRET <redacted>
RSTUDIO 1
RSTUDIO_CONSOLE_COLOR 256
RSTUDIO_CONSOLE_WIDTH 91
RSTUDIO_PANDOC /Applications/RStudio.app/Contents/MacOS/pandoc
RSTUDIO_SESSION_PORT 9090
RSTUDIO_USER_IDENTITY conrad
RSTUDIO_WINUTILS bin/winutils
SED /usr/bin/sed
SHELL /bin/tcsh
SSH_ASKPASS rpostback-askpass
SSH_AUTH_SOCK /private/tmp/com.apple.launchd.wBdDUnzsja/Listeners
TAR /usr/bin/tar
TERM xterm-256color
TMPDIR /var/folders/dr/ldgx2z697jv6b0b281qjcsw400019n/T/
USER conrad
XPC_FLAGS 0x0
XPC_SERVICE_NAME 0
(自然是发帖后马上就找到答案了:)
解决方法是删除
LIBXML_INCDIR=/usr/local/opt/libxml2
LIBXML_LIBDIR=/usr/local/opt/libxml2
来自 ~/.Renviron 并添加
XML_CONFIG=/usr/local/bin/xml2-config
这允许 XML 包编译和安装。
这个问题困扰我很久了。仅在 RStudio 中。在 R 上安装包并将其库化。转到 RStudio 并需要包。
请设置PKG_CONFIG_PATH，它应该包含一个libxml-2.0.pc文件。 对我来说，我通过 brew 安装了 libxml2，这段代码有效：
export PKG_CONFIG_PATH="/usr/local/Cellar/libxml2/2.9.8/lib/pkgconfig"