如何解决R软件包安装给出一个`:: std :: isxdigit'声明为致命错误` Rcpp的错误消息：安装脚本 R会话 Hombrew版本
我最近在Mac（10.14.6（18G6020））上更新了 Homebrew ，并继续重新编译R的开发版本。我构建了一个安装脚本，以确保执行相同的步骤。每次拍摄（见下文）。 R成功编译并通过所有检查。但是，当我开始安装Rcpp，devtools，ape，lme4等软件包时，在编译过程中会得到::std::isxdigit declared here ，并且安装失败。
我在这里发布Rcpp，安装脚本，sessionInfo（）和brew版本的错误消息。解决该问题的任何帮助将不胜感激，
谢谢！
Rcpp的错误消息：
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks//R.framework/Resources/include" -DNDEBUG -I../inst/include/ -isysroot /Library/Developer/CommandLinetools/SDKs/MacOSX.sdk -I/usr\
/local/opt/icu4c/include -I/usr/local/opt/gettext/include -I/usr/local/opt/curl/include -I/usr/local/include -I/usr/local/opt/cairo/include -I/usr/local/opt/pango/include/pa\
ngo-1.0/pango -I/usr/local/opt/tcl-tk/include -fPIC -Wall -g -O3 -c api.cpp -o api.o
In file included from api.cpp:24:
In file included from ../inst/include/Rcpp.h:27:
In file included from ../inst/include/RcppCommon.h:51:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/iostream:38:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/ios:216:
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:116:20: error: use
of undeclared identifier 'LC_COLLATE_MASK'
collate = LC_COLLATE_MASK,^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:117:20: error: use
of undeclared identifier 'LC_CTYPE_MASK'
ctype = LC_CTYPE_MASK,^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:118:20: error: use
of undeclared identifier 'LC_MONETARY_MASK'
monetary = LC_MONETARY_MASK,^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:119:20: error: use
of undeclared identifier 'LC_NUMERIC_MASK'
numeric = LC_NUMERIC_MASK,^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:120:20: error: use
of undeclared identifier 'LC_TIME_MASK'
time = LC_TIME_MASK,^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:121:20: error: use
of undeclared identifier 'LC_MESSAGES_MASK'
messages = LC_MESSAGES_MASK,^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:330:5: error:
unkNown type name 'locale_t'; did you mean 'locale'?
locale_t __l;
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:105:24: note:
'locale' declared here
class _LIBCPP_TYPE_VIS locale
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:349:5: error:
unkNown type name 'locale_t'; did you mean 'locale'?
locale_t __l;
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:105:24: note:
'locale' declared here
class _LIBCPP_TYPE_VIS locale
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:708:5: error:
unkNown type name 'locale_t'; did you mean 'locale'?
locale_t __l;
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:105:24: note:
'locale' declared here
class _LIBCPP_TYPE_VIS locale
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:726:5: error:
unkNown type name 'locale_t'; did you mean 'locale'?
locale_t __l;
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:105:24: note:
'locale' declared here
class _LIBCPP_TYPE_VIS locale
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:958:5: error:
unkNown type name 'locale_t'; did you mean 'locale'?
locale_t __l;
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__locale:105:24: note:
'locale' declared here
class _LIBCPP_TYPE_VIS locale
^
In file included from api.cpp:24:
In file included from ../inst/include/Rcpp.h:27:
In file included from ../inst/include/RcppCommon.h:51:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/iostream:40:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/istream:163:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/ostream:140:
/Library/Developer/CommandLinetools/usr/include/c++/v1/locale:739:26: error: use of
undeclared identifier 'strtoll_l'
long long __ll = strtoll_l(__a,&__p2,__base,_LIBCPP_GET_C_LOCALE);
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/locale:779:35: error: use of
undeclared identifier 'strtoull_l'
unsigned long long __ll = strtoull_l(__a,_LIBCPP_GET...
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/locale:808:12: error: use of
undeclared identifier 'strtof_l'
return strtof_l(__a,__p2,_LIBCPP_GET_C_LOCALE);
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/locale:814:12: error: use of
undeclared identifier 'strtod_l'
return strtod_l(__a,_LIBCPP_GET_C_LOCALE);
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/locale:820:12: error: use of
undeclared identifier 'strtold_l'; did you mean 'strtoll'?
return strtold_l(__a,_LIBCPP_GET_C_LOCALE);
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/cstdlib:117:9: note:
'strtoll' declared here
using ::strtoll;
^
In file included from api.cpp:24:
In file included from ../inst/include/Rcpp.h:27:
In file included from ../inst/include/RcppCommon.h:51:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/iostream:40:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/istream:163:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/ostream:140:
/Library/Developer/CommandLinetools/usr/include/c++/v1/locale:1094:9: error: use of
undeclared identifier 'sscanf_l'
if (__libcpp_sscanf_l(__buf.c_str(),_LIBCPP_GET_C_LOCALE,"%p",&__v) != 1)
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/__bsd_locale_defaults.h:35:61: note:
expanded from macro '__libcpp_sscanf_l'
#define __libcpp_sscanf_l(...) sscanf_l(__VA_ARGS__)
^
In file included from api.cpp:24:
In file included from ../inst/include/Rcpp.h:27:
In file included from ../inst/include/RcppCommon.h:51:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/iostream:40:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/istream:163:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/ostream:140:
/Library/Developer/CommandLinetools/usr/include/c++/v1/locale:1199:18: error: use of
undeclared identifier 'isxdigit_l'; did you mean 'isxdigit'?
if (!isxdigit_l(*__ns,_LIBCPP_GET_C_LOCALE))
^
/Library/Developer/CommandLinetools/usr/include/c++/v1/cctype:115:9: note:
'isxdigit' declared here
using ::isxdigit;
^
In file included from api.cpp:24:
In file included from ../inst/include/Rcpp.h:27:
In file included from ../inst/include/RcppCommon.h:51:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/iostream:40:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/istream:163:
In file included from /Library/Developer/CommandLinetools/usr/include/c++/v1/ostream:140:
/Library/Developer/CommandLinetools/usr/include/c++/v1/locale:1199:18: error: too
many arguments to function call,expected 1,have 2; did you mean
'::std::isxdigit'?
if (!isxdigit_l(*__ns,_LIBCPP_GET_C_LOCALE))
^~~~~~~~~~
/Library/Developer/CommandLinetools/usr/include/c++/v1/cctype:115:9: note:
'::std::isxdigit' declared here
using ::isxdigit;
^
Fatal error: too many errors emitted,stopping Now [-ferror-limit=]
20 errors generated.
make: *** [api.o] Error 1
ERROR: compilation Failed for package ‘Rcpp’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp’
ERROR: dependency ‘Rcpp’ is not available for package ‘minqa’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/minqa’
ERROR: dependency ‘Rcpp’ is not available for package ‘RcppEigen’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen’
ERROR: dependencies ‘minqa’,‘nloptr’,‘Rcpp’,‘RcppEigen’ are not available for package ‘lme4’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/lme4’
The downloaded source packages are in
‘/private/var/folders/f7/v_vt_5bn07z9tljnh56n9crnrzdbg9/T/RtmpuouQQU/downloaded_packages’
Warning messages:
1: In install.packages("lme4") :
installation of package ‘nloptr’ had non-zero exit status
2: In install.packages("lme4") :
installation of package ‘Rcpp’ had non-zero exit status
3: In install.packages("lme4") :
installation of package ‘minqa’ had non-zero exit status
4: In install.packages("lme4") :
installation of package ‘RcppEigen’ had non-zero exit status
5: In install.packages("lme4") :
installation of package ‘lme4’ had non-zero exit status
安装脚本
## remove binaries,etc
make distclean
## update
svn update
## get recommended tools
./tools/rsync-recommended
## other variables
PKG_CONfig_PATH=/opt/X11/lib/pkgconfig:/usr/local/opt/curl/lib/pkgconfig
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-15.jdk/Contents/Home/
JAVA_CPPFLAGS="-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin"
JAVA_LD_LIBRARY_PATH="${JAVA_HOME}/jre/lib/server"
JAVA_LIBS="-L/${JAVA_HOME}/jre/lib/server -ljvm"
export LDFLAGS="-L/usr/local/opt/curl/lib -L/usr/local/opt/tcl-tk/lib"
export CPPFLAGS="-isysroot /Library/Developer/CommandLinetools/SDKs/MacOSX.sdk -I/usr/local/opt/icu4c/include -I/usr/local/opt/gettext/include -I/usr/local/opt/curl/include -\
I/usr/local/include -I/usr/local/opt/cairo/include -I/usr/local/opt/pango/include/pango-1.0/pango -I/usr/local/opt/tcl-tk/include"
export PKG_CONfig_PATH="/usr/local/opt/tcl-tk/lib/pkgconfig:/usr/local/opt/curl/lib/pkgconfig:$PKG_CONfig_PATH"
export CC=clang
export CXX=clang++
export FC=/usr/local/bin/gfortran
export OBJC=clang
export CFLAGS='-Wall -g -O3'
export CXXFLAGS='-Wall -g -O3'
export OBJCFLAGS='-Wall -g -O3'
export FFLAGS='-Wall -g -O3 -mtune=generic'
export LC_ALL='C'
./configure --enable-R-framework=/Library/Frameworks/ \
--with-blas="-framework Accelerate" --with-lapack \
--x-includes=/opt/X11/include --x-libraries=/opt/X11/lib \
--with-internal-tzcode --with-cairo=yes
make
make install
R会话
> sessionInfo()
R Under development (unstable) (2020-09-29 r79274)
Platform: x86_64-apple-darwin18.7.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics Grdevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0 tcltk_4.1.0
Hombrew版本
bash-3.2$ brew --version
Homebrew 2.5.2
Homebrew/homebrew-core (git revision f5bfb; last commit 2020-09-25)
Homebrew/homebrew-cask (git revision a5844b; last commit 2020-09-25)
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