I recently updated the Homebrew on my Mac (10.14.6 (18G6020)), and went ahead to recompile the development version of R. I built an installation script to make sure the same steps are taken every time (see below). R compiles successfully and passes all checks. However, when I begin to install packages, such as Rcpp, devtools, ape, lme4, among others, I get a ::std::isxdigit declared here during the compilation, and installation fails.
I'm posting here the error message for Rcpp, installation script, sessionInfo(), and brew version. Any help to resolve this will be much appreciated,
Thank you !
Error message for Rcpp:
* 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, &__p2, __base, _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, __p2, _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, __p2, _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
Installation script
## 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:$PKG_CONFIG_PATH"
export CC=clang
export CXX=clang++
export FC=/usr/local/bin/gfortran
export OBJC=clang
export CFLAGS='-Wall -g -O3'
export CXXFLAGS='-Wall -g -O3'
export OBJCFLAGS='-Wall -g -O3'
export FFLAGS='-Wall -g -O3 -mtune=generic'
export LC_ALL='C'
./configure --enable-R-framework=/Library/Frameworks/ \
--with-blas="-framework Accelerate" --with-lapack \
--x-includes=/opt/X11/include --x-libraries=/opt/X11/lib \
--with-internal-tzcode --with-cairo=yes
make
make install
R session
> sessionInfo()
R Under development (unstable) (2020-09-29 r79274)
Platform: x86_64-apple-darwin18.7.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0 tcltk_4.1.0
Hombrew Version
bash-3.2$ 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)