Installation fails
Closed this issue · 2 comments
ramay commented
Hi,
I am trying to install readxl from github
devtools::install_github("hadley/readxl")This is the error I get:
Downloading GitHub repo hadley/readxl@master
✔ checking for file ‘/private/var/folders/jn/zp890ymn4vn6wb76rf0hpz7c0000gn/T/Rtmpzgy9Z0/remotesf1137e51a17f/tidyverse-readxl-4572ade/DESCRIPTION’ ...
─ preparing ‘readxl’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘readxl_1.3.1.9000.tar.gz’
* installing *source* package ‘readxl’ ...
** libs
g++-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c RcppExports.cpp -o RcppExports.o
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/utils/tinyformat.h:40,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:70,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27,
from RcppExports.cpp:4:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:928:21: warning: conversion from 'long unsigned int' to 'int' may change value [-Wconversion]
detail::FormatListN<sizeof...(Args)> makeFormatList(const Args&... args)
^~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h: In function 'tinyformat::detail::FormatListN<sizeof... (Args)> tinyformat::makeFormatList(const Args& ...)':
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:930:32: warning: conversion from 'long unsigned int' to 'int' may change value [-Wconversion]
return detail::FormatListN<sizeof...(args)>(args...);
^~~~~~~~~~~~~~~
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/Vector.h:69,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:40,
from RcppExports.cpp:4:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/String.h: In member function 'SEXPREC* Rcpp::String::get_sexp_impl() const':
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/String.h:376:62: warning: conversion from 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion]
return Rf_mkCharLenCE(buffer.c_str(), buffer.size(), enc);
~~~~~~~~~~~^~
g++-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c XlsWorkBook.cpp -o XlsWorkBook.o
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/utils/tinyformat.h:40,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:70,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27,
from XlsWorkBook.cpp:1:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:928:21: warning: conversion from 'long unsigned int' to 'int' may change value [-Wconversion]
detail::FormatListN<sizeof...(Args)> makeFormatList(const Args&... args)
^~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h: In function 'tinyformat::detail::FormatListN<sizeof... (Args)> tinyformat::makeFormatList(const Args& ...)':
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:930:32: warning: conversion from 'long unsigned int' to 'int' may change value [-Wconversion]
return detail::FormatListN<sizeof...(args)>(args...);
^~~~~~~~~~~~~~~
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/Vector.h:69,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:40,
from XlsWorkBook.cpp:1:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/String.h: In member function 'SEXPREC* Rcpp::String::get_sexp_impl() const':
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/String.h:376:62: warning: conversion from 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion]
return Rf_mkCharLenCE(buffer.c_str(), buffer.size(), enc);
~~~~~~~~~~~^~
In file included from XlsWorkBook.h:6,
from XlsWorkBook.cpp:3:
ColSpec.h: In function 'Rcpp::List removeSkippedColumns(Rcpp::List, Rcpp::CharacterVector, std::vector<ColType>)':
ColSpec.h:258:20: warning: conversion from 'R_xlen_t' {aka 'long int'} to 'int' may change value [-Wconversion]
int p = cols.size();
~~~~~~~~~^~
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/Vector.h:52,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:40,
from XlsWorkBook.cpp:1:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h: In instantiation of 'Rcpp::Vector<RTYPE, StoragePolicy>::const_iterator Rcpp::Vector<RTYPE, StoragePolicy>::end() const [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage; Rcpp::Vector<RTYPE, StoragePolicy>::const_iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::const_string_proxy<16> >]':
StringSet.h:20:74: required from here
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:335:65: warning: conversion from 'R_xlen_t' {aka 'long int'} to 'Rcpp::internal::Proxy_Iterator<Rcpp::internal::const_string_proxy<16> >::difference_type' {aka 'int'} may change value [-Wconversion]
inline const_iterator end() const{ return cache.get_const() + size() ; }
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h: In instantiation of 'Rcpp::Vector<RTYPE, StoragePolicy>::iterator Rcpp::Vector<RTYPE, StoragePolicy>::end() [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage; Rcpp::Vector<RTYPE, StoragePolicy>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::string_proxy<16> >]':
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:1115:18: required from 'void Rcpp::Vector<RTYPE, StoragePolicy>::fill__dispatch(Rcpp::traits::true_type, const U&) [with U = SEXPREC*; int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage; Rcpp::traits::true_type = Rcpp::traits::integral_constant<bool, true>]'
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:329:9: required from 'void Rcpp::Vector<RTYPE, StoragePolicy>::fill(const U&) [with U = SEXPREC*; int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]'
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:97:9: required from 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&, const stored_type&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage; Rcpp::Vector<RTYPE, StoragePolicy>::stored_type = SEXPREC*]'
ColSpec.h:247:46: required from here
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:333:48: warning: conversion from 'R_xlen_t' {aka 'long int'} to 'Rcpp::internal::Proxy_Iterator<Rcpp::internal::string_proxy<16> >::difference_type' {aka 'int'} may change value [-Wconversion]
inline iterator end() { return cache.get() + size() ; }
g++-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Iunix -I. -DRCPP_DEFAULT_INCLUDE_CALL=false -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c XlsWorkSheet.cpp -o XlsWorkSheet.o
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/utils/tinyformat.h:40,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:70,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27,
from XlsWorkSheet.cpp:1:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:928:21: warning: conversion from 'long unsigned int' to 'int' may change value [-Wconversion]
detail::FormatListN<sizeof...(Args)> makeFormatList(const Args&... args)
^~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h: In function 'tinyformat::detail::FormatListN<sizeof... (Args)> tinyformat::makeFormatList(const Args& ...)':
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:930:32: warning: conversion from 'long unsigned int' to 'int' may change value [-Wconversion]
return detail::FormatListN<sizeof...(args)>(args...);
^~~~~~~~~~~~~~~
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/Vector.h:69,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:40,
from XlsWorkSheet.cpp:1:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/String.h: In member function 'SEXPREC* Rcpp::String::get_sexp_impl() const':
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/String.h:376:62: warning: conversion from 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion]
return Rf_mkCharLenCE(buffer.c_str(), buffer.size(), enc);
~~~~~~~~~~~^~
In file included from XlsWorkSheet.cpp:2:
ColSpec.h: In function 'Rcpp::List removeSkippedColumns(Rcpp::List, Rcpp::CharacterVector, std::vector<ColType>)':
ColSpec.h:258:20: warning: conversion from 'R_xlen_t' {aka 'long int'} to 'int' may change value [-Wconversion]
int p = cols.size();
~~~~~~~~~^~
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:72,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:6,
from Spinner.h:4,
from XlsWorkSheet.h:7,
from XlsWorkSheet.cpp:3:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/unistd.h: At global scope:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/unistd.h:208:40: error: 'gid_t' has not been declared
int fchownat(int, const char *, uid_t, gid_t, int) __OSX_AVAILABLE_STARTING(__MAC_10_10, __IPHONE_8_0);
^~~~~
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:6,
from Spinner.h:4,
from XlsWorkSheet.h:7,
from XlsWorkSheet.cpp:3:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:434:33: error: 'gid_t' has not been declared
int chown(const char *, uid_t, gid_t);
^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:449:1: error: 'gid_t' does not name a type; did you mean 'uid_t'?
gid_t getegid(void);
^~~~~
uid_t
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:451:1: error: 'gid_t' does not name a type; did you mean 'uid_t'?
gid_t getgid(void);
^~~~~
uid_t
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:455:21: error: 'gid_t' has not been declared
int getgroups(int, gid_t []);
^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:474:13: error: 'gid_t' was not declared in this scope
int setgid(gid_t);
^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:474:13: note: suggested alternative:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/types.h:109,
from ./libxls/xlstypes.h:40,
from ./libxls/xls.h:42,
from ColSpec.h:5,
from XlsWorkSheet.cpp:2:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_gid_t.h:31:24: note: 'xls::gid_t'
typedef __darwin_gid_t gid_t;
^~~~~
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:6,
from Spinner.h:4,
from XlsWorkSheet.h:7,
from XlsWorkSheet.cpp:3:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:570:34: error: 'gid_t' has not been declared
int lchown(const char *, uid_t, gid_t) __DARWIN_ALIAS(lchown);
^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:596:15: error: 'gid_t' was not declared in this scope
int setregid(gid_t, gid_t) __DARWIN_ALIAS(setregid);
^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:596:15: note: suggested alternative:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/types.h:109,
from ./libxls/xlstypes.h:40,
from ./libxls/xls.h:42,
from ColSpec.h:5,
from XlsWorkSheet.cpp:2:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_gid_t.h:31:24: note: 'xls::gid_t'
typedef __darwin_gid_t gid_t;
^~~~~
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:6,
from Spinner.h:4,
from XlsWorkSheet.h:7,
from XlsWorkSheet.cpp:3:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:596:22: error: 'gid_t' was not declared in this scope
int setregid(gid_t, gid_t) __DARWIN_ALIAS(setregid);
^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:596:22: note: suggested alternative:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/types.h:109,
from ./libxls/xlstypes.h:40,
from ./libxls/xls.h:42,
from ColSpec.h:5,
from XlsWorkSheet.cpp:2:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_gid_t.h:31:24: note: 'xls::gid_t'
typedef __darwin_gid_t gid_t;
^~~~~
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:6,
from Spinner.h:4,
from XlsWorkSheet.h:7,
from XlsWorkSheet.cpp:3:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:596:27: error: expression list treated as compound expression in initializer [-fpermissive]
int setregid(gid_t, gid_t) __DARWIN_ALIAS(setregid);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:603:1: error: 'useconds_t' does not name a type; did you mean 'user_off_t'?
useconds_t ualarm(useconds_t, useconds_t);
^~~~~~~~~~
user_off_t
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:604:13: error: 'useconds_t' was not declared in this scope
int usleep(useconds_t) __DARWIN_ALIAS_C(usleep);
^~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:604:13: note: suggested alternative:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/types.h:167,
from ./libxls/xlstypes.h:40,
from ./libxls/xls.h:42,
from ColSpec.h:5,
from XlsWorkSheet.cpp:2:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_useconds_t.h:31:29: note: 'xls::useconds_t'
typedef __darwin_useconds_t useconds_t;
^~~~~~~~~~
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:6,
from Spinner.h:4,
from XlsWorkSheet.h:7,
from XlsWorkSheet.cpp:3:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:624:25: error: 'gid_t' has not been declared
int fchown(int, uid_t, gid_t);
^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:627:14: error: 'gid_t' was not declared in this scope
int setegid(gid_t);
^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:627:14: note: suggested alternative:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/types.h:109,
from ./libxls/xlstypes.h:40,
from ./libxls/xls.h:42,
from ColSpec.h:5,
from XlsWorkSheet.cpp:2:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_gid_t.h:31:24: note: 'xls::gid_t'
typedef __darwin_gid_t gid_t;
^~~~~
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:638,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:6,
from Spinner.h:4,
from XlsWorkSheet.h:7,
from XlsWorkSheet.cpp:3:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/select.h:114:19: error: 'fd_set' has not been declared
int pselect(int, fd_set * __restrict, fd_set * __restrict,
^~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/select.h:114:40: error: 'fd_set' has not been declared
int pselect(int, fd_set * __restrict, fd_set * __restrict,
^~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/select.h:115:3: error: 'fd_set' has not been declared
fd_set * __restrict, const struct timespec * __restrict,
^~~~~~
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/select.h:129,
from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:638,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:6,
from Spinner.h:4,
from XlsWorkSheet.h:7,
from XlsWorkSheet.cpp:3:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_select.h:39:18: error: 'fd_set' has not been declared
int select(int, fd_set * __restrict, fd_set * __restrict,
^~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_select.h:39:39: error: 'fd_set' has not been declared
int select(int, fd_set * __restrict, fd_set * __restrict,
^~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_select.h:40:3: error: 'fd_set' has not been declared
fd_set * __restrict, struct timeval * __restrict)
^~~~~~
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:6,
from Spinner.h:4,
from XlsWorkSheet.h:7,
from XlsWorkSheet.cpp:3:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:664:31: error: 'gid_t' has not been declared
int getpeereid(int, uid_t *, gid_t *);
^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:702:32: error: 'gid_t' has not been declared
int pthread_setugid_np(uid_t, gid_t);
^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:703:35: error: 'gid_t' has not been declared
int pthread_getugid_np( uid_t *, gid_t *);
^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:718:27: error: 'gid_t' does not name a type; did you mean 'uid_t'?
int setgroups(int, const gid_t *);
^~~~~
uid_t
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:728:14: error: 'gid_t' was not declared in this scope
int setrgid(gid_t);
^~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:728:14: note: suggested alternative:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/types.h:109,
from ./libxls/xlstypes.h:40,
from ./libxls/xls.h:42,
from ColSpec.h:5,
from XlsWorkSheet.cpp:2:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_gid_t.h:31:24: note: 'xls::gid_t'
typedef __darwin_gid_t gid_t;
^~~~~
In file included from Spinner.h:4,
from XlsWorkSheet.h:7,
from XlsWorkSheet.cpp:3:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h: In member function 'void RProgress::RProgress::render()':
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:176:45: warning: conversion from 'long int' to 'double' may change value [-Wconversion]
double complete_len = round(bar_width * ratio_now);
^~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h: In static member function 'static double RProgress::RProgress::time_now()':
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:313:16: warning: conversion from '__darwin_time_t' {aka 'long int'} to 'double' may change value [-Wconversion]
return now.tv_sec + now.tv_usec / 1000000.0;
~~~~^~~~~~
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h: In static member function 'static std::__cxx11::string RProgress::RProgress::pretty_bytes(long int)':
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:365:16: warning: conversion from 'long int' to 'double' may change value [-Wconversion]
if (idx >= num_units) { idx = num_units - 1; }
^~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:365:45: warning: conversion from 'long int' to 'double' may change value [-Wconversion]
if (idx >= num_units) { idx = num_units - 1; }
~~~~~~~~~~^~~
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include/RProgress.h:367:52: warning: conversion from 'long int' to 'double' may change value [-Wconversion]
double res = round(bytes / std::pow(1000.0, idx) * 100.0) / 100.0;
^
In file included from XlsWorkSheet.cpp:3:
XlsWorkSheet.h: In member function 'Rcpp::List XlsWorkSheet::readCols(Rcpp::CharacterVector, const std::vector<ColType>&, const StringSet&, bool, bool)':
XlsWorkSheet.h:197:38: warning: choosing 'Rcpp::internal::generic_proxy<RTYPE, StoragePolicy>::operator U() const [with U = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' over 'Rcpp::RObject_Impl<StoragePolicy>::RObject_Impl(const Rcpp::GenericProxy<Proxy>&) [with Proxy = Rcpp::internal::generic_proxy<19>; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion]
Rcpp::RObject column = cols[col];
^
XlsWorkSheet.h:197:38: warning: for conversion from 'Rcpp::Vector<19>::Proxy' {aka 'Rcpp::internal::generic_proxy<19>'} to 'Rcpp::RObject' {aka 'Rcpp::RObject_Impl<Rcpp::PreserveStorage>'} [-Wconversion]
XlsWorkSheet.h:197:38: note: because conversion sequence for the argument is better
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/Vector.h:52,
from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:40,
from XlsWorkSheet.cpp:1:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h: In instantiation of 'Rcpp::Vector<RTYPE, StoragePolicy>::const_iterator Rcpp::Vector<RTYPE, StoragePolicy>::end() const [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage; Rcpp::Vector<RTYPE, StoragePolicy>::const_iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::const_string_proxy<16> >]':
StringSet.h:20:74: required from here
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:335:65: warning: conversion from 'R_xlen_t' {aka 'long int'} to 'Rcpp::internal::Proxy_Iterator<Rcpp::internal::const_string_proxy<16> >::difference_type' {aka 'int'} may change value [-Wconversion]
inline const_iterator end() const{ return cache.get_const() + size() ; }
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h: In instantiation of 'Rcpp::Vector<RTYPE, StoragePolicy>::iterator Rcpp::Vector<RTYPE, StoragePolicy>::end() [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage; Rcpp::Vector<RTYPE, StoragePolicy>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::string_proxy<16> >]':
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:1115:18: required from 'void Rcpp::Vector<RTYPE, StoragePolicy>::fill__dispatch(Rcpp::traits::true_type, const U&) [with U = SEXPREC*; int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage; Rcpp::traits::true_type = Rcpp::traits::integral_constant<bool, true>]'
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:329:9: required from 'void Rcpp::Vector<RTYPE, StoragePolicy>::fill(const U&) [with U = SEXPREC*; int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]'
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:97:9: required from 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&, const stored_type&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage; Rcpp::Vector<RTYPE, StoragePolicy>::stored_type = SEXPREC*]'
ColSpec.h:247:46: required from here
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:333:48: warning: conversion from 'R_xlen_t' {aka 'long int'} to 'Rcpp::internal::Proxy_Iterator<Rcpp::internal::string_proxy<16> >::difference_type' {aka 'int'} may change value [-Wconversion]
inline iterator end() { return cache.get() + size() ; }
make: *** [XlsWorkSheet.o] Error 1
ERROR: compilation failed for package ‘readxl’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/readxl’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/readxl’
Error in i.p(...) :
(converted from warning) installation of package ‘/var/folders/jn/zp890ymn4vn6wb76rf0hpz7c0000gn/T//Rtmpzgy9Z0/filef1133bb11b73/readxl_1.3.1.9000.tar.gz’ had non-zero exit status
Please guide on how to fix this. I have installed the latest version of Rcpp from github.
jennybc commented
I can build it successfully right now on macOS. FWIW I am using clang++ from Xcode command line tools.
Can you build the current CRAN version from source? With Rcpp from CRAN? That would be a good test to see if there is some problem with your dev setup. Are you successfully building other R packages w/ both C and C++ in them from source?
ramay commented
Thanks @jennybc for you reply. My problem was in .R/Makevars files where the right compilers were not being used. I updated it to
F77 = /usr/local/bin/gfortran
FC = $F77
CXX = /usr/local/opt/llvm/bin/clang++ -Wall
LDFLAGS=-L/usr/local/opt/llvm/lib/clang/7.0.1/lib/
CC= /usr/local/opt/llvm/bin/clang
SHLIB_CXXLD=/usr/local/opt/llvm/bin/clang++
CXX11 = /usr/local/opt/llvm/bin/clang++
CXX98 = /usr/local/opt/llvm/bin/clang++
CXX14 = /usr/local/opt/llvm/bin/clang++
Also for Mojave, I had to install header files. RcppCore/Rcpp#922
The package has been installed now!