gcc 4.8.5 compatibility #69

VincentGardeux · 2020-08-03T09:53:16Z

Hi,

I'm trying to install another package (tidyr) on CentOS7 which is apparently trying to use cpp11 library.
It throws multiple errors:

g++ -std=gnu++11 -I"/software/R-3.6.2/include" -DNDEBUG  -I"/data/software/R-3.6.2/library/cpp11/include" -I/usr/include -I/software/CLAPACK-3.2.1/INCLUDE -I/software/gsl-2.6/include -I/software/proj-6.0.0/include/proj -I/software/hdf5-1.10.4/include/  -fpic  -g -O2  -c cpp11.cpp -o cpp11.o
In file included from /data/software/R-3.6.2/library/cpp11/include/cpp11/as.hpp:8:0,
                 from /data/software/R-3.6.2/library/cpp11/include/cpp11.hpp:5,
                 from /data/software/R-3.6.2/library/cpp11/include/cpp11/declarations.hpp:8,
                 from cpp11.cpp:4:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In lambda function:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: parameter packs not expanded with ‘...’:
       return unwind_protect([&] { return ptr_(a...); });
                                               ^
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: note:         ‘a’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:48: error: expansion pattern ‘a’ contains no argument packs
       return unwind_protect([&] { return ptr_(a...); });
                                                ^
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In lambda function:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:199:38: error: parameter packs not expanded with ‘...’:
   unwind_protect([&] { Rf_error(fmt, args...); });
                                      ^
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:199:38: note:         ‘args’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:199:42: error: expansion pattern ‘args’ contains no argument packs
   unwind_protect([&] { Rf_error(fmt, args...); });
                                          ^
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In lambda function:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:206:46: error: parameter packs not expanded with ‘...’:
   unwind_protect([&] { Rf_error(fmt.c_str(), args...); });
                                              ^
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:206:46: note:         ‘args’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:206:50: error: expansion pattern ‘args’ contains no argument packs
   unwind_protect([&] { Rf_error(fmt.c_str(), args...); });
                                                  ^
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::protect::function<F>::operator()(A ...) const [with A = {}; F = void(); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = void]::__lambda2’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55:   required from ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {}; F = void(); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = void]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:195:65:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: using invalid field ‘cpp11::protect::function<F>::operator()(A ...) const::__lambda2::__a’
       return unwind_protect([&] { return ptr_(a...); });
                                               ^
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {}; F = void(); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = void]’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:195:65:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55: error: return-statement with a value, in function returning 'void' [-fpermissive]
       return unwind_protect([&] { return ptr_(a...); });
                                                       ^
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::protect::function<F>::operator()(A ...) const [with A = {const char*, cetype_t}; F = SEXPREC*(const char*, cetype_t); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]::__lambda2’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55:   required from ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {const char*, cetype_t}; F = SEXPREC*(const char*, cetype_t); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/r_string.hpp:16:69:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: using invalid field ‘cpp11::protect::function<F>::operator()(A ...) const::__lambda2::__a’
       return unwind_protect([&] { return ptr_(a...); });
                                               ^
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::protect::function<F>::operator()(A ...) const [with A = {int, long unsigned int}; F = SEXPREC*(unsigned int, long int); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]::__lambda2’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55:   required from ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {int, long unsigned int}; F = SEXPREC*(unsigned int, long int); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/list.hpp:75:67:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: using invalid field ‘cpp11::protect::function<F>::operator()(A ...) const::__lambda2::__a’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::protect::function<F>::operator()(A ...) const [with A = {int, long int}; F = SEXPREC*(unsigned int, long int); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]::__lambda2’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55:   required from ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {int, long int}; F = SEXPREC*(unsigned int, long int); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/list.hpp:107:74:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: using invalid field ‘cpp11::protect::function<F>::operator()(A ...) const::__lambda2::__a’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::protect::function<F>::operator()(A ...) const [with A = {SEXPREC*, long int}; F = SEXPREC*(SEXPREC*, long int); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]::__lambda2’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55:   required from ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {SEXPREC*, long int}; F = SEXPREC*(SEXPREC*, long int); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/list.hpp:108:73:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: using invalid field ‘cpp11::protect::function<F>::operator()(A ...) const::__lambda2::__a’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::protect::function<F>::operator()(A ...) const [with A = {const char*}; F = SEXPREC*(const char*); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]::__lambda2’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55:   required from ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {const char*}; F = SEXPREC*(const char*); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/function.hpp:59:50:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: using invalid field ‘cpp11::protect::function<F>::operator()(A ...) const::__lambda2::__a’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::protect::function<F>::operator()(A ...) const [with A = {SEXPREC*, SEXPREC*}; F = SEXPREC*(SEXPREC*, SEXPREC*); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]::__lambda2’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55:   required from ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {SEXPREC*, SEXPREC*}; F = SEXPREC*(SEXPREC*, SEXPREC*); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/function.hpp:59:58:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: using invalid field ‘cpp11::protect::function<F>::operator()(A ...) const::__lambda2::__a’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::protect::function<F>::operator()(A ...) const [with A = {SEXPREC*, cpp11::sexp}; F = SEXPREC*(SEXPREC*, SEXPREC*); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]::__lambda2’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55:   required from ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {SEXPREC*, cpp11::sexp}; F = SEXPREC*(SEXPREC*, SEXPREC*); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/function.hpp:69:66:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: using invalid field ‘cpp11::protect::function<F>::operator()(A ...) const::__lambda2::__a’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::protect::function<F>::operator()(A ...) const [with A = {SEXPREC*, SEXPREC*, Rboolean}; F = SEXPREC*(SEXPREC*, SEXPREC*, Rboolean); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]::__lambda2’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55:   required from ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {SEXPREC*, SEXPREC*, Rboolean}; F = SEXPREC*(SEXPREC*, SEXPREC*, Rboolean); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/environment.hpp:36:81:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: using invalid field ‘cpp11::protect::function<F>::operator()(A ...) const::__lambda2::__a’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::protect::function<F>::operator()(A ...) const [with A = {cpp11::sexp, SEXPREC*, Rboolean}; F = SEXPREC*(SEXPREC*, SEXPREC*, Rboolean); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]::__lambda2’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55:   required from ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {cpp11::sexp, SEXPREC*, Rboolean}; F = SEXPREC*(SEXPREC*, SEXPREC*, Rboolean); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/environment.hpp:47:58:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: using invalid field ‘cpp11::protect::function<F>::operator()(A ...) const::__lambda2::__a’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::protect::function<F>::operator()(A ...) const [with A = {int, int}; F = SEXPREC*(unsigned int, long int); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]::__lambda2’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55:   required from ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {int, int}; F = SEXPREC*(unsigned int, long int); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/strings.hpp:71:70:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: using invalid field ‘cpp11::protect::function<F>::operator()(A ...) const::__lambda2::__a’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::protect::function<F>::operator()(A ...) const [with A = {SEXPREC*}; F = SEXPREC*(SEXPREC*); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]::__lambda2’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55:   required from ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {SEXPREC*}; F = SEXPREC*(SEXPREC*); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/strings.hpp:73:45:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: using invalid field ‘cpp11::protect::function<F>::operator()(A ...) const::__lambda2::__a’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::protect::function<F>::operator()(A ...) const [with A = {cpp11::sexp, SEXPREC*}; F = SEXPREC*(SEXPREC*, SEXPREC*); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]::__lambda2’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:55:   required from ‘decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) cpp11::protect::function<F>::operator()(A ...) const [with A = {cpp11::sexp, SEXPREC*}; F = SEXPREC*(SEXPREC*, SEXPREC*); decltype (declval<F*>()(cpp11::protect::function::operator()::a ...)) = SEXPREC*]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/function.hpp:27:43:   required from ‘cpp11::sexp cpp11::function::operator()(Args&& ...) const [with Args = {SEXPREC*&, cpp11::named_arg&}]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/environment.hpp:60:35:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:183:47: error: using invalid field ‘cpp11::protect::function<F>::operator()(A ...) const::__lambda2::__a’
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp: In instantiation of ‘struct cpp11::stop(const char*, Args ...) [with Args = {}]::__lambda3’:
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:199:49:   required from ‘void cpp11::stop(const char*, Args ...) [with Args = {}]’
/data/software/R-3.6.2/library/cpp11/include/cpp11/as.hpp:98:39:   required from ‘cpp11::is_logical<T> cpp11::as_cpp(SEXP) [with T = bool; cpp11::is_logical<T> = bool; SEXP = SEXPREC*]’
cpp11.cpp:24:452:   required from here
/data/software/R-3.6.2/library/cpp11/include/cpp11/protect.hpp:199:38: error: using invalid field ‘cpp11::stop(const char*, Args ...)::__lambda3::__args’
   unwind_protect([&] { Rf_error(fmt, args...); });
                                      ^
make: *** [cpp11.o] Error 1
ERROR: compilation failed for package ‘tidyr’

Apparently the compilation errors are coming from several hpp files.
If you have any idea of a simple flag to add to make it work? Or if I need to recompile the cpp11 library with specific flags.

Thanks in advance

The text was updated successfully, but these errors were encountered:

yousefi138 · 2020-08-03T10:28:13Z

I'm having the same issue. Also on CentOS. Also trying to install tidyr.

Suggestions would be appreciated.

jimhester · 2020-08-03T11:08:44Z

cpp11 requires a compiler with full support for C++11.

What version of CentOS are you using, and what version of GNU compiler? e.g. what is the value of g++ --version

VincentGardeux · 2020-08-03T11:24:28Z

Hello @jimhester

As I said, I'm with CentOS 7

Here is the version of the C++ compiler:

$ g++ --version
g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)

yousefi138 · 2020-08-03T11:28:15Z

I'm on:
CentOS Linux release 7.7.1908

On the exact same version of C++ as @VincentGardeux

jimhester · 2020-08-03T11:55:18Z

I think this is possibly due to a bug with parameter packs in variadic templates in older gcc versions like 4.8.5 (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=47226)

I reproduced the issue in a centos 7 docker container using gcc 4.8.5. I was then able to compile tidyr successfully after installing a newer gcc version from the devtoolset-7 software collection, following the instructions at https://linuxize.com/post/how-to-install-gcc-compiler-on-centos-7/#installing-multiple-gcc-versions

VincentGardeux · 2020-08-03T12:17:53Z

Very good catch @jimhester it works for me.
It also solves the installation of other packages.

Thanks!

jimhester · 2020-08-03T12:56:07Z

Easy way to reproduce this is the following docker file.

FROM rstudio/r-base:4.0-centos7

RUN R -e 'install.packages("tidyr", repos = c(CRAN = "https://cloud.r-project.org"))'

stefanoborini · 2020-08-06T14:47:05Z

When is a new release going to be available for this fix?

VincentGardeux mentioned this issue Aug 3, 2020

Error trying to install the package on CentOS 7 philchalmers/mirt#191

Closed

hadley mentioned this issue Aug 3, 2020

tidyr 1.1.1 cannot be installed on centOS 7 tidyverse/tidyr#1016

Closed

jimhester changed the title ~~Bug when compiling another package with cpp11~~ gcc 4.8.5 compatibility Aug 3, 2020

bkietz mentioned this issue Aug 4, 2020

capture parameter pack as a tuple to work around gcc4.8 #71

Merged

hadley mentioned this issue Aug 5, 2020

Compilation on RHEL/CentOS 7 fails tidyverse/tidyr#1019

Closed

jimhester closed this as completed in #71 Aug 5, 2020

harrismcgehee mentioned this issue Aug 19, 2020

nanodbc.cpp compile issue with codecvt header file r-dbi/odbc#377

Closed

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gcc 4.8.5 compatibility #69

gcc 4.8.5 compatibility #69

VincentGardeux commented Aug 3, 2020

yousefi138 commented Aug 3, 2020

jimhester commented Aug 3, 2020

VincentGardeux commented Aug 3, 2020

yousefi138 commented Aug 3, 2020

jimhester commented Aug 3, 2020

VincentGardeux commented Aug 3, 2020

jimhester commented Aug 3, 2020

stefanoborini commented Aug 6, 2020

gcc 4.8.5 compatibility #69

gcc 4.8.5 compatibility #69

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VincentGardeux commented Aug 3, 2020

yousefi138 commented Aug 3, 2020

jimhester commented Aug 3, 2020

VincentGardeux commented Aug 3, 2020

yousefi138 commented Aug 3, 2020

jimhester commented Aug 3, 2020

VincentGardeux commented Aug 3, 2020

jimhester commented Aug 3, 2020

stefanoborini commented Aug 6, 2020