compilation error

[nvpatin]

Hi,

I'm trying to install wk on a Linux HPC system and am running into a compilation error. I have tried specifying different C compilers with no luck. I tried using both install.packages("wk") and remotes::install_github("paleolimbot/wk") and both produce the same error. It seems to be specific to the 'orient-filter' function but I suspect it has to do with the C compiler; can you tell me which compiler should be used and any edits to the .R/Makevars file that might help? The full output of the installation command is below.

Thanks,
Nastassia

remotes::install_github("paleolimbot/wk")
Downloading GitHub repo paleolimbot/wk@HEAD
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/RtmpWRYXtu/remotesbfca58d27712/paleolimbot-wk-279dffa/DESCRIPTION’ ...
─ preparing ‘wk’:
✔ 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
Removed empty directory ‘wk/vignettes’
─ building ‘wk_0.8.0.9000.tar.gz’

Installing package into ‘/home/nvp29/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)

• installing source package ‘wk’ ...
  ** using staged installation
  ** libs
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c bbox-handler.c -o bbox-handler.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c count-handler.c -o count-handler.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c debug-filter.c -o debug-filter.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c flatten-filter.c -o flatten-filter.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c handle-crc.c -o handle-crc.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c handle-rct.c -o handle-rct.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c handle-sfc.c -o handle-sfc.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c handle-wkb.c -o handle-wkb.o
  g++ -std=gnu++11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c handle-wkt.cpp -o handle-wkt.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c handle-xy.c -o handle-xy.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c identity-filter.c -o identity-filter.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c make-collection-filter.c -o make-collection-filter.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c make-linestring-filter.c -o make-linestring-filter.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c make-polygon-filter.c -o make-polygon-filter.o
  gcc -std=c11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c meta-handler.c -o meta-handler.o
  g++ -std=gnu++11 -I"/apps/R-4.2.0/lib64/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c orient-filter.cpp -o orient-filter.o
  orient-filter.cpp: In member function ‘virtual int OrientFilter::coord(const wk_meta_t, const double, uint32_t)’:
  orient-filter.cpp:58:54: error: no matching function for call to ‘std::vector::insert(std::vector::const_iterator, const double*&, const double*)’
  coords.insert(coords.cend(), coord, coord + n_dim);**
  ^
  orient-filter.cpp:58:54: note: candidates are:
  In file included from /usr/include/c++/4.8.2/vector:69:0,
  from orient-filter.cpp:1:
  /usr/include/c++/4.8.2/bits/vector.tcc:107:5: note: std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::iterator, const value_type&) [with _Tp = double; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::iterator = __gnu_cxx::__normal_iterator<double*, std::vector >; typename std::_Vector_base<_Tp, _Alloc>::pointer = double*; std::vector<_Tp, _Alloc>::value_type = double]
  vector<_Tp, _Alloc>::
  ^
  /usr/include/c++/4.8.2/bits/vector.tcc:107:5: note: candidate expects 2 arguments, 3 provided
  In file included from /usr/include/c++/4.8.2/vector:64:0,
  from orient-filter.cpp:1:
  /usr/include/c++/4.8.2/bits/stl_vector.h:988:7: note: std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = double; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::iterator = __gnu_cxx::__normal_iterator<double*, std::vector >; typename std::_Vector_base<_Tp, _Alloc>::pointer = double*; std::vector<_Tp, _Alloc>::value_type = double]
  insert(iterator __position, value_type&& __x)
  ^
  /usr/include/c++/4.8.2/bits/stl_vector.h:988:7: note: candidate expects 2 arguments, 3 provided
  /usr/include/c++/4.8.2/bits/stl_vector.h:1005:7: note: void std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::iterator, std::initializer_list<_Tp>) [with _Tp = double; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::iterator = __gnu_cxx::__normal_iterator<double*, std::vector >; typename std::_Vector_base<_Tp, _Alloc>::pointer = double*]
  insert(iterator __position, initializer_list<value_type> __l)
  ^
  /usr/include/c++/4.8.2/bits/stl_vector.h:1005:7: note: candidate expects 2 arguments, 3 provided
  /usr/include/c++/4.8.2/bits/stl_vector.h:1023:7: note: void std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::iterator = __gnu_cxx::__normal_iterator<double*, std::vector >; typename std::_Vector_base<_Tp, _Alloc>::pointer = double*; std::vector<_Tp, _Alloc>::size_type = long unsigned int; std::vector<_Tp, _Alloc>::value_type = double]
  insert(iterator __position, size_type __n, const value_type& __x)
  ^
  /usr/include/c++/4.8.2/bits/stl_vector.h:1023:7: note: no known conversion for argument 1 from ‘std::vector::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector >}’ to ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector >}’
  /usr/include/c++/4.8.2/bits/stl_vector.h:1044:9: note: template<class _InputIterator, class> void std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::iterator, _InputIterator, _InputIterator) [with _InputIterator = _InputIterator; = ; _Tp = double; _Alloc = std::allocator]
  insert(iterator __position, _InputIterator __first,
  ^
  /usr/include/c++/4.8.2/bits/stl_vector.h:1044:9: note: template argument deduction/substitution failed:
  orient-filter.cpp:58:54: note: cannot convert ‘((OrientFilter*)this)->OrientFilter::coords.std::vector<_Tp, _Alloc>::cend<double, std::allocator >()’ (type ‘std::vector::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector >}’) to type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector >}’
  coords.insert(coords.cend(), coord, coord + n_dim);
  ^
  make: *** [orient-filter.o] Error 1
  ERROR: compilation failed for package ‘wk’
• removing ‘/home/nvp29/R/x86_64-pc-linux-gnu-library/4.2/wk’
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/RtmpWRYXtu/filebfca3a2550f4/wk_0.8.0.9000.tar.gz’ had non-zero exit status

[paleolimbot]

Thanks for opening! It looks like we didn't test properly on gcc4.8 before releasing the last version. As a workaround, you should be able to install a previous version using remotes::install_github("cran/wk@0.7.2") until we fix + release the next version.

[nvpatin]

Thanks so much for the quick response! That worked, glad it was an easy fix.

[anthonynorth]

Appears that std::vector<>.cend isn't defined for gcc 4.8

'class std::vector' has no member named 'cend'

Problem here

wk/src/orient-filter.cpp

Line 58 in 279dffa

coords.insert(coords.cend(), coord, coord + n_dim);

Looks like it could a 1-liner to fix? https://godbolt.org/z/eeq3MfbY1

Edit: context

[paleolimbot]

Thanks for tracking that down! I'll put up a PR shortly + add R 3.6/Windows back on CI (which uses gcc 4.8).