"--coverage" flag does not seem to be working

[aadler]

When I try to use covr for my package, I get errors indicating that the needed compile and linker flags are not being passed:

Warning: unknown option '--with-keep.parse.data'
* installing *source* package 'Delaporte' ...
** libs
c:/Rtools/mingw_64/bin/gfortran  -fopenmp   -O3  -march=native -pipe -O0 --coverage -c  utils.f95 -o utils.o
c:/Rtools/mingw_64/bin/gfortran  -fopenmp   -O3  -march=native -pipe -O0 --coverage -c  lgamma.f95 -o lgamma.o
c:/Rtools/mingw_64/bin/gfortran  -fopenmp   -O3  -march=native -pipe -O0 --coverage -c  delaporte.f95 -o delaporte.o
c:/Rtools/mingw_64/bin/gcc  -I"C:/R/RCurrent/R-35~1.0PA/include" -DNDEBUG   -march=native -pipe  -I"C:/R/extsoft/include"     -O3 -Wall  -std=gnu99 -march=native -pipe -O0 --coverage -c utils_and_wrappers.c -o utils_and_wrappers.o
c:/Rtools/mingw_64/bin/gfortran -shared -s -static-libgcc -o Delaporte.dll tmp.def delaporte.o lgamma.o utils.o utils_and_wrappers.o -LC:/R/RCurrent/R-35~1.0PA/bin/x64 -lRlapack -LC:/R/RCurrent/R-35~1.0PA/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/R/extsoft/lib/x64 -LC:/R/extsoft/lib -LC:/R/RCurrent/R-35~1.0PA/bin/x64 -lR
delaporte.o:delaporte.f95:(.text+0x2cb8): undefined reference to `__gcov_init'
delaporte.o:delaporte.f95:(.data+0x60): undefined reference to `__gcov_merge_add'
lgamma.o:lgamma.f95:(.text+0x66b): undefined reference to `__gcov_init'
lgamma.o:lgamma.f95:(.data+0x60): undefined reference to `__gcov_merge_add'
utils.o:utils.f95:(.text+0x200): undefined reference to `__gcov_init'
utils.o:utils.f95:(.data+0x60): undefined reference to `__gcov_merge_add'
utils_and_wrappers.o:utils_and_wrappers.c:(.text+0xc84): undefined reference to `__gcov_init'
utils_and_wrappers.o:utils_and_wrappers.c:(.data+0x60): undefined reference to `__gcov_merge_add'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'Delaporte'
* removing 'D:/Rtemp/Rtmp8AkZTR/R_LIBS39c86e094a60/Delaporte'
In R CMD INSTALL
Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: In utils::install.packages(repos = NULL, lib = tmp_lib, pkg$path,  :
  installation of package ‘D:/Users/Parents/Documents/Avi/GitRepos/delaporte’ had non-zero exit status
2: In file(con, "r") :
  cannot open file 'D:/Rtemp/Rtmp8AkZTR/R_LIBS39c86e094a60/Delaporte/R/Delaporte': No such file or directory

However, when I manually put the proper flags in Makevars, it does work. Shouldn't --coverage alone be sufficient?

> package_coverage(quiet = FALSE, tests = "none", code = 'testthat::test_file("./tests/testthat/test-delap.r")', function_exclusions = "\\.onUnload*")
Warning: unknown option '--with-keep.parse.data'
* installing *source* package 'Delaporte' ...
** libs
c:/Rtools/mingw_64/bin/gfortran  -fopenmp -ftest-coverage -fprofile-arcs  -O3  -march=native -pipe -O0 --coverage -c  utils.f95 -o utils.o
c:/Rtools/mingw_64/bin/gfortran  -fopenmp -ftest-coverage -fprofile-arcs  -O3  -march=native -pipe -O0 --coverage -c  lgamma.f95 -o lgamma.o
c:/Rtools/mingw_64/bin/gfortran  -fopenmp -ftest-coverage -fprofile-arcs  -O3  -march=native -pipe -O0 --coverage -c  delaporte.f95 -o delaporte.o
c:/Rtools/mingw_64/bin/gcc  -I"C:/R/RCurrent/R-35~1.0PA/include" -DNDEBUG   -march=native -pipe  -I"C:/R/extsoft/include"     -O3 -Wall  -std=gnu99 -march=native -pipe -O0 --coverage -c utils_and_wrappers.c -o utils_and_wrappers.o
c:/Rtools/mingw_64/bin/gfortran -shared -s -static-libgcc -o Delaporte.dll tmp.def delaporte.o lgamma.o utils.o utils_and_wrappers.o -LC:/R/RCurrent/R-35~1.0PA/bin/x64 -lRlapack -LC:/R/RCurrent/R-35~1.0PA/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -fprofile-arcs -LC:/R/extsoft/lib/x64 -LC:/R/extsoft/lib -LC:/R/RCurrent/R-35~1.0PA/bin/x64 -lR
installing to D:/Rtemp/Rtmp6561Jg/R_LIBS44b84063750c/Delaporte/libs/x64
** R
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Delaporte'
    finding HTML links ... done
    Delaporte-defunct                       html  
    Delaporte-internal                      html  
    Delaporte-package                       html  
    Delaporte                               html  example
** building package indices
** testing if installed package can be loaded
* DONE (Delaporte)
In R CMD INSTALL
Running specific tests for package ‘Delaporte’
  Running ‘test-all.R’
Delaporte Coverage: 77.78%
R/Delaporte.R: 77.78%

[jimhester]

This is compiler dependant, perhaps the gfortran version you are using needs them explicitly set...

[aadler]

I guess that's a question for @jeroen then, as he builds Rtools for windows :)

[cjvanlissa]

This issue has been closed, but has it been resolved? I get the same issue in all of my packages with Fortran code.

[aadler]

No, I don't think so.

[jimhester]

Feel free to open a PR with the settings you need for fortran code, and please ensure it works across the major compilers, clang + gcc and the RTools toolchain on windows.

[cjvanlissa]

I'd love to, but I don't understand how to!

[jimhester]

Change

covr/R/zzz.R

Lines 18 to 19 in 26066d3

	FFLAGS = "-O0 --coverage",
	FCFLAGS = "-O0 --coverage",

to what it needs to be.