Rcpp/fortran support?

[hadley]

Is there any chance you might be able to combine covr with an existing C++ code coverage tool in order to also give C++ code coverage stats?

[jimhester]

Yeah that is something I want to add, I had a few links in #4 about it. Should be able to use https://gcc.gnu.org/onlinedocs/gcc/Gcov.html with a little work.

[jimhester]

I believe the same flags -fprofile-arcs -ftest-coverage should also work with for fortran code as well.

[hadley]

Looks like it's built into llvm: http://www.llvm.org/docs/CoverageMappingFormat.html

[jimhester]

@hadley what is the preferred way to pass compiler flags to devtools::load_all()? I tried adding

  old <- devtools:::set_envvar(c(CFLAGS = "-fprofile-arcs -ftest-coverage", CXXFLAGS = "-fprofile-arcs -ftest-coverage", FFLAGS = "-fprofile-arcs -ftest-coverage"), "prefix")
  on.exit(devtools:::set_envvar(old), add = TRUE)

before covr.R#L181 which does set CFLAGS, CXXFLAGS, and FFLAGS environment variables, but those values don't seem to be used when compiling. (The flags from devtools::compiler_flags() also seem to be ignored). I tried compiling dplyr and devtools, in both cases the environment variables don't seem to be used.

Am I doing something obviously wrong, or is there an alternative method we need to use to force the profiling flags?

[jimhester]

the answer to the above is you need to use PKG_CFLAGS PKG_CXXFLAGS etc. I think this is also a bug in devtools::compiler_flags() as well.

[hadley]

Do you have latest devtools? There was a problem previously - I'm pretty use CFLAGS etc is the right choice because it's for user overrides on the compilation of all packages .PKG_CFLAGS etc is for options for a specific package.

[jimhester]

devtools * 1.6.1.9000 2014-12-30 Github (hadley/devtools@6192843)

It may be that the packages I have tested against all define PKG_CFLAGS variables in Makevars so they are overriding the values in CFLAGS. In which case devtools is probably ok.

[jimhester]

preliminary support is now on master via 572d3da.

Outstanding issues

• complier optimization needs to be at -O0 as lines can get optimized out completely which makes the output impossible to interpret.
• source files which are not run at all by tests will not get counted as uncovered.
• need to verify gcov is available on windows.

[jimhester]

So the only real issue I am running into here is forcing R to use -O0 when compiling. From @eddelbuettel's answer at http://stackoverflow.com/a/23414789/2055486 it seems like the only way to override the default CFLAGS is by adding values to ~/.R/Makevars. Doing that temporarily seems hacky, but I don't really see another way to go unless there is another way to override the values. Setting the CFLAGS environment variable has no effect.

[eddelbuettel]

From memory, I may have seen something lately in R NEWS changes (which I read daily via RSS) that they allow overriding now. Hitherto $RHOME/etc/Makeconf always won making this an issue. Not really sure if it changed, but may be worth checking with R-devel.

[jimhester]

Ok I will look around some more and see if I can find anything, thanks Dirk!

On Thu, Jan 8, 2015 at 2:52 PM, Dirk Eddelbuettel notifications@github.com
wrote:

From memory, I may have seen something lately in R NEWS changes
http://developer.r-project.org/blosxom.cgi/R-devel (which I read daily
via RSS) that they allow overriding now. Hitherto $RHOME/etc/Makeconf
always won making this an issue. Not really sure if it changed, but may be
worth checking with R-devel.

—
Reply to this email directly or view it on GitHub
#9 (comment).

[jimhester]

As of 18d9210 this is now working locally by using a subprocess R session, but failing when trying to use R CMD check or on travis, possibly because of issues mentioned in r-lib/testthat#144. I added `R_TEST="" and NOT_CRAN="true" and it got further, but there is still an issue of some kind. Will keep trying though!

[jimhester]

Ok now seems to be working on everything but covr itself. Here is an example of the digest package.

https://coveralls.io/builds/1749592

[helske]

I see that this works for C/C++, but for some reason coveralls does not check the Fortran code in my package: https://coveralls.io/r/helske/KFAS

I am new to both Travis and Coveralls so it might be just me. Any hints?

[helske]

Tested this also locally on Linux, I compiled with -O0 and changed package Makevars to
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -fprofile-arcs
PKG_FCFLAGS = -fprofile-arcs -ftest-coverage

This seems to make the necessary gcov files but package_coverage still does not report any info about .f95 files.

[jimhester]

@helske this is because the function used to detect source files does not find extension .f95 like you used in your project. https://github.com/jimhester/covr/blob/master/R/compiled.R#L81-L82. It needs to be updated to handle all of the common FORTRAN extensions, http://fortranwiki.org/fortran/show/File+extensions seems like a decent list.

Right now the only FORTRAN extension that is found is .f

[helske]

Thanks, should have figured that out by debugging the code a bit. I updated the compiled function (and package_coverage) accordingly and created a pull request: #64