Quick guess. After changing > SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -pthread -O3 -Wextra -Wall > -Wno-unknown-pragmas -Wno-return-type -Wno-ignored-attributes > -Wno-cast-function-type -Wno-error=cast-function-type")
to > SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -pthread -O3 -Wextra > -Wall") I managed to `R CMD INSTALL` the package with gcc-8 on Ubuntu. Then doing `cd ~/R/x86_64-pc-linux-gnu-library/3.6/gpboost/libs/` and - nm *.so -C | grep exit - nm *.so -C | grep abort - nm *.so -C | grep printf yields nothing. However, doing `nm *.so -C | grep assert` yields U __assert_fail@@GLIBC_2.2.5 and doing `grep "assert" -nr .` shows that `assert` is being called. Thus, is everything build with `-NDEBUG`? See https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#DOCF76 Den fre. 17. jul. 2020 kl. 14.52 skrev Spencer Graves <spencer.gra...@effectivedefense.org>: > > Can you run the checks only on the subdirectory containing the > compiled code? If yes, then you can run it only on half of that > directory and identify it with a binary search. > > > Some years ago, I found a particularly difficult bug that way. > If I recall correctly, I made a copy of the package, deleted half of the > *.Rd files, etc., until I identified which *.Rd file. Then I deleted > ~half of the contents of that *.Rd file until I isolated the problem. > It was neither easy nor fun, but it was what I did to find and then fix > the problem. > > > Hope this helps, > Spencer > > > On 2020-07-17 07:34, Marcin Jurek wrote: > > So maybe you tried that already but I noticed that sometimes when I do the > > check on the package directory rather than on the tarball I get similar > > errors. I don't know if that's the problem but it should be a quick thing > > to try. > > > > On Fri, Jul 17, 2020 at 5:05 AM Fabio Sigrist <fabiosigr...@gmail.com> > > wrote: > > > >> Dear all, > >> > >> I am trying to get an R package with C++ code on CRAN and I have one NOTE > >> remaining, for which I can't find a solution: > >> > >> Note: information on .o files for x64 is not available > >> File > >> 'd:/RCompile/CRANincoming/R-devel/lib/gpboost/libs/x64/lib_gpboost.dll': > >> Found '_exit', possibly from '_exit' (C) > >> Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) > >> Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) > >> Found 'printf', possibly from 'printf' (C) > >> > >> As much as I search through my code, I can't find the place / headers where > >> these calls / symbols originate. Also, I have no idea how to add > >> information on .o files (apart from the shared library, there are no .o > >> files). The .tar.gz file for the package can be found on > >> https://github.com/fabsig/GPBoost/blob/master/gpboost_0.2.0.tar.gz. Note > >> that the shared library is compiled using install.libs.R (this is a > >> deliberate choice) and the flag "GPB_R_BUILD" is set when compiling for the > >> R package (I have tried to put "#ifndef GPB_R_BUILD" around all headers > >> that could cause the problems with exit / abort calls, but apparently I > >> have not been able to find all). > >> > >> Any help is greatly appreciated. > >> > >> Best regards, > >> Fabio Sigrist > >> > >> [[alternative HTML version deleted]] > >> > >> ______________________________________________ > >> R-package-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > >> > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > ______________________________________________ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel