[R-pkg-devel] Errors in the pre-test after submitting the R package

[Tan, Senren]

Dear Dirk,


Thank you very much for your reply.


I have been trying to look at the R package fftw developed by Olaf and Uwe over the last few days. And I have tried to make use of the configure.ac. file in their source package to generate the configure script. I tried R CMD Check on my Mac, as well as on some machines running Linux. It seems that I could pass all the R CMD Checks on these Unix / Linux machines.


Also, I have come across the following website https://cran.r-project.org/bin/windows/contrib/ThirdPartySoftware.html, on which it seems to suggest that the C library fftw3 (with the make variable LIB_FFTW) is installed on the CRAN build machine for Windows.


So, I tried the following Makevars.win.


PKG_CPPFLAGS = -I$(LIB_FFTW)/include  -I$(LIB_FFTW)
CXX11 = g++
PKG_CXXFLAGS = -std=c++11
PKG_LIBS = -L$(LIB_FFTW)/lib${R_ARCH} -lfftw3



However, when I tried to re-submit the package to CRAN, I still got the same error message on the pre-test as follows, suggesting that the machine had not detected the fftw3 library.




 **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs

*** arch - i386
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include -Id:/Rcompile/CRANpkg/extralibs215/local215 -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include -Id:/Rcompile/CRANpkg/extralibs215/local215 -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -O2 -Wall  -mtune=core2 -c cont_ks_dist.cpp -o cont_ks_dist.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include -Id:/Rcompile/CRANpkg/extralibs215/local215 -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -O2 -Wall  -mtune=core2 -c crossprob_new.cc -o crossprob_new.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include -Id:/Rcompile/CRANpkg/extralibs215/local215 -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -O2 -Wall  -mtune=core2 -c fftw_wrappers.cc -o fftw_wrappers.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include -Id:/Rcompile/CRANpkg/extralibs215/local215 -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -O2 -Wall  -mtune=core2 -c fftwconvolver.cc -o fftwconvolver.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include -Id:/Rcompile/CRANpkg/extralibs215/local215 -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -O2 -Wall  -mtune=core2 -c one_sided_noncrossing_probability.cc -o one_sided_noncrossing_probability.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include -Id:/Rcompile/CRANpkg/extralibs215/local215 -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -O2 -Wall  -mtune=core2 -c one_sided_noncrossing_probability_n2.cc -o one_sided_noncrossing_probability_n2.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include -Id:/Rcompile/CRANpkg/extralibs215/local215 -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -O2 -Wall  -mtune=core2 -c one_sided_noncrossing_probability_n2logn.cc -o one_sided_noncrossing_probability_n2logn.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include -Id:/Rcompile/CRANpkg/extralibs215/local215 -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -O2 -Wall  -mtune=core2 -c poisson_pmf.cc -o poisson_pmf.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include -Id:/Rcompile/CRANpkg/extralibs215/local215 -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -O2 -Wall  -mtune=core2 -c read_boundaries_file.cc -o read_boundaries_file.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include -Id:/Rcompile/CRANpkg/extralibs215/local215 -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -O2 -Wall  -mtune=core2 -c string_utils.cc -o string_utils.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -std=gnu++11 -I"D:/RCompile/recent/R/include" -DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include -Id:/Rcompile/CRANpkg/extralibs215/local215 -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -O2 -Wall  -mtune=core2 -c two_sided_noncrossing_probability.cc -o two_sided_noncrossing_probability.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/g++ -shared -s -static-libgcc -o KSgeneral.dll tmp.def RcppExports.o cont_ks_dist.o crossprob_new.o fftw_wrappers.o fftwconvolver.o one_sided_noncrossing_probability.o one_sided_noncrossing_probability_n2.o one_sided_noncrossing_probability_n2logn.o poisson_pmf.o read_boundaries_file.o string_utils.o two_sided_noncrossing_probability.o -Ld:/Rcompile/CRANpkg/extralibs215/local215/lib/i386 -lfftw3 -Ld:/Compiler/gcc-4.9.3/local330/lib/i386 -Ld:/Compiler/gcc-4.9.3/local330/lib -LD:/RCompile/recent/R/bin/i386 -lR
fftw_wrappers.o:fftw_wrappers.cc:(.text+0x125): undefined reference to `_imp__fftw_plan_dft_r2c_1d'
fftw_wrappers.o:fftw_wrappers.cc:(.text+0x14f): undefined reference to `_imp__fftw_destroy_plan'
fftw_wrappers.o:fftw_wrappers.cc:(.text+0x29b): undefined reference to `_imp__fftw_execute'
fftw_wrappers.o:fftw_wrappers.cc:(.text+0x315): undefined reference to `_imp__fftw_plan_dft_c2r_1d'
fftw_wrappers.o:fftw_wrappers.cc:(.text+0x33f): undefined reference to `_imp__fftw_destroy_plan'
fftw_wrappers.o:fftw_wrappers.cc:(.text+0x3bb): undefined reference to `_imp__fftw_execute'
collect2.exe: error: ld returned 1 exit status
no DLL was created


I was wondering whether I should include in the configure.ac file a few lines about downloading the library fftw3 when it is not available on the machine? Or have I made some mistakes in the Makevars.win file?

Thank you very much and I apologize for any inconvenience I may have caused you.

Best regards,
Senren



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