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ropensci / phylocomr

Phylocom R interface
https://docs.ropensci.org/phylocomr
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windows build errors #14

Closed sckott closed 5 years ago

sckott commented 7 years ago

Winbuilder install notes

* installing *source* package 'phylocomr' ...
** libs

*** arch - i386
rm -Rf nothing.o register.o libphylocom/*.o libphylocom.a phylocom ecovolve phylomatic
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/io.c -o libphylocom/io.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/new2fy.c -o libphylocom/new2fy.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/aot.c -o libphylocom/aot.o
libphylocom/aot.c: In function 'TipStats':
libphylocom/aot.c:274:9: warning: variable 'RXY' set but not used [-Wunused-but-set-variable]
   float RXY; 
         ^
libphylocom/aot.c:273:15: warning: variable 'y' set but not used [-Wunused-but-set-variable]
   int i,j,k,x,y,node;
               ^
libphylocom/aot.c: In function 'PIC':
libphylocom/aot.c:338:13: warning: variable 'upn' set but not used [-Wunused-but-set-variable]
   int node, upn;
             ^
libphylocom/aot.c: In function 'AOT':
libphylocom/aot.c:403:14: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
           if (pick > size)
              ^
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/traits.c -o libphylocom/traits.o
libphylocom/traits.c: In function 'PSigRun':
libphylocom/traits.c:22:16: warning: variable 'cx' set but not used [-Wunused-but-set-variable]
   int i, j, k, cx, run, depth, node, dtx, dtxlow, dtxhi, swap, tmp, bin;
                ^
libphylocom/traits.c: In function 'RandArrayT':
libphylocom/traits.c:1780:12: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
         if (pick > size) {
            ^
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/comstruct.c -o libphylocom/comstruct.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/nrutil.c -o libphylocom/nrutil.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/fy2new.c -o libphylocom/fy2new.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/bladj.c -o libphylocom/bladj.o
libphylocom/bladj.c: In function 'Bladj':
libphylocom/bladj.c:16:7: warning: variable 'matched' set but not used [-Wunused-but-set-variable]
   int matched;
       ^
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/comnode.c -o libphylocom/comnode.o
libphylocom/comnode.c: In function 'Comnode':
libphylocom/comnode.c:25:9: warning: variable 'Out' set but not used [-Wunused-but-set-variable]
   phylo Out[1];
         ^
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/prune.c -o libphylocom/prune.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/comtrait.c -o libphylocom/comtrait.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/stats.c -o libphylocom/stats.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/combase.c -o libphylocom/combase.o
mkdir -p ../inst/bin/i386
d:/Compiler/gcc-4.9.3/mingw_32/bin/ar rcs libphylocom.a libphylocom/io.o libphylocom/new2fy.o libphylocom/aot.o libphylocom/traits.o libphylocom/comstruct.o libphylocom/nrutil.o libphylocom/fy2new.o libphylocom/bladj.o libphylocom/comnode.o libphylocom/prune.o libphylocom/comtrait.o libphylocom/stats.o libphylocom/nrutil.o libphylocom/combase.o libphylocom/prune.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/main.c -o libphylocom/main.o
libphylocom/main.c: In function 'main':
libphylocom/main.c:193:13: warning: ISO C forbids zero-size array 'IntreeV' [-Wpedantic]
       phylo IntreeV[0];
             ^
libphylocom/main.c:205:13: warning: ISO C forbids zero-size array 'IntreeV' [-Wpedantic]
       phylo IntreeV[0];
             ^
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc   -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -o phylocom libphylocom/main.o -L. -lphylocom -lm
cp -f phylocom ../inst/bin/i386
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/ecomain.c -o libphylocom/ecomain.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc   -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -o ecovolve libphylocom/ecomain.o -L. -lphylocom -lm
cp -f ecovolve ../inst/bin/i386
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/phylomatic.c -o libphylocom/phylomatic.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc   -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -o phylomatic libphylocom/phylomatic.o -L. -lphylocom -lm
cp -f phylomatic ../inst/bin/i386
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c nothing.c -o nothing.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O3 -Wall  -std=gnu99 -mtune=core2 -c register.c -o register.o
d:/Compiler/gcc-4.9.3/mingw_32/bin/gcc -shared -s -static-libgcc -o phylocomr.dll tmp.def nothing.o register.o -Ld:/Compiler/gcc-4.9.3/local330/lib/i386 -Ld:/Compiler/gcc-4.9.3/local330/lib -LD:/RCompile/recent/R/bin/i386 -lR
installing to d:/RCompile/CRANguest/R-devel/lib/phylocomr/libs/i386

*** arch - x64
rm -Rf nothing.o register.o libphylocom/*.o libphylocom.a phylocom ecovolve phylomatic
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/io.c -o libphylocom/io.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/new2fy.c -o libphylocom/new2fy.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/aot.c -o libphylocom/aot.o
libphylocom/aot.c: In function 'TipStats':
libphylocom/aot.c:274:9: warning: variable 'RXY' set but not used [-Wunused-but-set-variable]
   float RXY; 
         ^
libphylocom/aot.c:273:15: warning: variable 'y' set but not used [-Wunused-but-set-variable]
   int i,j,k,x,y,node;
               ^
libphylocom/aot.c: In function 'PIC':
libphylocom/aot.c:338:13: warning: variable 'upn' set but not used [-Wunused-but-set-variable]
   int node, upn;
             ^
libphylocom/aot.c: In function 'RandArray':
libphylocom/aot.c:403:14: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
           if (pick > size)
              ^
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/traits.c -o libphylocom/traits.o
libphylocom/traits.c: In function 'PSigRun':
libphylocom/traits.c:22:16: warning: variable 'cx' set but not used [-Wunused-but-set-variable]
   int i, j, k, cx, run, depth, node, dtx, dtxlow, dtxhi, swap, tmp, bin;
                ^
libphylocom/traits.c: In function 'RandArrayT':
libphylocom/traits.c:1780:12: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
         if (pick > size) {
            ^
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/comstruct.c -o libphylocom/comstruct.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/nrutil.c -o libphylocom/nrutil.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/fy2new.c -o libphylocom/fy2new.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/bladj.c -o libphylocom/bladj.o
libphylocom/bladj.c: In function 'Bladj':
libphylocom/bladj.c:16:7: warning: variable 'matched' set but not used [-Wunused-but-set-variable]
   int matched;
       ^
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/comnode.c -o libphylocom/comnode.o
libphylocom/comnode.c: In function 'Comnode':
libphylocom/comnode.c:25:9: warning: variable 'Out' set but not used [-Wunused-but-set-variable]
   phylo Out[1];
         ^
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/prune.c -o libphylocom/prune.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/comtrait.c -o libphylocom/comtrait.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/stats.c -o libphylocom/stats.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/combase.c -o libphylocom/combase.o
mkdir -p ../inst/bin/x64
d:/Compiler/gcc-4.9.3/mingw_64/bin/ar rcs libphylocom.a libphylocom/io.o libphylocom/new2fy.o libphylocom/aot.o libphylocom/traits.o libphylocom/comstruct.o libphylocom/nrutil.o libphylocom/fy2new.o libphylocom/bladj.o libphylocom/comnode.o libphylocom/prune.o libphylocom/comtrait.o libphylocom/stats.o libphylocom/nrutil.o libphylocom/combase.o libphylocom/prune.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/main.c -o libphylocom/main.o
libphylocom/main.c: In function 'main':
libphylocom/main.c:193:13: warning: ISO C forbids zero-size array 'IntreeV' [-Wpedantic]
       phylo IntreeV[0];
             ^
libphylocom/main.c:205:13: warning: ISO C forbids zero-size array 'IntreeV' [-Wpedantic]
       phylo IntreeV[0];
             ^
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64  -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -o phylocom libphylocom/main.o -L. -lphylocom -lm
cp -f phylocom ../inst/bin/x64
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/ecomain.c -o libphylocom/ecomain.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64  -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -o ecovolve libphylocom/ecomain.o -L. -lphylocom -lm
cp -f ecovolve ../inst/bin/x64
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c libphylocom/phylomatic.c -o libphylocom/phylomatic.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64  -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -o phylomatic libphylocom/phylomatic.o -L. -lphylocom -lm
cp -f phylomatic ../inst/bin/x64
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c nothing.c -o nothing.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -I"D:/RCompile/recent/R/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -pedantic -O2 -Wall  -std=gnu99 -mtune=core2 -c register.c -o register.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gcc -m64 -shared -s -static-libgcc -o phylocomr.dll tmp.def nothing.o register.o -Ld:/Compiler/gcc-4.9.3/local330/lib/x64 -Ld:/Compiler/gcc-4.9.3/local330/lib -LD:/RCompile/recent/R/bin/x64 -lR
installing to d:/RCompile/CRANguest/R-devel/lib/phylocomr/libs/x64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* MD5 sums
packaged installation of 'phylocomr' as phylocomr_0.1.0.zip
* DONE (phylocomr)

and some of the check notes

* checking whether package 'phylocomr' can be installed ... WARNING
Found the following significant warnings:
  libphylocom/main.c:193:13: warning: ISO C forbids zero-size array 'IntreeV' [-Wpedantic]
  libphylocom/main.c:205:13: warning: ISO C forbids zero-size array 'IntreeV' [-Wpedantic]
See 'd:/RCompile/CRANguest/R-devel/phylocomr.Rcheck/00install.out' for details.
sckott commented 7 years ago

@jeroenooms going to ask you about this pkg tomorrow during our chat - pkg seems to be having trouble on windows in general despite usually (random failures here and there, out of our control) working fine on *nix platforms

jeroen commented 7 years ago

Maybe report this bug upstream:

libphylocom/main.c: In function 'main':
libphylocom/main.c:193:13: warning: ISO C forbids zero-size array 'IntreeV' [-Wpedantic]
       phylo IntreeV[0];
             ^
libphylocom/main.c:205:13: warning: ISO C forbids zero-size array 'IntreeV' [-Wpedantic]
       phylo IntreeV[0];
             ^