On Thu Jan 9 2014 03:47 Henrik Bengtsson wrote: > This is is an issue that bugged me for a while. I encountered a year > ago (April 2012) when I first tried to build R from source on Windows. > I never figured out what the solution is or if I'm doing something > wrong myself (but I have found a tedious workaround). I'm still on > the same Windows 7 Ultimate machine with NTFS, but I now made sure I > started from scratch so I have a completely fresh setup (see details > at the end). > > PROBLEM: > At the very first step I do: > > C:\R\src\gnuwin32>make all > [... Waiting. No errors until ...] > cp R.dll ../../bin/i386 > -------- Building ../../../bin/i386/Rblas.dll -------- > gcc -std=gnu99 -shared -o ../../../bin/i386/Rblas.dll blas.o > cmplxblas.o ../../gnuwin32/dllversion.o Rblas.def -L../../../bin/i386 > -lR -lgfortran > c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: > cannot find -lR > collect2: ld returned 1 exit status > make[2]: *** [../../../bin/i386/Rblas.dll] Error 1 > make[1]: *** [Rblas] Error 2 > make: *** [rbuild] Error 2 > > However: > > C:\R\src\gnuwin32>dir ..\..\bin\i386\ > Volume in drive C is Windows7_OS > Volume Serial Number is E038-51CC > > Directory of C:\R\bin\i386 > > 01/08/2014 06:18 PM <DIR> . > 01/08/2014 06:18 PM <DIR> .. > 01/08/2014 06:18 PM 3,059,712 R.dll > 01/08/2014 06:18 PM 348,995 Rgraphapp.dll > 01/08/2014 06:18 PM 102,975 Riconv.dll > 01/08/2014 06:18 PM 154,917 Rzlib.dll > 4 File(s) 3,666,599 bytes > 2 Dir(s) 22,424,739,840 bytes free > > What's weird is that these files have **read permission disabled**: > > C:\R\src\gnuwin32>file ..\..\bin\i386\*.dll > ..\..\bin\i386\R.dll: writable, executable, regular file, no > read permission > ..\..\bin\i386\Rgraphapp.dll: writable, executable, regular file, no > read permission > ..\..\bin\i386\Riconv.dll: writable, executable, regular file, no > read permission > ..\..\bin\i386\Rzlib.dll: writable, executable, regular file, no > read permission > > What is going on? Have anyone else seen this? I've also tried > running as Administrator - no difference. Hi Henrik,
Old thread, but I think I'm experiencing exactly the same problem. I tried running as administrator and as a normal user, and no luck. I noticed, though, that resetting permissions on the build tree makes the error go away, and replaces it with another one stating that headers in include/ could not be created due to permission issues. This is on a machine where I was able to build R 3.0.1 successfully, though I also remember having permission issues I eventually fixed by resetting permissions on the build tree. Not sure what's changed since then... To add bit of information to the debugging you've already done: I noticed that when opening the directory/file property dialog, a user with a very long name including letters and numbers appears in the permissions list for a second, and then disappears. This user reappears every time I run 'make'. So maybe 'mkdir' or other tools use wrong user IDs, creating bogus users. Just a guess. Have you found a solution or workaround since January? I really need to build an R installer and I seem to be stuck... Thanks for your help > TROUBLESHOOTING / WORKAROUND: > It appears that 'mkdir' (of Rtools) causes this problem, because if I > manually pre-create 'C:\R\src\gnuwin32\bin\i386' using Windows' mkdir > it works, e.g. > > C:\R\src\gnuwin32>rm -fR ..\..\bin\ > C:\R\src\gnuwin32>cmd /C mkdir ..\..\bin\i386 > C:\R\src\gnuwin32>make rbuild > [...] > -------- Building ../../../bin/i386/Rblas.dll -------- > gcc -std=gnu99 -shared -o ../../../bin/i386/Rblas.dll blas.o > cmplxblas.o ../../gnuwin32/dllversion.o Rblas.def -L../../../bin/i386 > -lR -lgfortran > make --no-print-directory -C front-ends > mkdir -p ../../../bin/i386 > cp Rgui.exe ../../../bin/i386/Rgui.exe > mkdir -p ../../../bin/i386 > cp Rterm.exe ../../../bin/i386/Rterm.exe > mkdir -p ../../../bin/i386 > cp Rcmd.exe ../../../bin/i386/Rcmd.exe > mkdir -p ../../../bin/i386 > cp RSetReg.exe ../../../bin/i386/RSetReg.exe > mkdir -p ../../../bin/i386 > cp R.exe ../../../bin/i386/R.exe > mkdir -p ../../../bin/i386 > cp Rscript.exe ../../../bin/i386/Rscript.exe > mkdir -p ../../../bin/i386 > cp open.exe ../../../bin/i386/open.exe > mkdir -p ../../../bin > cp Rfe.exe ../../../bin/R.exe > mkdir -p ../../../bin > cp Rfe.exe ../../../bin/Rscript.exe > make[1]: `COPYRIGHTS' is up to date. > make --no-print-directory -C ../modules -f Makefile.win \ > CFLAGS='-O3 -Wall -pedantic -mtune=core2' FFLAGS='-O3 -mtune=core2' > gcc -std=gnu99 -shared -s -o ../../../bin/i386/Rlapack.dll dlamch.o > dlapack.o cmplx.o init_win.o Rlapackrc.o -L../../../bin/i386 -lR > -lRblas -lgfortran > cp lapack.dll ../../../modules/i386/lapack.dll > > and there is (obviously) read permissions on those files: > > C:\R\src\gnuwin32>file ..\..\bin\i386\*.dll > ..\..\bin\i386\R.dll: PE32 executable for MS Windows (DLL) > (GUI) Intel 80386 32-bit > ..\..\bin\i386\Rblas.dll: PE32 executable for MS Windows (DLL) > (console) Intel 80386 32-bit > ..\..\bin\i386\Rgraphapp.dll: PE32 executable for MS Windows (DLL) > (GUI) Intel 80386 32-bit > ..\..\bin\i386\Riconv.dll: PE32 executable for MS Windows (DLL) > (console) Intel 80386 32-bit > ..\..\bin\i386\Rlapack.dll: PE32 executable for MS Windows (DLL) > (console) Intel 80386 32-bit > ..\..\bin\i386\Rzlib.dll: PE32 executable for MS Windows (DLL) > (console) Intel 80386 32-bit > > Pre-creating the proper directories is tedious and only works up to > the point of 'make distribution', where I haven't found a similar > workaround (without modifying the Makefiles). Note, I can get to the > point where I have build and check everything (including recommended > packages). > > > Just to convince you that mkdir is the problem, I can reproduce the > problem from this point, by removing the bin/ directory again and > relying on Rtools mkdir again; > > C:\R\src\gnuwin32>rm -fR ..\..\bin > C:\R\src\gnuwin32>make rbuild > make[3]: Nothing to be done for `svnonly'. > installing C headers > make[1]: `libRblas.dll.a' is up to date. > make[4]: Nothing to be done for `svnonly'. > installing C headers > make --no-print-directory -C ../extra/intl CFLAGS='-O3 -Wall -pedantic > -mtune=core2' -f Makefile.win > make --no-print-directory -C ../appl CFLAGS='-O3 -Wall -pedantic > -mtune=core2' FFLAGS='-O3 -mtune=core2' -f Makefile.win > make --no-print-directory -C ../nmath CFLAGS='-O3 -Wall -pedantic > -mtune=core2' FFLAGS='-O3 -mtune=core2' -f Makefile.win > make --no-print-directory -C ../main CFLAGS='-O3 -Wall -pedantic > -mtune=core2' FFLAGS='-O3 -mtune=core2' malloc-DEFS='-DLEA_MALLOC' -f > Makefile.win > make --no-print-directory -C ./getline CFLAGS='-O3 -Wall -pedantic > -mtune=core2' > > make[3]: `gl.a' is up to date. > make -f Makefile.win makeMakedeps > make -f Makefile.win libpcre.a > make[4]: `libpcre.a' is up to date. > make[3]: Nothing to be done for `all'. > make -f Makefile.win makeMakedeps > make -f Makefile.win libtre.a > make[4]: `libtre.a' is up to date. > make[3]: Nothing to be done for `all'. > make[4]: `stamp' is up to date. > make[4]: `liblzma.a' is up to date. > make[2]: `R.dll' is up to date. > cp R.dll ../../bin/i386 > -------- Building ../../../bin/i386/Rblas.dll -------- > gcc -std=gnu99 -shared -o ../../../bin/i386/Rblas.dll blas.o > cmplxblas.o ../../gnuwin32/dllversion.o Rblas.def -L../../../bin/i386 > -lR -lgfortran > c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: > cannot find -lR > collect2: ld returned 1 exit status > make[2]: *** [../../../bin/i386/Rblas.dll] Error 1 > make[1]: *** [Rblas] Error 2 > make: *** [rbuild] Error 2 > > > MORE TROUBLESHOOTING: > The MD5 checksum when it fails (reproducible): > C:\R\src\gnuwin32>md5sum ../../bin/i386/*.dll > 75b2e64d3847e768631681922df5a81d *../../bin/i386/R.dll > 12a35b63a28ad0e0fee8cae04f76e907 *../../bin/i386/Rgraphapp.dll > e2c40ae15d13dc17af33c1367f78817d *../../bin/i386/Riconv.dll > c5ea5a5cd2b7d3c07970f5314ce7296a *../../bin/i386/Rzlib.dll > > The MD5 checksum when it works (reproducible): > C:\R\src\gnuwin32>md5sum ../../bin/i386/*.dll > 75b2e64d3847e768631681922df5a81d *../../bin/i386/R.dll > 12a35b63a28ad0e0fee8cae04f76e907 *../../bin/i386/Rgraphapp.dll > e2c40ae15d13dc17af33c1367f78817d *../../bin/i386/Riconv.dll > c5ea5a5cd2b7d3c07970f5314ce7296a *../../bin/i386/Rzlib.dll > + > c81b3399027ec9c24ca80ba92199327c *../../bin/i386/Rblas.dll > 20d32cee2e561d1826af1a538844472b *../../bin/i386/Rlapack.dll > > > Thanks for any help, > > Henrik > > > SETUP: > 1. Downloaded/svn checkout the R source to C:\R\. > 2. Installed most recent Rtools to C:\Rtools (completely removed previously) > (3. Modifying the MkRules.* files has no impact for reproducing this > problem. Same with 'make rsync-recommended') > > C:\R\src\gnuwin32>path > PATH=;C:\Rtools\bin;C:\Rtools\gcc-4.6.3\bin;C:\Windows;C:\Windows\system32 > > C:\R\src\gnuwin32>cat C:\Rtools\VERSION.txt > Rtools version 3.1.0.1939 > > C:\R\src\gnuwin32>ls ../.. > COPYING Makefile.fw VERSION configure.ac po tmp > ChangeLog Makefile.in VERSION-NICK doc share tools > INSTALL README config.site etc src > Makeconf.in Tcl configure m4 tests ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
