Le lundi 30 juin 2014 à 15:32 -0400, Duncan Murdoch a écrit : > On 30/06/2014 2:41 PM, Milan Bouchet-Valat wrote: > > Le lundi 30 juin 2014 à 05:23 -0400, Duncan Murdoch a écrit : > > > On 30/06/2014, 4:44 AM, Milan Bouchet-Valat wrote: > > > > 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... > > > > > > I have seen this, but I don't see it on every machine. One one where I > > > do see it is the Windows builder machine in Dortmund. The following is > > > inserted into the script after building the 32 bit build > > > > > > cacls %name32% /T /E /G VORDEFINIERT\Benutzer:R > NUL > > > > > > and similar after the 64 bit build. (I don't remember whether > > > VORDEFINIERT\Benutzer is the current user name, or is some generic thing > > > saying "current user". I think Uwe Ligges came up with this...) > > Thanks. VORDEFINIERT\Benutzer appears to mean BUILTIN\Users (BUILTIN > > \Utilisateurs in French), and refers to any user on the system (more or > > less). > > > > Unfortunately, I've run that, and it doesn't make any difference to the > > error I'm seeing. But I don't understand what you mean by "after > > building the 32 bit build" since the problem is precisely that this step > > does not complete successfully. > > > > Here is what I get: > > > > Microsoft Windows [version 6.1.7600] > > Copyright (c) 2009 Microsoft Corporation. Tous droits réservés. > > > > C:\Windows\system32>cd C:\Rbuild\R-3.1.0-32bit > > > > C:\Rbuild\R-3.1.0-32bit>cacls %name32% /T /E /G BUILTIN\UTILISATEURS:R > NUL > > > > C:\Rbuild\R-3.1.0-32bit>cacls %name32% /T /E /G BUILTIN\UTILISATEURS:W > NUL > > > > C:\Rbuild\R-3.1.0-32bit>cd src/gnuwin32 > > > > C:\Rbuild\R-3.1.0-32bit\src\gnuwin32>set TMPDIR=C:\Rbuild\tmp > > > > C:\Rbuild\R-3.1.0-32bit\src\gnuwin32>make -j4 all > > make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make > > rule > > I doubt if this warning is the cause of your troubles, but I wouldn't > bother with the -j4 option because of it. > > On a more positive note: our scripts are more complicated than yours. > I've cc'd a copy of our R-devel script. It has lots of hard-coded > directories in it, so it would take some work to get it going, but maybe > it'll be helpful. Thanks, it's very interesting to see the full script you are using. It may be worth adding a link to it in the docs, I would have used it instead of my half-automated solution if I had seen it.
I've taken inspiration from it and run the build again, in a different directory, and it succeeded. Though it seems the real difference is the directory: for some obscure reason I suspect the old one contaminated the whole tree below it with its broken permission, even if I had removed the source tree itself. So, if anybody in the future is in the same situation: start from an entirely different directory under e.g. C:\. Thanks for the support > Duncan Murdoch > > . > > make[1]: `MkRules' is up to date. > > make[1]: warning: jobserver unavailable: using -j1. Add `+' to parent make > > rule > > . > > make[4]: Nothing to be done for `svnonly'. > > installing C headers > > make[2]: Nothing to be done for `all'. > > make[2]: `libRblas.dll.a' is up to date. > > make[5]: 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 > > gcc -std=gnu99 -m32 -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD > > -DR_ARCH='"i386"' -I../extra/xdr -O3 -Wall -pedantic -mtune=core2 -c > > serialize.c -o serialize.o > > In file included from serialize.c:28:0: > > ../include/Defn.h:1244:21: fatal error: ../include/libintl.h: Permission > > denied > > compilation terminated. > > make[4]: *** [serialize.o] Error 1 > > make[3]: *** [rlibs] Error 2 > > make[2]: *** [../../bin/i386/R.dll] Error 2 > > make[1]: *** [rbuild] Error 2 > > make: *** [all] Error 2 > > > > C:\Rbuild\R-3.1.0-32bit\src\gnuwin32>ls ../include/libintl.h -l > > ---------- 1 Milan mkpasswd 14384 Jun 29 20:15 ../include/libintl.h > > > > I see this weird permission pattern for most of the files in the build > > tree. Running > > cacls %name32% /T /E /G BUILTIN\UTILISATEURS:R > NUL > > does not have any effect on the output of 'ls -l'. > > > > > > Regards > > > > > Duncan Murdoch > > > > > > > > > > > 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 > > > > > > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
