From nalimilan at club.fr  Mon Jun 30 20:41:18 2014
From: nalimilan at club.fr (Milan Bouchet-Valat)
Date: Mon, 30 Jun 2014 20:41:18 +0200
Subject: [Rd] Building R on Windows: mkdir of Rtools creates directories
 with read-only permissions [WEIRD]
In-Reply-To: <53B12C98.2000007@gmail.com>
References: <1404117853.25972.8.camel@milan.mobile.lan>
	<53B12C98.2000007@gmail.com>
Message-ID: <1404153678.32183.41.camel@milan.mobile.lan>

Le lundi 30 juin 2014 ? 05:23 -0400, Duncan Murdoch a ?crit :
> 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 r?serv?s.

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
.
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 at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >



[Rd] Building R on Windows: mkdir of Rtools creates directories with read-only permissions [WEIRD]
Milan Bouchet-Valat