From nalimilan at club.fr  Mon Jun 30 10:44:13 2014
From: nalimilan at club.fr (Milan Bouchet-Valat)
Date: Mon, 30 Jun 2014 10:44:13 +0200
Subject: [Rd] Building R on Windows: mkdir of Rtools creates directories
 with read-only permissions [WEIRD]
Message-ID: <1404117853.25972.8.camel@milan.mobile.lan>

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



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