Henrik Bengtsson
2014-Jan-09 02:47 UTC
[Rd] Building R on Windows: mkdir of Rtools creates directories with read-only permissions [WEIRD]
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.
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
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