R devel - Jun 2014 - Building R on Windows: mkdir of Rtools creates directories with read-only permissions [WEIRD]

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

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...)

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
> 
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