Re: [R-SIG-Mac] building R under Lion

2012-08-29 Thread Kasper Daniel Hansen
For other readers of the thread: apply the patch Simon gave and still
use  --with-blas='-framework vecLib'

Peter: Accelerate.h just includes vecLib.h (and also vImage.h), nothing else.

Simon: after looking at the header files, I agree that it seems
easiest to just define __ACCELERATE__.  It might also be possible to
define __ENVIRONMENT_MAC_OS_X_VERSION_MIN_REQUIRED, but I guess that
is likely to have other consequences.

Kasper


On Wed, Aug 29, 2012 at 9:27 AM, Simon Urbanek
 wrote:
>
> On Aug 29, 2012, at 2:29 AM, peter dalgaard wrote:
>
>>
>> On Aug 29, 2012, at 02:51 , Simon Urbanek wrote:
>>
>>> You were on the right path - it's only about renaming vecLib to Accelerate, 
>>> so you just have to apply the patch below. It is annoying, since -framework 
>>> vecLib still works just fine so you don't even need to change the configure 
>>> flags. The patch will in some modified form make it to R eventually.
>>
>> Just to clarify: This is due to quite recent XCode changes? In my versions 
>> on Lion and Snow Leopard, Accelerate.h just #includes vecLib.h.
>>
>
> It's just yet another Apple nonsense in Mountain Lion - it still just 
> includes vecLib but now vecLib checks whether __ACCELERATE__ is defined and 
> bails out with an error if it's not ... So another work-around is to set 
> CPPFLAGS=-D__ACCELERATE__
>
> Cheers,
> Simon
>
>
>>
>>>
>>> Cheers,
>>> Simon
>>>
>>>
>>> Index: vecLibg95c.c
>>> ===
>>> --- vecLibg95c.c (revision 59442)
>>> +++ vecLibg95c.c (working copy)
>>> @@ -2,7 +2,7 @@
>>> #include 
>>> #endif
>>>
>>> -#include 
>>> +#include 
>>>
>>> void F77_FUNC_(rcblas_cdotu_sub,)(const int *N, const void *X, const int 
>>> *incX,
>>>   const void *Y, const int *incY, void *dotu)
>>>
>>>
>>>
>>>
>>>
>>> On Aug 28, 2012, at 5:22 PM, Kasper Daniel Hansen wrote:
>>>
 I am running Lion, with the newest version of Xcode, and the 5666
 build of gcc+gfortran from Simon's page.  This is on Macbook pro last
 generation, with a quad core i7.  I have installed the latest stable
 release of Xquartz.

 I am building R, not as a framework (--disable-framework), but I am
 using --with-blas='-framework vecLib' which at least used to be much
 better than the built-in BLAS.

 My entire configure call is
 ../${SRCDIR}/configure SHELL='/bin/bash' \
 --prefix=/usr/local/R/R-${R_VERSION} --disable-R-framework\
 CC="/usr/bin/gcc-4.2 -arch x86_64 -std=gnu99" \
 CFLAGS="-g -O2 -std=gnu99 -march=nocona" \
 CXX="/usr/bin/g++-4.2 -arch x86_64" \
 CXXFLAGS="-g -O2 -march=nocona" \
 OBJC="/usr/bin/gcc-4.2 -arch x86_64" \
 F77="/usr/bin/gfortran-4.2 -arch x86_64" \
 FFLAGS="-g -O2 -march=nocona" \
 FC="/usr/bin/gfortran-4.2 -arch x86_64" \
 FCFLAGS="-g -O2 -march=nocona" \
 --enable-memory-profiling\
 --x-includes=/usr/X11/include --x-libraries=/usr/X11/lib\
 --with-system-zlib\
 --with-blas='-framework vecLib' --with-lapack

 When I build R-2.15.1-patched, I get

 making internet.d from 
 ../../../../R-2.15.x-src/src/modules/internet/internet.c
 In file included from
 ../../../../R-2.15.x-src/src/modules/lapack/vecLibg95c.c:5:
 /System/Library/Frameworks/vecLib.framework/Headers/vecLib.h:22:4:
 error: #error " is deprecated.  Please #include
  and link to Accelerate.framework."
 make[3]: *** [vecLibg95c.d] Error 1
 make[2]: *** [make.lapack] Error 2
 make[2]: *** Waiting for unfinished jobs
 making nanoftp.d from 
 ../../../../R-2.15.x-src/src/modules/internet/nanoftp.c

 

 /usr/bin/gcc-4.2 -arch x86_64 -std=gnu99 -I. -I../../../src/include
 -I../../../../R-2.15.x-src/src/include -I/usr/local/include
 -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2 -std=gnu99 -march=nocona   -c
 ../../../../R-2.15.x-src/src/modules/internet/sockconn.c -o sockconn.o
 /usr/bin/gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib
 -Wl,-headerpad_max_install_names  -undefined dynamic_lookup
 -single_module -multiply_defined suppress -L/usr/local/lib -o
 internet.so Rhttpd.o Rsock.o internet.o nanoftp.o nanohttp.o sock.o
 sockconn.o   -Wl,-framework -Wl,CoreFoundation
 mkdir /Users/khansen/build/R/R-2.15.x-build/modules
 make[1]: *** [R] Error 1
 make: *** [R] Error 1

 So it seems that it does not like -framework vecLib.  I tried with
 -framework Accelerate, but I get the same error.

 My guess is that there is some new thing I have to do here, but I
 tried reading the admin guide for R-devel and could not see anything
 particular (except I do not need -arch x86_64 anymore).

 Thanks,
 Kasper

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>>>
>>> __

Re: [R-SIG-Mac] building R under Lion

2012-08-29 Thread Simon Urbanek

On Aug 29, 2012, at 2:29 AM, peter dalgaard wrote:

> 
> On Aug 29, 2012, at 02:51 , Simon Urbanek wrote:
> 
>> You were on the right path - it's only about renaming vecLib to Accelerate, 
>> so you just have to apply the patch below. It is annoying, since -framework 
>> vecLib still works just fine so you don't even need to change the configure 
>> flags. The patch will in some modified form make it to R eventually.
> 
> Just to clarify: This is due to quite recent XCode changes? In my versions on 
> Lion and Snow Leopard, Accelerate.h just #includes vecLib.h.
> 

It's just yet another Apple nonsense in Mountain Lion - it still just includes 
vecLib but now vecLib checks whether __ACCELERATE__ is defined and bails out 
with an error if it's not ... So another work-around is to set 
CPPFLAGS=-D__ACCELERATE__

Cheers,
Simon


> 
>> 
>> Cheers,
>> Simon
>> 
>> 
>> Index: vecLibg95c.c
>> ===
>> --- vecLibg95c.c (revision 59442)
>> +++ vecLibg95c.c (working copy)
>> @@ -2,7 +2,7 @@
>> #include 
>> #endif
>> 
>> -#include 
>> +#include 
>> 
>> void F77_FUNC_(rcblas_cdotu_sub,)(const int *N, const void *X, const int 
>> *incX,
>>   const void *Y, const int *incY, void *dotu) 
>> 
>> 
>> 
>> 
>> 
>> On Aug 28, 2012, at 5:22 PM, Kasper Daniel Hansen wrote:
>> 
>>> I am running Lion, with the newest version of Xcode, and the 5666
>>> build of gcc+gfortran from Simon's page.  This is on Macbook pro last
>>> generation, with a quad core i7.  I have installed the latest stable
>>> release of Xquartz.
>>> 
>>> I am building R, not as a framework (--disable-framework), but I am
>>> using --with-blas='-framework vecLib' which at least used to be much
>>> better than the built-in BLAS.
>>> 
>>> My entire configure call is
>>> ../${SRCDIR}/configure SHELL='/bin/bash' \
>>> --prefix=/usr/local/R/R-${R_VERSION} --disable-R-framework\
>>> CC="/usr/bin/gcc-4.2 -arch x86_64 -std=gnu99" \
>>> CFLAGS="-g -O2 -std=gnu99 -march=nocona" \
>>> CXX="/usr/bin/g++-4.2 -arch x86_64" \
>>> CXXFLAGS="-g -O2 -march=nocona" \
>>> OBJC="/usr/bin/gcc-4.2 -arch x86_64" \
>>> F77="/usr/bin/gfortran-4.2 -arch x86_64" \
>>> FFLAGS="-g -O2 -march=nocona" \
>>> FC="/usr/bin/gfortran-4.2 -arch x86_64" \
>>> FCFLAGS="-g -O2 -march=nocona" \
>>> --enable-memory-profiling\
>>> --x-includes=/usr/X11/include --x-libraries=/usr/X11/lib\
>>> --with-system-zlib\
>>> --with-blas='-framework vecLib' --with-lapack
>>> 
>>> When I build R-2.15.1-patched, I get
>>> 
>>> making internet.d from 
>>> ../../../../R-2.15.x-src/src/modules/internet/internet.c
>>> In file included from
>>> ../../../../R-2.15.x-src/src/modules/lapack/vecLibg95c.c:5:
>>> /System/Library/Frameworks/vecLib.framework/Headers/vecLib.h:22:4:
>>> error: #error " is deprecated.  Please #include
>>>  and link to Accelerate.framework."
>>> make[3]: *** [vecLibg95c.d] Error 1
>>> make[2]: *** [make.lapack] Error 2
>>> make[2]: *** Waiting for unfinished jobs
>>> making nanoftp.d from 
>>> ../../../../R-2.15.x-src/src/modules/internet/nanoftp.c
>>> 
>>> 
>>> 
>>> /usr/bin/gcc-4.2 -arch x86_64 -std=gnu99 -I. -I../../../src/include
>>> -I../../../../R-2.15.x-src/src/include -I/usr/local/include
>>> -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2 -std=gnu99 -march=nocona   -c
>>> ../../../../R-2.15.x-src/src/modules/internet/sockconn.c -o sockconn.o
>>> /usr/bin/gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib
>>> -Wl,-headerpad_max_install_names  -undefined dynamic_lookup
>>> -single_module -multiply_defined suppress -L/usr/local/lib -o
>>> internet.so Rhttpd.o Rsock.o internet.o nanoftp.o nanohttp.o sock.o
>>> sockconn.o   -Wl,-framework -Wl,CoreFoundation
>>> mkdir /Users/khansen/build/R/R-2.15.x-build/modules
>>> make[1]: *** [R] Error 1
>>> make: *** [R] Error 1
>>> 
>>> So it seems that it does not like -framework vecLib.  I tried with
>>> -framework Accelerate, but I get the same error.
>>> 
>>> My guess is that there is some new thing I have to do here, but I
>>> tried reading the admin guide for R-devel and could not see anything
>>> particular (except I do not need -arch x86_64 anymore).
>>> 
>>> Thanks,
>>> Kasper
>>> 
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> 
>> 
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> -- 
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd@cbs.dk  Priv: pda...@gmail.com
> 
> 
> 
> 
> 
> 
> 
> 
> 

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Re: [R-SIG-Mac] building R under Lion

2012-08-28 Thread peter dalgaard

On Aug 29, 2012, at 02:51 , Simon Urbanek wrote:

> You were on the right path - it's only about renaming vecLib to Accelerate, 
> so you just have to apply the patch below. It is annoying, since -framework 
> vecLib still works just fine so you don't even need to change the configure 
> flags. The patch will in some modified form make it to R eventually.

Just to clarify: This is due to quite recent XCode changes? In my versions on 
Lion and Snow Leopard, Accelerate.h just #includes vecLib.h.

-p


> 
> Cheers,
> Simon
> 
> 
> Index: vecLibg95c.c
> ===
> --- vecLibg95c.c  (revision 59442)
> +++ vecLibg95c.c  (working copy)
> @@ -2,7 +2,7 @@
> #include 
> #endif
> 
> -#include 
> +#include 
> 
> void F77_FUNC_(rcblas_cdotu_sub,)(const int *N, const void *X, const int 
> *incX,
>const void *Y, const int *incY, void *dotu) 
> 
> 
> 
> 
> 
> On Aug 28, 2012, at 5:22 PM, Kasper Daniel Hansen wrote:
> 
>> I am running Lion, with the newest version of Xcode, and the 5666
>> build of gcc+gfortran from Simon's page.  This is on Macbook pro last
>> generation, with a quad core i7.  I have installed the latest stable
>> release of Xquartz.
>> 
>> I am building R, not as a framework (--disable-framework), but I am
>> using --with-blas='-framework vecLib' which at least used to be much
>> better than the built-in BLAS.
>> 
>> My entire configure call is
>> ../${SRCDIR}/configure SHELL='/bin/bash' \
>> --prefix=/usr/local/R/R-${R_VERSION} --disable-R-framework\
>> CC="/usr/bin/gcc-4.2 -arch x86_64 -std=gnu99" \
>> CFLAGS="-g -O2 -std=gnu99 -march=nocona" \
>> CXX="/usr/bin/g++-4.2 -arch x86_64" \
>> CXXFLAGS="-g -O2 -march=nocona" \
>> OBJC="/usr/bin/gcc-4.2 -arch x86_64" \
>> F77="/usr/bin/gfortran-4.2 -arch x86_64" \
>> FFLAGS="-g -O2 -march=nocona" \
>> FC="/usr/bin/gfortran-4.2 -arch x86_64" \
>> FCFLAGS="-g -O2 -march=nocona" \
>> --enable-memory-profiling\
>> --x-includes=/usr/X11/include --x-libraries=/usr/X11/lib\
>> --with-system-zlib\
>> --with-blas='-framework vecLib' --with-lapack
>> 
>> When I build R-2.15.1-patched, I get
>> 
>> making internet.d from 
>> ../../../../R-2.15.x-src/src/modules/internet/internet.c
>> In file included from
>> ../../../../R-2.15.x-src/src/modules/lapack/vecLibg95c.c:5:
>> /System/Library/Frameworks/vecLib.framework/Headers/vecLib.h:22:4:
>> error: #error " is deprecated.  Please #include
>>  and link to Accelerate.framework."
>> make[3]: *** [vecLibg95c.d] Error 1
>> make[2]: *** [make.lapack] Error 2
>> make[2]: *** Waiting for unfinished jobs
>> making nanoftp.d from ../../../../R-2.15.x-src/src/modules/internet/nanoftp.c
>> 
>> 
>> 
>> /usr/bin/gcc-4.2 -arch x86_64 -std=gnu99 -I. -I../../../src/include
>> -I../../../../R-2.15.x-src/src/include -I/usr/local/include
>> -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2 -std=gnu99 -march=nocona   -c
>> ../../../../R-2.15.x-src/src/modules/internet/sockconn.c -o sockconn.o
>> /usr/bin/gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib
>> -Wl,-headerpad_max_install_names  -undefined dynamic_lookup
>> -single_module -multiply_defined suppress -L/usr/local/lib -o
>> internet.so Rhttpd.o Rsock.o internet.o nanoftp.o nanohttp.o sock.o
>> sockconn.o   -Wl,-framework -Wl,CoreFoundation
>> mkdir /Users/khansen/build/R/R-2.15.x-build/modules
>> make[1]: *** [R] Error 1
>> make: *** [R] Error 1
>> 
>> So it seems that it does not like -framework vecLib.  I tried with
>> -framework Accelerate, but I get the same error.
>> 
>> My guess is that there is some new thing I have to do here, but I
>> tried reading the admin guide for R-devel and could not see anything
>> particular (except I do not need -arch x86_64 anymore).
>> 
>> Thanks,
>> Kasper
>> 
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> 
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R-SIG-Mac] building R under Lion

2012-08-28 Thread Simon Urbanek
You were on the right path - it's only about renaming vecLib to Accelerate, so 
you just have to apply the patch below. It is annoying, since -framework vecLib 
still works just fine so you don't even need to change the configure flags. The 
patch will in some modified form make it to R eventually.

Cheers,
Simon


Index: vecLibg95c.c
===
--- vecLibg95c.c(revision 59442)
+++ vecLibg95c.c(working copy)
@@ -2,7 +2,7 @@
 #include 
 #endif
 
-#include 
+#include 
 
 void F77_FUNC_(rcblas_cdotu_sub,)(const int *N, const void *X, const int *incX,
const void *Y, const int *incY, void *dotu) 





On Aug 28, 2012, at 5:22 PM, Kasper Daniel Hansen wrote:

> I am running Lion, with the newest version of Xcode, and the 5666
> build of gcc+gfortran from Simon's page.  This is on Macbook pro last
> generation, with a quad core i7.  I have installed the latest stable
> release of Xquartz.
> 
> I am building R, not as a framework (--disable-framework), but I am
> using --with-blas='-framework vecLib' which at least used to be much
> better than the built-in BLAS.
> 
> My entire configure call is
> ../${SRCDIR}/configure SHELL='/bin/bash' \
>  --prefix=/usr/local/R/R-${R_VERSION} --disable-R-framework\
>  CC="/usr/bin/gcc-4.2 -arch x86_64 -std=gnu99" \
>  CFLAGS="-g -O2 -std=gnu99 -march=nocona" \
>  CXX="/usr/bin/g++-4.2 -arch x86_64" \
>  CXXFLAGS="-g -O2 -march=nocona" \
>  OBJC="/usr/bin/gcc-4.2 -arch x86_64" \
>  F77="/usr/bin/gfortran-4.2 -arch x86_64" \
>  FFLAGS="-g -O2 -march=nocona" \
>  FC="/usr/bin/gfortran-4.2 -arch x86_64" \
>  FCFLAGS="-g -O2 -march=nocona" \
>  --enable-memory-profiling\
>  --x-includes=/usr/X11/include --x-libraries=/usr/X11/lib\
>  --with-system-zlib\
>  --with-blas='-framework vecLib' --with-lapack
> 
> When I build R-2.15.1-patched, I get
> 
> making internet.d from 
> ../../../../R-2.15.x-src/src/modules/internet/internet.c
> In file included from
> ../../../../R-2.15.x-src/src/modules/lapack/vecLibg95c.c:5:
> /System/Library/Frameworks/vecLib.framework/Headers/vecLib.h:22:4:
> error: #error " is deprecated.  Please #include
>  and link to Accelerate.framework."
> make[3]: *** [vecLibg95c.d] Error 1
> make[2]: *** [make.lapack] Error 2
> make[2]: *** Waiting for unfinished jobs
> making nanoftp.d from ../../../../R-2.15.x-src/src/modules/internet/nanoftp.c
> 
> 
> 
> /usr/bin/gcc-4.2 -arch x86_64 -std=gnu99 -I. -I../../../src/include
> -I../../../../R-2.15.x-src/src/include -I/usr/local/include
> -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2 -std=gnu99 -march=nocona   -c
> ../../../../R-2.15.x-src/src/modules/internet/sockconn.c -o sockconn.o
> /usr/bin/gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib
> -Wl,-headerpad_max_install_names  -undefined dynamic_lookup
> -single_module -multiply_defined suppress -L/usr/local/lib -o
> internet.so Rhttpd.o Rsock.o internet.o nanoftp.o nanohttp.o sock.o
> sockconn.o   -Wl,-framework -Wl,CoreFoundation
> mkdir /Users/khansen/build/R/R-2.15.x-build/modules
> make[1]: *** [R] Error 1
> make: *** [R] Error 1
> 
> So it seems that it does not like -framework vecLib.  I tried with
> -framework Accelerate, but I get the same error.
> 
> My guess is that there is some new thing I have to do here, but I
> tried reading the admin guide for R-devel and could not see anything
> particular (except I do not need -arch x86_64 anymore).
> 
> Thanks,
> Kasper
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> 

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[R-SIG-Mac] building R under Lion

2012-08-28 Thread Kasper Daniel Hansen
I am running Lion, with the newest version of Xcode, and the 5666
build of gcc+gfortran from Simon's page.  This is on Macbook pro last
generation, with a quad core i7.  I have installed the latest stable
release of Xquartz.

I am building R, not as a framework (--disable-framework), but I am
using --with-blas='-framework vecLib' which at least used to be much
better than the built-in BLAS.

My entire configure call is
../${SRCDIR}/configure SHELL='/bin/bash' \
  --prefix=/usr/local/R/R-${R_VERSION} --disable-R-framework\
  CC="/usr/bin/gcc-4.2 -arch x86_64 -std=gnu99" \
  CFLAGS="-g -O2 -std=gnu99 -march=nocona" \
  CXX="/usr/bin/g++-4.2 -arch x86_64" \
  CXXFLAGS="-g -O2 -march=nocona" \
  OBJC="/usr/bin/gcc-4.2 -arch x86_64" \
  F77="/usr/bin/gfortran-4.2 -arch x86_64" \
  FFLAGS="-g -O2 -march=nocona" \
  FC="/usr/bin/gfortran-4.2 -arch x86_64" \
  FCFLAGS="-g -O2 -march=nocona" \
  --enable-memory-profiling\
  --x-includes=/usr/X11/include --x-libraries=/usr/X11/lib\
  --with-system-zlib\
  --with-blas='-framework vecLib' --with-lapack

When I build R-2.15.1-patched, I get

making internet.d from ../../../../R-2.15.x-src/src/modules/internet/internet.c
In file included from
../../../../R-2.15.x-src/src/modules/lapack/vecLibg95c.c:5:
/System/Library/Frameworks/vecLib.framework/Headers/vecLib.h:22:4:
error: #error " is deprecated.  Please #include
 and link to Accelerate.framework."
make[3]: *** [vecLibg95c.d] Error 1
make[2]: *** [make.lapack] Error 2
make[2]: *** Waiting for unfinished jobs
making nanoftp.d from ../../../../R-2.15.x-src/src/modules/internet/nanoftp.c



/usr/bin/gcc-4.2 -arch x86_64 -std=gnu99 -I. -I../../../src/include
-I../../../../R-2.15.x-src/src/include -I/usr/local/include
-DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2 -std=gnu99 -march=nocona   -c
../../../../R-2.15.x-src/src/modules/internet/sockconn.c -o sockconn.o
/usr/bin/gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib
-Wl,-headerpad_max_install_names  -undefined dynamic_lookup
-single_module -multiply_defined suppress -L/usr/local/lib -o
internet.so Rhttpd.o Rsock.o internet.o nanoftp.o nanohttp.o sock.o
sockconn.o   -Wl,-framework -Wl,CoreFoundation
mkdir /Users/khansen/build/R/R-2.15.x-build/modules
make[1]: *** [R] Error 1
make: *** [R] Error 1

So it seems that it does not like -framework vecLib.  I tried with
-framework Accelerate, but I get the same error.

My guess is that there is some new thing I have to do here, but I
tried reading the admin guide for R-devel and could not see anything
particular (except I do not need -arch x86_64 anymore).

Thanks,
Kasper

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