[R-SIG-Mac] segfault with raster package

2019-12-16 Thread Marc Girondot via R-SIG-Mac 

When I load the last version of raster package in MacOS, I get a segfault:

This is similar to the problem described here:

https://r.789695.n4.nabble.com/Raster-package-crash-with-segmentation-fault-td4759487.html

or here

https://github.com/rspatial/raster/issues/63

The last working version for me is the 2.5-8 installed with:

require(devtools)
install_version("raster", version = "2.5-8", repos 
="http://cran.us.r-project.org;)


I would like know if the problem with the raster package is common in 
macOSX or if there is something special for me.


Thanks a lot

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Re: [R-SIG-Mac] Update of RcppParallel failed

2018-02-14 Thread Marc Girondot via R-SIG-Mac 

Hi Keith,

When I try just now, a new version of RcppParallel was available 
(4.3.20.2; previous one was 4.3.20.1):


essai de l'URL 
'https://cran.r-project.org/src/contrib/RcppParallel_4.3.20.2.tar.gz'

And it compiles without problem !

So the problem is solved !

Thanks

Marc




Le 14/02/2018 à 14:58, Keith O'Hara a écrit :

This looks like an issue to bring up with the Rcpp guys, not R… but can you 
provide a full printout of the error? I’m guessing this failed when compiling a 
C file, not C++.



On Feb 14, 2018, at 8:43 AM, Marc Girondot via R-SIG-Mac 
<r-sig-mac@r-project.org> wrote:

This morning I had an update to apply for RcppParallel but it failed

Here are some information:


update.packages()

RcppParallel :
  Version 4.3.20 installed in 
/Library/Frameworks/R.framework/Versions/3.5/Resources/library
  Version 4.3.20.1 available at https://cran.r-project.org

During instal, I had this error

error: invalid argument '-std=gnu++11' not allowed with 'C'

It failed with the two versions of clang that I have installed:

clang++ --version
clang version 5.0.1 (tags/RELEASE_501/final)
Target: x86_64-apple-darwin17.4.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin

or

clang++ --version
Apple LLVM version 9.0.0 (clang-900.0.39.2)
Target: x86_64-apple-darwin17.4.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Do you have some idea about what's happened and how to solve this problem ?

Thanks

Marc

_

Information on my R version:


R.Version()

$platform
[1] "x86_64-apple-darwin15.6.0"

$arch
[1] "x86_64"

$os
[1] "darwin15.6.0"

$system
[1] "x86_64, darwin15.6.0"

$status
[1] "Under development (unstable)"

$major
[1] "3"

$minor
[1] "5.0"

$year
[1] "2018"

$month
[1] "02"

$day
[1] "13"

$`svn rev`
[1] "74247"

$language
[1] "R"

$version.string
[1] "R Under development (unstable) (2018-02-13 r74247)"

$nickname
[1] "Unsuffered Consequences"

___
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

[R-SIG-Mac] Update of RcppParallel failed

2018-02-14 Thread Marc Girondot via R-SIG-Mac 

This morning I had an update to apply for RcppParallel but it failed

Here are some information:

> update.packages()
RcppParallel :
 Version 4.3.20 installed in 
/Library/Frameworks/R.framework/Versions/3.5/Resources/library

 Version 4.3.20.1 available at https://cran.r-project.org

During instal, I had this error

error: invalid argument '-std=gnu++11' not allowed with 'C'

It failed with the two versions of clang that I have installed:

clang++ --version
clang version 5.0.1 (tags/RELEASE_501/final)
Target: x86_64-apple-darwin17.4.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin

or

clang++ --version
Apple LLVM version 9.0.0 (clang-900.0.39.2)
Target: x86_64-apple-darwin17.4.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin


Do you have some idea about what's happened and how to solve this problem ?

Thanks

Marc

_

Information on my R version:

> R.Version()
$platform
[1] "x86_64-apple-darwin15.6.0"

$arch
[1] "x86_64"

$os
[1] "darwin15.6.0"

$system
[1] "x86_64, darwin15.6.0"

$status
[1] "Under development (unstable)"

$major
[1] "3"

$minor
[1] "5.0"

$year
[1] "2018"

$month
[1] "02"

$day
[1] "13"

$`svn rev`
[1] "74247"

$language
[1] "R"

$version.string
[1] "R Under development (unstable) (2018-02-13 r74247)"

$nickname
[1] "Unsuffered Consequences"

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Re: [R-SIG-Mac] rJava compilation on R 3.5 devel [SOLVED]

2018-01-31 Thread Marc Girondot via R-SIG-Mac 

I have found a solution based on the proposition of Keith. Thanks a lot



First I have made some cleaning because I had pieces of clang in many 
places.


Then with a clean version I installed 
clang-4.0.0-darwin15.6-Release.tar.gz using the version in

http://r.research.att.com/libs/clang-4.0.0-darwin15.6-Release.tar.gz

Note that it produced an error at the end when I run the command:
sudo tar xvzf clang-4.0.0-darwin15.6-Release.tar.gz -C /
The error is:
tar: Error exit delayed from previous errors.

But it seems to be ok

then I create the link as propose by Keith:
cd /usr/local/lib
sudo ln -s /usr/local/clang4/lib/libomp.dylib libomp.dylib

And it works perfectly if the install.packages("rJava") is ran as root: 
sudo R


##

Now, let try with clang 5.0.1 from homebrew.

First I delete all tracks of previous installation of clang4:
sudo cd 
# I use this trick to enter the root password firsttime; after it does 
not ask within the loop

for file in $(tar tfz clang-4.0.0-darwin15.6-Release.tar.gz); do
   sudo rm -f /$file;
done

# Remove empty _folders_ associated with the binary
for file in $(tar tfz clang-4.0.0-darwin15.6-Release.tar.gz); do
   sudo rmdir -p /$file;
done

Then I install llvm with homebrew:
brew install llvm

in /usr/local/opt/llvm/lib there is no libomp.dylib but libgomp.dylib 
and libiomp5.dylib. I don't know if I can use it instead of libomp.dylib.


But I see one in:
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libomp.dylib

Better to use this one:
cd /usr/local/lib
sudo ln -s 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libomp.dylib 
libomp.dylib



And the compilation ran correctly.

Thanks a lot !

Marc

Le 31/01/2018 à 11:52, Keith O'Hara a écrit :

Sorry, ignore the installation question, I missed the ‘brew install’ line.

Try adding a symbolic link from the brew install of libomp to /usr/local/lib.




On Jan 31, 2018, at 5:38 AM, Keith O'Hara <keith.oh...@nyu.edu> wrote:

Apple’s LLVM doesn’t support OpenMP, which explains the second error.

How did you install clang-5.0.1? If you installed using MacPorts, then you 
might need to create a symbolic link to libomp in /usr/local/lib. Check if the 
following exists:

/opt/local/lib/libomp/libomp.dylib




On Jan 31, 2018, at 5:22 AM, Marc Girondot via R-SIG-Mac 
<r-sig-mac@r-project.org> wrote:

Dear Experts,

I use now r-3.5 devel as it is stable (from http://r.research.att.com , version 
(2018/01/30, r74185) ) but I have a problem with compilation of rJava package.

In short (all the explanations are bellow):

If I use clang 4.0.0 from here: http://r.research.att.com/libs/, I get this 
error: ld: library not found for -lomp

If I use clang from xcode, I get this error: clang: error: unsupported option 
'-fopenmp'

If I use clang 5.0.1, I get this error: ld: library not found for -lomp

Any idea to have rJava in r-devel ?

Thanks a lot

Marc



First I ran:

sudo R CMD javareconf

I have the Java version : 1.8.0_162

I need to compile it from source but it failed with clang4 reporting an error.

I try various origin of clang:

at the beginning of the compilation, it said:

checking for gcc... /usr/local/clang4/bin/clang

I tried several version of clang:

belinda:local marcgirondot$ 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang
 --version
Apple LLVM version 9.0.0 (clang-900.0.39.2)
Target: x86_64-apple-darwin17.3.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

or (same version installed by: brew install llvm )

belinda:local marcgirondot$ 
/Applications/clang+llvm-5.0.1-final-x86_64-apple-darwin/bin/clang --version
clang version 5.0.1 (tags/RELEASE_501/final)
Target: x86_64-apple-darwin17.3.0
Thread model: posix
InstalledDir: /Applications/clang+llvm-5.0.1-final-x86_64-apple-darwin/bin

or

belinda:local marcgirondot$ /usr/local/clang4/bin/clang --version
clang version 4.0.0 (tags/RELEASE_400/final)
Target: x86_64-apple-darwin17.3.0
Thread model: posix
InstalledDir: /usr/local/clang4/bin

If I use the former, I get this error:
/usr/local/clang4/bin/clang -o libjri.jnilib Rengine.o jri.o Rcallbacks.o 
Rinit.o globals.o rjava.o  -dynamiclib -framework JavaVM -fopenmp 
-L/usr/local/lib -F/Library/Frameworks/R.framework/.. -framework R -lpcre 
-llzma -lbz2 -lz -licucore -lm -liconv
ld: library not found for -lomp
clang-4.0: error: linker command failed with exit code 1 (use -v to see 
invocation)
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’

Then I tried more recent versions:

I make a symbolic link to clang 5.0.1 or the one within xcode:
cd /usr/local
sudo ln -s /Applications/clang+llvm-5.0.1-final-x86_64-apple-darwin clang4

I get this error: (after running sudo R and within R: install.packages("rJava")
/usr/local/c

[R-SIG-Mac] rJava compilation on R 3.5 devel

2018-01-31 Thread Marc Girondot via R-SIG-Mac 

Dear Experts,

I use now r-3.5 devel as it is stable (from http://r.research.att.com , 
version (2018/01/30, r74185) ) but I have a problem with compilation of 
rJava package.


In short (all the explanations are bellow):

If I use clang 4.0.0 from here: http://r.research.att.com/libs/, I get 
this error: ld: library not found for -lomp


If I use clang from xcode, I get this error: clang: error: unsupported 
option '-fopenmp'


If I use clang 5.0.1, I get this error: ld: library not found for -lomp

Any idea to have rJava in r-devel ?

Thanks a lot

Marc



First I ran:

sudo R CMD javareconf

I have the Java version : 1.8.0_162

I need to compile it from source but it failed with clang4 reporting an 
error.


I try various origin of clang:

at the beginning of the compilation, it said:

checking for gcc... /usr/local/clang4/bin/clang

I tried several version of clang:

belinda:local marcgirondot$ 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang 
--version

Apple LLVM version 9.0.0 (clang-900.0.39.2)
Target: x86_64-apple-darwin17.3.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin


or (same version installed by: brew install llvm )

belinda:local marcgirondot$ 
/Applications/clang+llvm-5.0.1-final-x86_64-apple-darwin/bin/clang --version

clang version 5.0.1 (tags/RELEASE_501/final)
Target: x86_64-apple-darwin17.3.0
Thread model: posix
InstalledDir: /Applications/clang+llvm-5.0.1-final-x86_64-apple-darwin/bin

or

belinda:local marcgirondot$ /usr/local/clang4/bin/clang --version
clang version 4.0.0 (tags/RELEASE_400/final)
Target: x86_64-apple-darwin17.3.0
Thread model: posix
InstalledDir: /usr/local/clang4/bin

If I use the former, I get this error:
/usr/local/clang4/bin/clang -o libjri.jnilib Rengine.o jri.o 
Rcallbacks.o Rinit.o globals.o rjava.o  -dynamiclib -framework JavaVM 
-fopenmp -L/usr/local/lib -F/Library/Frameworks/R.framework/.. 
-framework R -lpcre -llzma -lbz2 -lz -licucore -lm -liconv

ld: library not found for -lomp
clang-4.0: error: linker command failed with exit code 1 (use -v to see 
invocation)

make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’

Then I tried more recent versions:

I make a symbolic link to clang 5.0.1 or the one within xcode:
cd /usr/local
sudo ln -s /Applications/clang+llvm-5.0.1-final-x86_64-apple-darwin clang4

I get this error: (after running sudo R and within R: 
install.packages("rJava")
/usr/local/clang4/bin/clang -o libjri.jnilib Rengine.o jri.o 
Rcallbacks.o Rinit.o globals.o rjava.o  -dynamiclib -framework JavaVM 
-fopenmp -L/usr/local/lib -F/Library/Frameworks/R.framework/.. 
-framework R -lpcre -llzma -lbz2 -lz -licucore -lm -liconv

ld: library not found for -lomp
clang-5.0: error: linker command failed with exit code 1 (use -v to see 
invocation)

make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’


If I make the symbolic link to
cd /usr/local
sudo ln -s 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr 
clang4


I get this error: (after running sudo R and within R: 
install.packages("rJava")
/usr/local/clang4/bin/clang -o libjri.jnilib Rengine.o jri.o 
Rcallbacks.o Rinit.o globals.o rjava.o  -dynamiclib -framework JavaVM 
-fopenmp -L/usr/local/lib -F/Library/Frameworks/R.framework/.. 
-framework R -lpcre -llzma -lbz2 -lz -licucore -lm -liconv

clang: error: unsupported option '-fopenmp'
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Re: [R-SIG-Mac] Install rJava produce an error

2017-10-15 Thread Marc Girondot via R-SIG-Mac 

The temporary solution was to load the compiled version of the package:
https://cran.r-project.org/bin/macosx/el-capitan/contrib/3.4/rJava_0.9-9.tgz

Uncompress with double-click,

and replace the rJava (from previous installation) folder with this new 
one in:

> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/3.4/Resources/library"

It is not very elegant but until now it works.

Marc

Le 14/10/2017 à 17:01, Marc Girondot via R-SIG-Mac a écrit :
I would be most interested to get a solution for my problem in rJava 
install.


R 3.4.2

MacOSx 10.12.6, Sierra

Xcode 9.

If I install the rJava package, I get this error:

###

> install.packages("rJava")
essai de l'URL 
'https://cran.r-project.org/src/contrib/rJava_0.9-9.tar.gz'

Content type 'application/x-gzip' length 660454 bytes (644 KB)
==
downloaded 644 KB

* installing *source* package ‘rJava’ ...

### many lines

clang -o libjri.jnilib Rengine.o jri.o Rcallbacks.o Rinit.o globals.o 
rjava.o  -dynamiclib -framework JavaVM -fopenmp -L/usr/local/lib 
-F/Library/Frameworks/R.framework/.. -framework R -lpcre -llzma -lbz2 
-lz -licucore -lm -liconv

clang: error: unsupported option '-fopenmp'
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’

###

clang does not understand the option -fopenmp

This version of clang comes with xCode 9:
Apple LLVM version 9.0.0 (clang-900.0.37)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin


Then I install clang 5.0.0

clang version 5.0.0 (tags/RELEASE_500/final)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin

This time, the error is:

###

clang -o libjri.jnilib Rengine.o jri.o Rcallbacks.o Rinit.o globals.o 
rjava.o  -dynamiclib -framework JavaVM -fopenmp -L/usr/local/lib 
-F/Library/Frameworks/R.framework/.. -framework R -lpcre -llzma -lbz2 
-lz -licucore -lm -liconv

ld: library not found for -lomp
clang-5.0: error: linker command failed with exit code 1 (use -v to 
see invocation)


###

Has someone a solution to compile rJava ?

Thanks

Marc

___
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

[R-SIG-Mac] Install rJava produce an error

2017-10-14 Thread Marc Girondot via R-SIG-Mac 
I would be most interested to get a solution for my problem in rJava 
install.


R 3.4.2

MacOSx 10.12.6, Sierra

Xcode 9.

If I install the rJava package, I get this error:

###

> install.packages("rJava")
essai de l'URL 'https://cran.r-project.org/src/contrib/rJava_0.9-9.tar.gz'
Content type 'application/x-gzip' length 660454 bytes (644 KB)
==
downloaded 644 KB

* installing *source* package ‘rJava’ ...

### many lines

clang -o libjri.jnilib Rengine.o jri.o Rcallbacks.o Rinit.o globals.o 
rjava.o  -dynamiclib -framework JavaVM -fopenmp -L/usr/local/lib 
-F/Library/Frameworks/R.framework/.. -framework R -lpcre -llzma -lbz2 
-lz -licucore -lm -liconv

clang: error: unsupported option '-fopenmp'
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’

###

clang does not understand the option -fopenmp

This version of clang comes with xCode 9:
Apple LLVM version 9.0.0 (clang-900.0.37)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin


Then I install clang 5.0.0

clang version 5.0.0 (tags/RELEASE_500/final)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin

This time, the error is:

###

clang -o libjri.jnilib Rengine.o jri.o Rcallbacks.o Rinit.o globals.o 
rjava.o  -dynamiclib -framework JavaVM -fopenmp -L/usr/local/lib 
-F/Library/Frameworks/R.framework/.. -framework R -lpcre -llzma -lbz2 
-lz -licucore -lm -liconv

ld: library not found for -lomp
clang-5.0: error: linker command failed with exit code 1 (use -v to see 
invocation)


###

Has someone a solution to compile rJava ?

Thanks

Marc

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac