Re: [R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

2017-05-23 Thread Simon Urbanek 
Christofer,

> On May 23, 2017, at 7:44 PM, Christofer Bogaso  
> wrote:
> 
> Hi David,
> 
> The file 'rJava.so' exists in my machine :
> 
>> file.exists('/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so')
> 
> [1] TRUE
> 
> Also the Javac version that I have :
> 
>> system('javac -version')
> 
> javac 1.6.0_65
> 
> Looks like mine is older than you. Do I need to download the latest?
> In that case, do you suggest any link? As far as I know, javac comes
> with Mac installed.
> 

Apple has dropped Java support many years ago - what you have a is a left-over 
from a very old OS X version as you likely upgraded your OS X over the years 
without re-installing.
Since R 3.4.0 the CRAN binary uses Java 1.8, because too many users have 
complained about incompatibilities with old Java version, so you have two 
options
1) recompile rJava from sources against your ancient Java
2) install Java 1.8 from Oracle[1], then run R CMD javareconf

[1] 
http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

Cheers,
Simon



> On Peter's suggestion I also did sudo R CMD javareconf. However still
> rJava couldnt be loaded.
> 
> Any other idea? Thanks,
> 
> On Wed, May 24, 2017 at 4:28 AM, peter dalgaard  wrote:
>> [Christofer seemed to have fallen off the cc: list, now included]
>> 
>>> On 24 May 2017, at 00:18 , David Winsemius  wrote:
>>> 
>>> What version of the Java Runtime Environment is available? What do you get 
>>> for:
>>> 
>>> system('javac -version')
>>> #I get:
>>> #javac 1.8.0_65
>>> 
>>> I think that version was working with rJava, but I followed the "critical" 
>>> advice on the Java SDK webpage ...
>>> 
>>> ... and after updating I now  get
>>> #javac 1.8.0_131
>>> 
>>> And rJava still loads without error. I'm not on Sierra, however.
>>> 
>> 
>> I am, and rJava doesn't load here either. However after
>> 
>> sudo R CMD javareconf
>> 
>> it seems happy as a clam.
>> 
>> 
>>> Good luck;
>>> David,
>> 
>> --
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email: pd@cbs.dk  Priv: pda...@gmail.com
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> 
> ___
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Re: [R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

2017-05-23 Thread David Winsemius 

> On May 23, 2017, at 5:29 PM, David Winsemius  wrote:
> 
> 
>> On May 23, 2017, at 4:44 PM, Christofer Bogaso  
>> wrote:
>> 
>> Hi David,
>> 
>> The file 'rJava.so' exists in my machine :
>> 
>>> file.exists('/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so')
>> 
>> [1] TRUE
>> 
>> Also the Javac version that I have :
>> 
>>> system('javac -version')
>> 
>> javac 1.6.0_65
>> 
>> Looks like mine is older than you. Do I need to download the latest?
>> In that case, do you suggest any link? As far as I know, javac comes
>> with Mac installed.
> 
> Yes, it does and some people seem to get success with that. I found that 
> installing 1.8 (also confusingly known as "Java 8") resolved my difficulties 
> with loading rJava. I'm not an expert, just reporting my ezxperience
>> 
>> On Peter's suggestion I also did sudo R CMD javareconf. However still
>> rJava couldnt be loaded.
> 
> For my machine:
> 
>> Sys.getenv()  # returns (among many other values)
> 
> 
> DYLD_LIBRARY_PATH
> /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/

And I just notice another value in the returns from that command:

LD_LIBRARY_PATH   :@JAVA_LD@

-- 
David.
> 
> 
>> 
>> Any other idea? Thanks,
>> 
>> On Wed, May 24, 2017 at 4:28 AM, peter dalgaard  wrote:
>>> [Christofer seemed to have fallen off the cc: list, now included]
>>> 
 On 24 May 2017, at 00:18 , David Winsemius  wrote:
 
 What version of the Java Runtime Environment is available? What do you get 
 for:
 
 system('javac -version')
 #I get:
 #javac 1.8.0_65
 
 I think that version was working with rJava, but I followed the "critical" 
 advice on the Java SDK webpage ...
 
 ... and after updating I now  get
 #javac 1.8.0_131
 
 And rJava still loads without error. I'm not on Sierra, however.
 
>>> 
>>> I am, and rJava doesn't load here either. However after
>>> 
>>> sudo R CMD javareconf
>>> 
>>> it seems happy as a clam.
>>> 
>>> 
 Good luck;
 David,
>>> 
>>> --
>>> Peter Dalgaard, Professor,
>>> Center for Statistics, Copenhagen Business School
>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>> Phone: (+45)38153501
>>> Office: A 4.23
>>> Email: pd@cbs.dk  Priv: pda...@gmail.com
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
> 
> David Winsemius
> Alameda, CA, USA
> 
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Re: [R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

2017-05-23 Thread David Winsemius 

> On May 23, 2017, at 4:44 PM, Christofer Bogaso  
> wrote:
> 
> Hi David,
> 
> The file 'rJava.so' exists in my machine :
> 
>> file.exists('/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so')
> 
> [1] TRUE
> 
> Also the Javac version that I have :
> 
>> system('javac -version')
> 
> javac 1.6.0_65
> 
> Looks like mine is older than you. Do I need to download the latest?
> In that case, do you suggest any link? As far as I know, javac comes
> with Mac installed.

Yes, it does and some people seem to get success with that. I found that 
installing 1.8 (also confusingly known as "Java 8") resolved my difficulties 
with loading rJava. I'm not an expert, just reporting my ezxperience
> 
> On Peter's suggestion I also did sudo R CMD javareconf. However still
> rJava couldnt be loaded.

For my machine:

>Sys.getenv()  # returns (among many other values)


DYLD_LIBRARY_PATH
/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/


> 
> Any other idea? Thanks,
> 
> On Wed, May 24, 2017 at 4:28 AM, peter dalgaard  wrote:
>> [Christofer seemed to have fallen off the cc: list, now included]
>> 
>>> On 24 May 2017, at 00:18 , David Winsemius  wrote:
>>> 
>>> What version of the Java Runtime Environment is available? What do you get 
>>> for:
>>> 
>>> system('javac -version')
>>> #I get:
>>> #javac 1.8.0_65
>>> 
>>> I think that version was working with rJava, but I followed the "critical" 
>>> advice on the Java SDK webpage ...
>>> 
>>> ... and after updating I now  get
>>> #javac 1.8.0_131
>>> 
>>> And rJava still loads without error. I'm not on Sierra, however.
>>> 
>> 
>> I am, and rJava doesn't load here either. However after
>> 
>> sudo R CMD javareconf
>> 
>> it seems happy as a clam.
>> 
>> 
>>> Good luck;
>>> David,
>> 
>> --
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email: pd@cbs.dk  Priv: pda...@gmail.com
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 

David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

2017-05-23 Thread David Winsemius 

> On May 23, 2017, at 3:18 PM, David Winsemius  wrote:
> 
>> 
>> On May 23, 2017, at 1:05 PM, Duncan Murdoch  wrote:
>> 
>> On 23/05/2017 2:48 PM, Christofer Bogaso wrote:
>>> Hi again,
>>> 
>>> After I upgraded R to 3.4.0, I could not load rJava package. Below is
>>> the error :
>>> 
 library(rJava)
>>> 
>>> Error: package or namespace load failed for ‘rJava’:
>>> 
>>> .onLoad failed in loadNamespace() for 'rJava', details:
>>> 
>>> call: dyn.load(file, DLLpath = DLLpath, ...)
>>> 
>>> error: unable to load shared object
>>> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so':
> 
> To Christofer;
> 
> Does 
> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so'
>  exist?
> 
> (You may need to check libPaths() in your new installation. )

You might also want to report the value that Sys.getenv() returns for:

DYLD_LIBRARY_PATH  

For me it is now:

   /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/


> 
> 
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so,
>>> 6): Library not loaded: @rpath/libjvm.dylib
>>> 
> 
> What version of the Java Runtime Environment is available? What do you get 
> for:
> 
> system('javac -version')
> #I get:
> #javac 1.8.0_65
> 
> I think that version was working with rJava, but I followed the "critical" 
> advice on the Java SDK webpage ...
> 
> ... and after updating I now  get
> #javac 1.8.0_131
> 
> And rJava still loads without error. I'm not on Sierra, however.
> 
> Good luck;
> David,
> 
> 
> 
>>> Referenced from:
>>> /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so
>>> 
>>> Reason: image not found
>>> 
>>> I have installed latest version of Java.
>> 
>> Did you re-install rJava?  Generally speaking you need to re-install all 
>> packages when switching R versions (except if the only change is in the 
>> patch level z, where the version number is x.y.z, you can usually use the 
>> old version).
>> 
>> Duncan Murdoch
>> 
>>> 
>>> R version :
>>> 
>>> R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
>>> 
>>> Copyright (C) 2017 The R Foundation for Statistical Computing
>>> 
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> 
>>> iOS : Sierra
>>> 
>>> With previous version of R, rJava was working fine. Could you please
>>> help how to fix it.
>>> 
>>> Thanks for your time.
>>> 
>>> Regards,
>>> 
>>> ___
>>> 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
> 
> David Winsemius
> Alameda, CA, USA
> 
> ___
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> R-SIG-Mac@r-project.org
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David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

2017-05-23 Thread Christofer Bogaso 
Hi David,

The file 'rJava.so' exists in my machine :

> file.exists('/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so')

[1] TRUE

Also the Javac version that I have :

> system('javac -version')

javac 1.6.0_65

Looks like mine is older than you. Do I need to download the latest?
In that case, do you suggest any link? As far as I know, javac comes
with Mac installed.

On Peter's suggestion I also did sudo R CMD javareconf. However still
rJava couldnt be loaded.

Any other idea? Thanks,

On Wed, May 24, 2017 at 4:28 AM, peter dalgaard  wrote:
> [Christofer seemed to have fallen off the cc: list, now included]
>
>> On 24 May 2017, at 00:18 , David Winsemius  wrote:
>>
>> What version of the Java Runtime Environment is available? What do you get 
>> for:
>>
>> system('javac -version')
>> #I get:
>> #javac 1.8.0_65
>>
>> I think that version was working with rJava, but I followed the "critical" 
>> advice on the Java SDK webpage ...
>>
>> ... and after updating I now  get
>> #javac 1.8.0_131
>>
>> And rJava still loads without error. I'm not on Sierra, however.
>>
>
> I am, and rJava doesn't load here either. However after
>
> sudo R CMD javareconf
>
> it seems happy as a clam.
>
>
>> Good luck;
>> David,
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: pda...@gmail.com
>
>
>
>
>
>
>
>
>

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Re: [R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

2017-05-23 Thread peter dalgaard 
[Christofer seemed to have fallen off the cc: list, now included]

> On 24 May 2017, at 00:18 , David Winsemius  wrote:
> 
> What version of the Java Runtime Environment is available? What do you get 
> for:
> 
> system('javac -version')
> #I get:
> #javac 1.8.0_65
> 
> I think that version was working with rJava, but I followed the "critical" 
> advice on the Java SDK webpage ...
> 
> ... and after updating I now  get
> #javac 1.8.0_131
> 
> And rJava still loads without error. I'm not on Sierra, however.
> 

I am, and rJava doesn't load here either. However after

sudo R CMD javareconf

it seems happy as a clam.


> Good luck;
> David,

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

2017-05-23 Thread David Winsemius 

> On May 23, 2017, at 1:05 PM, Duncan Murdoch  wrote:
> 
> On 23/05/2017 2:48 PM, Christofer Bogaso wrote:
>> Hi again,
>> 
>> After I upgraded R to 3.4.0, I could not load rJava package. Below is
>> the error :
>> 
>>> library(rJava)
>> 
>> Error: package or namespace load failed for ‘rJava’:
>> 
>> .onLoad failed in loadNamespace() for 'rJava', details:
>> 
>>  call: dyn.load(file, DLLpath = DLLpath, ...)
>> 
>>  error: unable to load shared object
>> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so':

To Christofer;

Does 
'/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so'
 exist?

(You may need to check libPaths() in your new installation. )


>>  
>> dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so,
>> 6): Library not loaded: @rpath/libjvm.dylib
>> 

What version of the Java Runtime Environment is available? What do you get for:

system('javac -version')
#I get:
#javac 1.8.0_65

I think that version was working with rJava, but I followed the "critical" 
advice on the Java SDK webpage ...

... and after updating I now  get
#javac 1.8.0_131

And rJava still loads without error. I'm not on Sierra, however.

Good luck;
David,



>>  Referenced from:
>> /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so
>> 
>>  Reason: image not found
>> 
>> I have installed latest version of Java.
> 
> Did you re-install rJava?  Generally speaking you need to re-install all 
> packages when switching R versions (except if the only change is in the patch 
> level z, where the version number is x.y.z, you can usually use the old 
> version).
> 
> Duncan Murdoch
> 
>> 
>> R version :
>> 
>> R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
>> 
>> Copyright (C) 2017 The R Foundation for Statistical Computing
>> 
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> 
>> iOS : Sierra
>> 
>> With previous version of R, rJava was working fine. Could you please
>> help how to fix it.
>> 
>> Thanks for your time.
>> 
>> Regards,
>> 
>> ___
>> 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@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

2017-05-23 Thread Duncan Murdoch 

On 23/05/2017 2:48 PM, Christofer Bogaso wrote:

Hi again,

After I upgraded R to 3.4.0, I could not load rJava package. Below is
the error :


library(rJava)


Error: package or namespace load failed for ‘rJava’:

 .onLoad failed in loadNamespace() for 'rJava', details:

  call: dyn.load(file, DLLpath = DLLpath, ...)

  error: unable to load shared object
'/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so':

  
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so,
6): Library not loaded: @rpath/libjvm.dylib

  Referenced from:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so

  Reason: image not found

I have installed latest version of Java.


Did you re-install rJava?  Generally speaking you need to re-install all 
packages when switching R versions (except if the only change is in the 
patch level z, where the version number is x.y.z, you can usually use 
the old version).


Duncan Murdoch



R version :

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"

Copyright (C) 2017 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin15.6.0 (64-bit)

iOS : Sierra

With previous version of R, rJava was working fine. Could you please
help how to fix it.

Thanks for your time.

Regards,

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[R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

2017-05-23 Thread Christofer Bogaso 
Hi again,

After I upgraded R to 3.4.0, I could not load rJava package. Below is
the error :

> library(rJava)

Error: package or namespace load failed for ‘rJava’:

 .onLoad failed in loadNamespace() for 'rJava', details:

  call: dyn.load(file, DLLpath = DLLpath, ...)

  error: unable to load shared object
'/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so':

  
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so,
6): Library not loaded: @rpath/libjvm.dylib

  Referenced from:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so

  Reason: image not found

I have installed latest version of Java.

R version :

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"

Copyright (C) 2017 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin15.6.0 (64-bit)

iOS : Sierra

With previous version of R, rJava was working fine. Could you please
help how to fix it.

Thanks for your time.

Regards,

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