date:20180201

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

2018-02-01 Thread Simon Urbanek

That is, unfortunately, the reality of Oracle taking over Java. They have no 
idea what they are doing on macOS so once Apple stopped supporting system Java 
you have to re-run
R CMD javareconf
every time you upgrade Java version since they their binaries are broken. There 
is no way to link to Oracle Java as it changes paths without embedding the ID. 
It is sad that Oracle (unlike Apple) is not capable of providing a working 
solution, but since corporate Java is all you get on macOS there is no real 
choice and we have to live with it and its limitations.

Cheers,
Simon



> On Feb 1, 2018, at 6:02 AM, Keith O'Hara  wrote:
> 
> That looks like a bad idea to me—unless I am mistaken, you will need to 
> update your link with every update to the JDK, otherwise R and RStudio could 
> be out of sync when building/loading rJava.
> 
> (Consider contacting the RStudio people for a more permanent solution, as 
> Simon suggested.)
> 
>> On Feb 1, 2018, at 12:22 AM, Marc Girondot  wrote:
>> 
>> This is indeed a problem with Rstudio:
>> 
>> I used the Rstudio 1.2.308 (development version) but the same occurred with 
>> 1.1.419 version;
>>> library("rJava")
>> Erreur : package or namespace load failed for ‘rJava’:
>> .onLoad a échoué dans loadNamespace() pour 'rJava', détails :
>>  appel : dyn.load(file, DLLpath = DLLpath, ...)
>>  erreur : impossible de charger l'objet partagé 
>> '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
>> dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so,
>>  6): Library not loaded: @rpath/libjvm.dylib
>>  Referenced from: 
>> /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
>>  Reason: image not found
>> 
>> 1.1.419
>> Sys.getenv() gives
>> DYLD_FALLBACK_LIBRARY_PATH
>> /Library/Frameworks/R.framework/Resources/lib:/Users/marcgirondot/lib:/usr/local/lib:/usr/lib::
>> 1.2.308
>> Sys.getenv() gives
>> DYLD_FALLBACK_LIBRARY_PATH
>> /Library/Frameworks/R.framework/Resources/lib:/Users/marcgirondot/lib:/usr/local/lib:/usr/lib::
>> 
>> R in terminal
>> Sys.getenv() gives
>> DYLD_FALLBACK_LIBRARY_PATH
>> /Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server
>> 
>> I try:
>> 
>> cd /usr/local/lib
>> sudo ln -s 
>> /Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server/libjsig.dylib
>>  libjsig.dylib
>> sudo ln -s 
>> /Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server/libjvm.dylib
>>  libjvm.dylib
>> 
>> And I can load rJava package in Rstudio also now.
>> 
>> Thanks to everybody for your help !
>> 
>> Marc
>> 
>> 
>> 
>> Le 01/02/2018 à 01:23, Kevin Ushey a écrit :
>>> What version of RStudio are you using? This particular issue should be
>>> fixed in v1.1.419 of RStudio.
>>> 
>>> On Wed, Jan 31, 2018 at 11:48 AM, Marc Girondot  
>>> wrote:
 Hi Simon,
 
 Half solution ! Thanks !
 
 I remove JAVA_HOME and when R is ran as root or non-root in terminal, rJava
 package can be loaded. Great !
 
 But in Rstudio, I have still a problem (see bellow).
 
 Any suggestion ?
 
 Thanks
 
 Marc
 
> library(rJava)
 Erreur : package or namespace load failed for ‘rJava’:
 .onLoad a échoué dans loadNamespace() pour 'rJava', détails :
  appel : dyn.load(file, DLLpath = DLLpath, ...)
  erreur : impossible de charger l'objet partagé
 '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
 dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so,
 6): Library not loaded: @rpath/libjvm.dylib
  Referenced from:
 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
  Reason: image not found
 
 
 Here are the Sys.getenv() in the 3 cases (terminal R, root or not, and
 Rstudio):
 Rstudio
 
 DYLD_FALLBACK_LIBRARY_PATH
 /Library/Frameworks/R.framework/Resources/lib:/Library/Frameworks/R.framework/Resources/lib:/Users/marcgirondot/lib:/usr/local/lib:/usr/lib
 DYLD_LIBRARY_PATH
 /Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server
 
 R (in terminal, non-root)
 
 DYLD_FALLBACK_LIBRARY_PATH
 /Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server
 
 R (in terminal, root)
 
 DYLD_FALLBACK_LIBRARY_PATH
 /Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server
 
 
 
 
 Le 31/01/2018 à 19:49, Simon Urbanek a écrit :
> It means that you are likely setting JAVA_HOME incorrectly in your user
> account. Don't set JAVA_HOME - you'll only likely break things by doing

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

2018-02-01 Thread Keith O'Hara

That looks like a bad idea to me—unless I am mistaken, you will need to update 
your link with every update to the JDK, otherwise R and RStudio could be out of 
sync when building/loading rJava.

(Consider contacting the RStudio people for a more permanent solution, as Simon 
suggested.)

> On Feb 1, 2018, at 12:22 AM, Marc Girondot  wrote:
> 
> This is indeed a problem with Rstudio:
> 
> I used the Rstudio 1.2.308 (development version) but the same occurred with 
> 1.1.419 version;
> > library("rJava")
> Erreur : package or namespace load failed for ‘rJava’:
>  .onLoad a échoué dans loadNamespace() pour 'rJava', détails :
>   appel : dyn.load(file, DLLpath = DLLpath, ...)
>   erreur : impossible de charger l'objet partagé 
> '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
> dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so,
>  6): Library not loaded: @rpath/libjvm.dylib
>   Referenced from: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
>   Reason: image not found
> 
> 1.1.419
> Sys.getenv() gives
> DYLD_FALLBACK_LIBRARY_PATH
> /Library/Frameworks/R.framework/Resources/lib:/Users/marcgirondot/lib:/usr/local/lib:/usr/lib::
> 1.2.308
> Sys.getenv() gives
> DYLD_FALLBACK_LIBRARY_PATH
> /Library/Frameworks/R.framework/Resources/lib:/Users/marcgirondot/lib:/usr/local/lib:/usr/lib::
> 
> R in terminal
> Sys.getenv() gives
> DYLD_FALLBACK_LIBRARY_PATH
> /Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server
> 
> I try:
> 
> cd /usr/local/lib
> sudo ln -s 
> /Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server/libjsig.dylib
>  libjsig.dylib
> sudo ln -s 
> /Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server/libjvm.dylib
>  libjvm.dylib
> 
> And I can load rJava package in Rstudio also now.
> 
> Thanks to everybody for your help !
> 
> Marc
> 
> 
> 
> Le 01/02/2018 à 01:23, Kevin Ushey a écrit :
>> What version of RStudio are you using? This particular issue should be
>> fixed in v1.1.419 of RStudio.
>> 
>> On Wed, Jan 31, 2018 at 11:48 AM, Marc Girondot  
>> wrote:
>>> Hi Simon,
>>> 
>>> Half solution ! Thanks !
>>> 
>>> I remove JAVA_HOME and when R is ran as root or non-root in terminal, rJava
>>> package can be loaded. Great !
>>> 
>>> But in Rstudio, I have still a problem (see bellow).
>>> 
>>> Any suggestion ?
>>> 
>>> Thanks
>>> 
>>> Marc
>>> 
 library(rJava)
>>> Erreur : package or namespace load failed for ‘rJava’:
>>>  .onLoad a échoué dans loadNamespace() pour 'rJava', détails :
>>>   appel : dyn.load(file, DLLpath = DLLpath, ...)
>>>   erreur : impossible de charger l'objet partagé
>>> '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so,
>>> 6): Library not loaded: @rpath/libjvm.dylib
>>>   Referenced from:
>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
>>>   Reason: image not found
>>> 
>>> 
>>> Here are the Sys.getenv() in the 3 cases (terminal R, root or not, and
>>> Rstudio):
>>> Rstudio
>>> 
>>> DYLD_FALLBACK_LIBRARY_PATH
>>> /Library/Frameworks/R.framework/Resources/lib:/Library/Frameworks/R.framework/Resources/lib:/Users/marcgirondot/lib:/usr/local/lib:/usr/lib
>>> DYLD_LIBRARY_PATH
>>> /Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server
>>> 
>>> R (in terminal, non-root)
>>> 
>>> DYLD_FALLBACK_LIBRARY_PATH
>>> /Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server
>>> 
>>> R (in terminal, root)
>>> 
>>> DYLD_FALLBACK_LIBRARY_PATH
>>> /Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server
>>> 
>>> 
>>> 
>>> 
>>> Le 31/01/2018 à 19:49, Simon Urbanek a écrit :
 It means that you are likely setting JAVA_HOME incorrectly in your user
 account. Don't set JAVA_HOME - you'll only likely break things by doing so.
 
 Cheers,
 Simon
 
 
 
> On Jan 31, 2018, at 10:52 AM, Marc Girondot 
> wrote:
> 
> Thanks for your help:
> 
> Here are some results; First in terminal:
> 
> belinda:~ marcgirondot$ locate libjvm.dylib
> /Applications/Xcode.app/Contents/Applications/Application
> Loader.app/Contents/itms/java/lib/server/libjvm.dylib
> /Library/Internet
> Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/server/libjvm.dylib
> 
> /Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries/libjvm.dylib
> 
> /Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/jre/lib/server/libjvm.dylib
> 
>

Re: [R-SIG-Mac] help: change of e-mail address

2018-02-01 Thread peter dalgaard

Um, no we can't! 

You are writing to all subscribers of the list and we cannot mess with 
eachother's subscriptions. 

In case of administrative trouble, you need 

>  r-sig-mac-ow...@r-project.org

However, are you _sure_ that it didn't work to follow the instructions at 
https://stat.ethz.ch/mailman/listinfo/r-sig-mac ?

Notice in particular that the system cannot retroactively change recipients on 
things that have already been sent, and that mails can sit in mailer queues for 
some time. I.e., you may recieve mails to the old address for a while until the 
new address takes effect.

-pd

> On 1 Feb 2018, at 08:39 , Hagens, M. (Mathilde)  wrote:
> 
> To whom it may concern,
> 
> I've been trying to change my e-mail address unsuccessfully via the World 
> Wide Web. Could you please change my e-mail address to 
> mathilde.hag...@wur.nl? 
> 
> Thank you,
> Mathilde
> 
> Dr. M. (Mathilde) Hagens | Assistant Professor | Department of Soil Quality | 
> Wageningen University & Research | Droevendaalsesteeg 4, 6708 PB Wageningen, 
> the Netherlands | tel. +31 317 487 775 | 
> www.wur.nl/en/Persons/Mathilde-dr.-M-Mathilde-Hagens.htm | Please note new 
> e-mail address: mathilde.hag...@wur.nl
> 
> 
> 
> From: R-SIG-Mac [r-sig-mac-boun...@r-project.org] on behalf of 
> r-sig-mac-requ...@r-project.org [r-sig-mac-requ...@r-project.org]
> Sent: Thursday, February 01, 2018 06:22
> To: r-sig-mac@r-project.org
> Subject: R-SIG-Mac Digest, Vol 180, Issue 1
> 
> Send R-SIG-Mac mailing list submissions to
>r-sig-mac@r-project.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> or, via email, send a message with subject or body 'help' to
>r-sig-mac-requ...@r-project.org
> 
> You can reach the person managing the list at
>r-sig-mac-ow...@r-project.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of R-SIG-Mac digest..."
> ___
> 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
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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

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

Re: [R-SIG-Mac] help: change of e-mail address

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