[Rd] [BULK] Re: status of Java & rJava?
Simon Urbanek
@|mon@urb@nek @end|ng |rom R-project@org
Sun Mar 29 05:46:54 CEST 2020
Spencer,
1) you don't seem to have working tools on your Mac (check config.log)
2) on Windows you don't have JDK installed
I would strongly recommend using the CRAN binaries of rJava 0.9-12 unless you know what you're doing and have all the tools (for Mac use https://mac.R-project.org as mirror since there was a hiccup with macOS sync across mirrors).
Cheers,
Simon
> On 29/03/2020, at 4:29 PM, Spencer Graves <spencer.graves using prodsyse.com> wrote:
>
> Hi, Simon et al.:
>
>
> My attempts to install rJava 0.9-12 from source failed under both macOS 10.15.4 and Windows 10.
>
>
> Below please find what I got just now trying "update.packages()" and selecting "install from sources" on both computers followed by "sessionInfo()" in each case.
>
>
> Thanks for your help.
> Spencer Graves
>
>
> update.packages()
> rJava :
> Version 0.9-11 installed in /Library/Frameworks/R.framework/Versions/3.6/Resources/library
> Version 0.9-12 available at https://cran.rstudio.com
> Update? (Yes/no/cancel) y
> sf :
> Version 0.8-1 installed in /Library/Frameworks/R.framework/Versions/3.6/Resources/library
> Version 0.9-0 available at https://cran.rstudio.com
> Update? (Yes/no/cancel) n
> XLConnect :
> Version 0.2-15 installed in /Library/Frameworks/R.framework/Versions/3.6/Resources/library
> Version 1.0.1 available at https://cran.rstudio.com
> Update? (Yes/no/cancel) n
>
> There is a binary version available but the
> source version is later:
> binary source needs_compilation
> rJava 0.9-11 0.9-12 TRUE
>
> Do you want to install from sources the package which needs compilation? (Yes/no/cancel) y
> installing the source package ‘rJava’
>
> trying URL 'https://cran.rstudio.com/src/contrib/rJava_0.9-12.tar.gz'
> Content type 'application/x-gzip' length 1103629 bytes (1.1 MB)
> ==================================================
> downloaded 1.1 MB
>
> * installing *source* package ‘rJava’ ...
> ** package ‘rJava’ successfully unpacked and MD5 sums checked
> ** using staged installation
> checking for gcc... clang
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... configure: error: in `/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjr0000gn/T/Rtmpm3rVc5/R.INSTALL5d09696e941d/rJava':
> configure: error: cannot run C compiled programs.
> If you meant to cross compile, use `--host'.
> See `config.log' for more details
> ERROR: configuration failed for package ‘rJava’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava’
> * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava’
>
> The downloaded source packages are in
> ‘/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjr0000gn/T/RtmpbxyWRI/downloaded_packages’
> Warning message:
> In install.packages(update[instlib == l, "Package"], l, repos = repos, :
> installation of package ‘rJava’ had non-zero exit status
> > sessionInfo()
> R version 3.6.3 (2020-02-29)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Catalina 10.15.4
>
> Matrix products: default
> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets
> [6] methods base
>
> loaded via a namespace (and not attached):
> [1] compiler_3.6.3 tools_3.6.3
>
>
>
> > update.packages()
> rJava :
> Version 0.9-11 installed in C:/Program Files/R/R-3.6.3/library
> Version 0.9-12 available at https://cran.rstudio.com
>
> There is a binary version available but
> the source version is later:
> binary source needs_compilation
> rJava 0.9-11 0.9-12 TRUE
>
> installing the source package 'rJava'
>
> trying URL 'https://cran.rstudio.com/src/contrib/rJava_0.9-12.tar.gz'
> Content type 'application/x-gzip' length 1103629 bytes (1.1 MB)
> downloaded 1.1 MB
>
> * installing *source* package 'rJava' ...
> ** package 'rJava' successfully unpacked and MD5 sums checked
> ** using staged installation
> Generate Windows-specific files (src/jvm-w32) ...
> make: Entering directory '/Users/spenc/AppData/Local/Temp/RtmpQbnYkA/R.INSTALL8ec5478248a/rJava/src/jvm-w32'
> c:/Rtools/mingw_64/bin/dlltool --as c:/Rtools/mingw_64/bin/as --input-def jvm64.def --kill-at --dllname jvm.dll --output-lib libjvm.dll.a
> c:/Rtools/mingw_64/bin/gcc -O2 -c -o findjava.o findjava.c
> c:/Rtools/mingw_64/bin/gcc -s -o findjava.exe findjava.o
> make: Leaving directory '/Users/spenc/AppData/Local/Temp/RtmpQbnYkA/R.INSTALL8ec5478248a/rJava/src/jvm-w32'
> Find Java...
> JAVA_HOME=C:/PROGRA~1/Java/JRE18~1.0_2
> === Building JRI ===
> JAVA_HOME=C:/PROGRA~1/Java/JRE18~1.0_2
> R_HOME=C:/PROGRA~1/R/R-36~1.3
> JDK has no javah.exe - using javac -h . instead
> Creating Makefiles ...
> Configuration done.
> make -C src JRI.jar
> make[1]: Entering directory '/Users/spenc/AppData/Local/Temp/RtmpQbnYkA/R.INSTALL8ec5478248a/rJava/jri/src'
> C:/PROGRA~1/Java/JRE18~1.0_2/bin/javac -h . -d . ../RList.java ../RBool.java ../RVector.java ../RMainLoopCallbacks.java ../RConsoleOutputStream.java ../Mutex.java ../Rengine.java ../REXP.java ../RFactor.java ../package-info.java
> sh: C:/PROGRA~1/Java/JRE18~1.0_2/bin/javac: No such file or directory
> make[1]: *** [Makefile.all:41: org/rosuda/JRI/Rengine.class] Error 127
> make[1]: Leaving directory '/Users/spenc/AppData/Local/Temp/RtmpQbnYkA/R.INSTALL8ec5478248a/rJava/jri/src'
> make: *** [Makefile.all:19: src/JRI.jar] Error 2
> **** WARNING: JRI could NOT be built
> Set IGNORE=1 if you want to build rJava anyway.
> ERROR: configuration failed for package 'rJava'
> * removing 'C:/Program Files/R/R-3.6.3/library/rJava'
> * restoring previous 'C:/Program Files/R/R-3.6.3/library/rJava'
>
> The downloaded source packages are in
> 'C:\Users\spenc\AppData\Local\Temp\RtmpsDQIkn\downloaded_packages'
> Warning message:
> In install.packages(update[instlib == l, "Package"], l, repos = repos, :
> installation of package 'rJava' had non-zero exit status
>
> > sessionInfo()
> R version 3.6.3 (2020-02-29)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 18362)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils
> [5] datasets methods base
>
> loaded via a namespace (and not attached):
> [1] compiler_3.6.3 tools_3.6.3
>
>
> On 2020-03-28 22:07, Simon Urbanek wrote:
>> Spencer,
>>
>> you could argue that Java is dead since Oracle effectively killed it by removing all public downloads, but if you manage to get hold of a Java installation then it works just fine with R. To my best knowledge there has never been an issue if you installed rJava from source. macOS Catalina has made binary distributions impossible due to additional restrictions on run-time, but even that has been how solved with the release of rJava 0.9-12, so please make sure you use the latest rJava. In most cases that I have seen issues were caused by incorrect configuration (setting JAVA_HOME incorrectly [do NOT set it unless you know what you're doing!], not installing Java for the same architecture as R etc.). If you have any issues feel free to report them. rJava 0.9-12 has quite a few changes that try to detect user errors better and report them so I strongly suggest users to upgrade.
>>
>> Cheers,
>> Simon
>>
>>
>>> On 29/03/2020, at 9:18 AM, Spencer Graves <spencer.graves using prodsyse.com> wrote:
>>>
>>> Hello, All:
>>>
>>>
>>> Is Java being deprecated for R?
>>>
>>>
>>> I ask, because I've been unable to get rJava 0.9-11 to work under either macOS 10.15 or Windows 10, and I can't get rJava 0.9-12 to install -- and my Ecfun package uses it: I can't get "R CMD build Ecfun" to work on my Mac nor "R CMD check Ecfun_0.2-4" under Windows. Travis CI builds "https://github.com/sbgraves237/Ecfun" just fine.
>>>
>>>
>>> The rJava maintainer, Simon Urbanek, has kindly responded to two of my three emails on this since 2020-03-20, but I've so far been unable to translate his suggestions into fixes for these problems.
>>>
>>>
>>> Should I remove rJava from Ecfun and see what breaks, then see if I can work around that? Should I provide the error messages I get for rJava from "update.packages()" and / or library(rJava) on both machines, with sessionInfo() to this list or to Stack Exchange or Stack Overflow?
>>>
>>>
>>> Since I'm getting so many problems with rJava on under both macOS and Windows 10, that suggests to me that potential users could have similar problems, and I should try to remove rJava from Ecfun.
>>>
>>>
>>> What do you think?
>>> Thanks,
>>> Spencer Graves
>>>
>>> ______________________________________________
>>> R-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>
More information about the R-devel
mailing list