On 29/03/2020, at 4:29 PM, Spencer Graves <spencer.graves at 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
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
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
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 at 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