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.gra...@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.gra...@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@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
