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
Hi Spencer, I'm also having problems getting rJava to work on Mac OS X. -G On Sat, Mar 28, 2020 at 4:19 PM 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 > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- "Whereas true religion and good morals are the only solid foundations of public liberty and happiness . . . it is hereby earnestly recommended to the several States to take the most effectual measures for the encouragement thereof." Continental Congress, 1778 [[alternative HTML version deleted]]
I, too, had encountered problems with Java on Windows 10 while I was trying to install the package "xlsx." I tried the fixes I found online, but to no avail. Thanks & Best regards, Ravi ________________________________ From: R-devel <r-devel-bounces at r-project.org> on behalf of Gregory Warnes <greg at warnes.net> Sent: Saturday, March 28, 2020 8:14:45 PM To: Spencer Graves Cc: r-devel at r-project.org Subject: Re: [Rd] status of Java & rJava? Hi Spencer, I'm also having problems getting rJava to work on Mac OS X. -G On Sat, Mar 28, 2020 at 4:19 PM 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 > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- "Whereas true religion and good morals are the only solid foundations of public liberty and happiness . . . it is hereby earnestly recommended to the several States to take the most effectual measures for the encouragement thereof." Continental Congress, 1778 [[alternative HTML version deleted]] ______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]]
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 > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
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 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 >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >>
On 29/03/2020 04:07, 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.There is OpenJDK, and https://adoptopenjdk.net provides binaries for macOS, including the preferred Java 11 LTS. I just re-checked that, and after env JAVA_HOME=/Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/Home R CMD javareconf I was able to install from source and check rJava 0.9-12 in 4.0.0 alpha. For the CRAN binary of 3.6.3 I had to make sure I was using clang 7: 'clang' defaults to that in the Apple CLT which does not support -fopenmp -- but the binary package just worked. [All on Catalina.] -- Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford