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Morkus

2017-Oct-21 11:35 UTC

[R] Problem when trying to run Java in R:

Hello All,

Although running Java from R used to work, for some mysterious reason, it's
stopped.

Today when I tried to load a basic JDBC driver (or the sample .jinit()) code, I
got:

- JavaVM: requested Java version ((null)) not available. Using Java at
"" instead.

- JavaVM: Failed to load JVM: /bundle/Libraries/libserver.dylib

- JavaVM FATAL: Failed to load the jvm library.

I saw postings on StackOverflow about this issue, but none of the suggested
fixes helped.

I'm on Mac OS 10.13.

My JAVA_HOME is:
/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home

java -version
java version "1.8.0_144"
Java(TM) SE Runtime Environment (build 1.8.0_144-b01)
Java HotSpot(TM) 64-Bit Server VM (build 25.144-b01, mixed mode)

I'm using R: 3.3.3

Here is sample code that also throws this same error:

    library(rJava)
    .jinit() # this starts the JVM
    s <- .jnew("java/lang/String", "Hello World!")

(this is the "hello world" equivalent from the rJava site)

----

I also tried to use Java 7 (rev. 51), which used to work, but that still fails.

Also tried a fresh install of R/RStudio on another machine with the same results
(same Java version, etc., however).

I suspect Java itself is working fine since JDBC code from Java programs has no
issues.

Not sure why loading Java in R stopped working, but would appreciate any
suggestions.

Thanks very much,

Sent from [ProtonMail](https://protonmail.com), Swiss-based encrypted email.
	[[alternative HTML version deleted]]

Jeff Newmiller

2017-Oct-23 01:10 UTC

head link

[R] Problem when trying to run Java in R:

I suggest asking a Mac-OS-specific question like this on the r-sig-mac mailing
list. A common problem is attempting to access a 64-bit implementation of Java
from a 32-bit version of R, or vice versa, but you may want to include the
output of sessionInfo() and a reproducible example (both input and output) when
you ask your question again to help them help you.
-- 
Sent from my phone. Please excuse my brevity.

On October 21, 2017 4:35:19 AM PDT, Morkus via R-help <r-help at
r-project.org> wrote:>Hello All,
>
>Although running Java from R used to work, for some mysterious reason,
>it's stopped.
>
>Today when I tried to load a basic JDBC driver (or the sample .jinit())
>code, I got:
>
>- JavaVM: requested Java version ((null)) not available. Using Java at
>"" instead.
>
>- JavaVM: Failed to load JVM: /bundle/Libraries/libserver.dylib
>
>- JavaVM FATAL: Failed to load the jvm library.
>
>I saw postings on StackOverflow about this issue, but none of the
>suggested fixes helped.
>
>I'm on Mac OS 10.13.
>
>My JAVA_HOME is:
>/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home
>
>java -version
>java version "1.8.0_144"
>Java(TM) SE Runtime Environment (build 1.8.0_144-b01)
>Java HotSpot(TM) 64-Bit Server VM (build 25.144-b01, mixed mode)
>
>I'm using R: 3.3.3
>
>Here is sample code that also throws this same error:
>
>    library(rJava)
>    .jinit() # this starts the JVM
>    s <- .jnew("java/lang/String", "Hello World!")
>
>(this is the "hello world" equivalent from the rJava site)
>
>----
>
>I also tried to use Java 7 (rev. 51), which used to work, but that
>still fails.
>
>Also tried a fresh install of R/RStudio on another machine with the
>same results (same Java version, etc., however).
>
>I suspect Java itself is working fine since JDBC code from Java
>programs has no issues.
>
>Not sure why loading Java in R stopped working, but would appreciate
>any suggestions.
>
>Thanks very much,
>
>Sent from [ProtonMail](https://protonmail.com), Swiss-based encrypted
>email.
>	[[alternative HTML version deleted]]
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

David Winsemius

2017-Oct-23 02:17 UTC

head link

[R] Problem when trying to run Java in R:

> On Oct 21, 2017, at 4:35 AM, Morkus via R-help <r-help at
r-project.org> wrote:
> 
> Hello All,
> 
> Although running Java from R used to work, for some mysterious reason,
it's stopped.
> 
> Today when I tried to load a basic JDBC driver (or the sample .jinit())
code, I got:
> 
> - JavaVM: requested Java version ((null)) not available. Using Java at
"" instead.
> 
> - JavaVM: Failed to load JVM: /bundle/Libraries/libserver.dylib
> 
> - JavaVM FATAL: Failed to load the jvm library.
> 
> I saw postings on StackOverflow about this issue, but none of the suggested
fixes helped.
> 
> I'm on Mac OS 10.13.
> 
> My JAVA_HOME is:
/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home
> 
> java -version
> java version "1.8.0_144"
I am not sure why but I do notice that currently:  Java Recommended Version 8
Update 151

AND this quoted warning is on the current download page .. 

macOS Sierra 10.12 users: A few issues have been reported on Sierra. See FAQ for
more information.

Others have reported success with this at the Terminal command line:

sudo R CMD javareconf

export
JAVA_HOME="/Library/Java/JavaVirtualMachines/jdk1.8.0.jdk/Contents/Home"
export
LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home/jre/lib/server

#AND then ....  at the R command line:

install.packages('rJava', type='source')
> Java(TM) SE Runtime Environment (build 1.8.0_144-b01)
> Java HotSpot(TM) 64-Bit Server VM (build 25.144-b01, mixed mode)
> 
> I'm using R: 3.3.3
> 
> Here is sample code that also throws this same error:
> 
>    library(rJava)
>    .jinit() # this starts the JVM
>    s <- .jnew("java/lang/String", "Hello World!")
I don't get any error running:

 sessionInfo()

R version 3.4.2 Patched (2017-10-04 r73465)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.4/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] grDevices utils     datasets  graphics  stats     methods   base     

other attached packages:
 [1] rJava_0.9-8     dplyr_0.7.2     gmodels_2.16.2  Matrix_1.2-11  
xgboost_0.6-4
 [6] rms_5.1-1       SparseM_1.77    Hmisc_4.0-3     ggplot2_2.2.1  
Formula_1.2-1
[11] survival_2.41-3 sos_2.0-0       brew_1.0-6      lattice_0.20-35

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11        mvtnorm_1.0-6       gtools_3.5.0       
visNetwork_1.0.3
 [5] zoo_1.8-0           assertthat_0.2.0    digest_0.6.12       R6_2.2.2
 [9] plyr_1.8.4          backports_1.1.0     acepack_1.4.1      
MatrixModels_0.4-1
[13] rlang_0.1.2         lazyeval_0.2.0      mxnet_0.10.1        multcomp_1.4-6
[17] gdata_2.17.0        rstudioapi_0.6      data.table_1.10.4   rpart_4.1-11
[21] gamlss.data_5.0-0   checkmate_1.8.3     DiagrammeR_0.9.0    splines_3.4.2
[25] stringr_1.2.0       foreign_0.8-69      htmlwidgets_0.8     igraph_1.0.1
[29] munsell_0.4.3       compiler_3.4.2      influenceR_0.1.0    rgexf_0.15.3
[33] pkgconfig_2.0.1     gamlss_5.0-2        base64enc_0.1-3    
gamlss.dist_5.0-0
[37] htmltools_0.3.6     nnet_7.3-12         tibble_1.3.1        gridExtra_2.2.1
[41] htmlTable_1.9       codetools_0.2-15    XML_3.98-1.7       
viridisLite_0.2.0
[45] MASS_7.3-47         grid_3.4.2          nlme_3.1-131       
polspline_1.1.12
[49] jsonlite_1.5        gtable_0.2.0        magrittr_1.5        scales_0.4.1
[53] stringi_1.1.5       viridis_0.4.0       bindrcpp_0.2       
latticeExtra_0.6-28
[57] sandwich_2.3-4      TH.data_1.0-8       RColorBrewer_1.1-2  tools_3.4.2
[61] glue_1.1.1          Rook_1.1-1          parallel_3.4.2     
colorspace_1.3-2
[65] cluster_2.0.6       knitr_1.15.1        bindr_0.1           quantreg_5.33

Running this produces:

Sys.getenv()[grep("jre", Sys.getenv())]
#DYLD_LIBRARY_PATH          
/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/lib/server


--
David. > 
> (this is the "hello world" equivalent from the rJava site)
> 
> ----
> 
> I also tried to use Java 7 (rev. 51), which used to work, but that still
fails.
> 
> Also tried a fresh install of R/RStudio on another machine with the same
results (same Java version, etc., however).
> 
> I suspect Java itself is working fine since JDBC code from Java programs
has no issues.
> 
> Not sure why loading Java in R stopped working, but would appreciate any
suggestions.
> 
> Thanks very much,
> 
> Sent from [ProtonMail](https://protonmail.com), Swiss-based encrypted
email.
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.' 
-Gehm's Corollary to Clarke's Third Law

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