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Cannot load rJava | unable to load shared object rJava.so #283

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isaac2lord opened this issue Nov 5, 2021 · 3 comments
Closed

Cannot load rJava | unable to load shared object rJava.so #283

isaac2lord opened this issue Nov 5, 2021 · 3 comments

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@isaac2lord
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isaac2lord commented Nov 5, 2021 •
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Hello there,

I am unable to load the library after installation.

SessionInfo

R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.3 (Ootpa)

Matrix products: default
BLAS:   /opt/microsoft/ropen/4.0.2/lib64/R/lib/libRblas.so
LAPACK: /opt/microsoft/ropen/4.0.2/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DBI_1.1.0            RevoUtils_11.0.2     RevoUtilsMath_11.0.0

loaded via a namespace (and not attached):
[1] compiler_4.0.2 parallel_4.0.2 tools_4.0.2

R_HOME/etc permissions

xxx@yyyy:/opt/microsoft/ropen/4.0.2/lib64/R/etc
$ ls -al
total 36
drwxrwxrwx.  2 root root  131 Nov  5 10:16 .
drwxr-xr-x. 11 root root  157 Sep 29 20:22 ..
-rwxrwxrwx.  1 root root  209 Aug 12  2020 javaconf
-rw-rwxrwx.  1 root root  830 Nov  5 10:16 ldpaths
-rw-rwxrwx.  1 root root 6200 Nov  5 10:16 Makeconf
-rwxrwxrwx.  1 root root 1447 Sep  3  2020 Renviron
-rw-rwxrwx.  1 root root   72 Sep  3  2020 Renviron.site
-rwxrwxrwx.  1 root root 1095 Aug 12  2020 repositories
-rw-rwxrwx.  1 root root 7187 Sep  3  2020 Rprofile.site

JAVA Version

$ java -version
openjdk version "1.8.0_242"
OpenJDK Runtime Environment (AdoptOpenJDK)(build 1.8.0_242-b08)
OpenJDK 64-Bit Server VM (AdoptOpenJDK)(build 25.242-b08, mixed mode)

Commands Ran and outputs

install.packages("rJava")

Installing package into ‘.../app/R40_Library’
(as ‘lib’ is unspecified)
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  649k  100  649k    0     0   287k      0  0:00:02  0:00:02 --:--:--  287k
Microsoft R Open 4.0.2
The enhanced R distribution from Microsoft
Microsoft packages Copyright (C) 2020 Microsoft Corporation

Using the Intel MKL for parallel mathematical computing (using 8 cores).

Default CRAN mirror snapshot taken on 2020-07-16.
See: https://mran.microsoft.com/.

* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc -std=gnu99
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... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc -std=gnu99 supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/bin/java'
archiver    : '/bin/jar'
compiler    : '/bin/javac'
header prep.: '/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux'
java libs   : '-L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/lib/amd64/server -ljvm'
checking whether Java run-time works... yes
checking whether -Xrs is supported... yes
checking whether -Xrs will be used... yes
checking whether JVM will be loaded dynamically... no
checking whether JNI programs can be compiled... yes
checking whether JNI programs run... yes
checking JNI data types... ok
checking whether JRI should be compiled (autodetect)... yes
checking whether debugging output should be enabled... no
checking whether memory profiling is desired... no
checking whether threads support is requested... no
checking whether callbacks support is requested... no
checking whether JNI cache support is requested... no
checking whether headless init is enabled... no
checking whether JRI is requested... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
=== configuring in jri (/tmp/Rtmp9CxMGW/R.INSTALL21c6f633549029/rJava/jri)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local'  --cache-file=/dev/null --srcdir=.
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc -std=gnu99
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... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking Java version... 1.8.0_302
checking Java compatibility version (integer)... 8
checking whether /bin/javah actually works... yes
checking for target flags...  -target 1.4 -source 1.4
checking whether Java interpreter works... checking whether JNI programs can be compiled... yes
checking whether JNI programs can be run... yes
checking JNI data types... ok
checking whether Rinterface.h exports R_CStackXXX variables... yes
checking whether Rinterface.h exports R_SignalHandlers... yes
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating Makefile
config.status: creating run
config.status: creating src/config.h
** libs
gcc -std=gnu99 -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c Rglue.c -o Rglue.o
gcc -std=gnu99 -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c arrayc.c -o arrayc.o
gcc -std=gnu99 -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c callJNI.c -o callJNI.o
gcc -std=gnu99 -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c callback.c -o callback.o
gcc -std=gnu99 -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c fields.c -o fields.o
gcc -std=gnu99 -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c jri_glue.c -o jri_glue.o
gcc -std=gnu99 -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c loader.c -o loader.o
gcc -std=gnu99 -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c otables.c -o otables.o
gcc -std=gnu99 -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c rJava.c -o rJava.o
gcc -std=gnu99 -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c registration.c -o registration.o
gcc -std=gnu99 -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG -I. -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c tools.c -o tools.o
gcc -std=gnu99 -shared -L/opt/microsoft/ropen/4.0.2/lib64/R/lib -o rJava.so Rglue.o arrayc.o callJNI.o callback.o fields.o init.o jri_glue.o loader.o otables.o rJava.o registration.o tools.o -L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/lib/amd64/server -ljvm -L/opt/microsoft/ropen/4.0.2/lib64/R/lib -lR
(cd ../jri && make)
make[1]: Entering directory '/tmp/Rtmp9CxMGW/R.INSTALL21c6f633549029/rJava/jri'
make -C src JRI.jar
make[2]: Entering directory '/tmp/Rtmp9CxMGW/R.INSTALL21c6f633549029/rJava/jri/src'
/bin/javac -target 1.4 -source 1.4 -d . ../RConsoleOutputStream.java ../RFactor.java ../REXP.java ../Rengine.java ../RList.java ../Mutex.java ../package-info.java ../RMainLoopCallbacks.java ../RVector.java ../RBool.java
warning: [options] bootstrap class path not set in conjunction with -source 1.4
warning: [options] source value 1.4 is obsolete and will be removed in a future release
warning: [options] target value 1.4 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
4 warnings
if [ -n "/bin/javah" ]; then /bin/javah -d . -classpath . org.rosuda.JRI.Rengine; fi
gcc -std=gnu99 -c -o Rengine.o Rengine.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DU_STATIC_IMPLEMENTATION -O2 -g  -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -fpic -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux -I/opt/microsoft/ropen/4.0.2/lib64/R/include -I/opt/microsoft/ropen/4.0.2/lib64/R/include
gcc -std=gnu99 -c -o jri.o jri.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DU_STATIC_IMPLEMENTATION -O2 -g  -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -fpic -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux -I/opt/microsoft/ropen/4.0.2/lib64/R/include -I/opt/microsoft/ropen/4.0.2/lib64/R/include
gcc -std=gnu99 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DU_STATIC_IMPLEMENTATION -O2 -g  -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -fpic -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux -I/opt/microsoft/ropen/4.0.2/lib64/R/include -I/opt/microsoft/ropen/4.0.2/lib64/R/include
gcc -std=gnu99 -c -o Rinit.o Rinit.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DU_STATIC_IMPLEMENTATION -O2 -g  -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -fpic -I/opt/microsoft/ropen/4.0.2/lib64/R/include -I/opt/microsoft/ropen/4.0.2/lib64/R/include
gcc -std=gnu99 -c -o globals.o globals.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DU_STATIC_IMPLEMENTATION -O2 -g  -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -fpic -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux
gcc -std=gnu99 -c -o rjava.o rjava.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DU_STATIC_IMPLEMENTATION -O2 -g  -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux  -fpic -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/../include/linux
gcc -std=gnu99 -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o  -shared -L/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64/jre/lib/amd64/server -ljvm -Wl,--export-dynamic -fopenmp  -L/opt/microsoft/ropen/4.0.2/lib64/R/lib -lR 
/bin/javac -target 1.4 -source 1.4 -d . ../package-info.java ../RFactor.java ../REXP.java ../RList.java ../Mutex.java ../RVector.java ../RBool.java ../RConsoleOutputStream.java ../Rengine.java ../RMainLoopCallbacks.java
warning: [options] bootstrap class path not set in conjunction with -source 1.4
warning: [options] source value 1.4 is obsolete and will be removed in a future release
warning: [options] target value 1.4 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
4 warnings
/bin/jar fc JRI.jar org libjri.so
make[2]: Leaving directory '/tmp/Rtmp9CxMGW/R.INSTALL21c6f633549029/rJava/jri/src'
rm -f libjri.so
cp src/libjri.so libjri.so
/bin/javac -target 1.4 -source 1.4 -classpath src/JRI.jar -d examples examples/rtest.java
warning: [options] bootstrap class path not set in conjunction with -source 1.4
warning: [options] source value 1.4 is obsolete and will be removed in a future release
warning: [options] target value 1.4 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
Note: examples/rtest.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
4 warnings
/bin/javac -target 1.4 -source 1.4 -classpath src/JRI.jar -d examples examples/rtest2.java
warning: [options] bootstrap class path not set in conjunction with -source 1.4
warning: [options] source value 1.4 is obsolete and will be removed in a future release
warning: [options] target value 1.4 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
Note: examples/rtest2.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
4 warnings
make[1]: Leaving directory '/tmp/Rtmp9CxMGW/R.INSTALL21c6f633549029/rJava/jri'
installing via 'install.libs.R' to /.../app/R40_Library/00LOCK-rJava/00new/rJava
** R
** inst
** byte-compile and prepare package for lazy loading
Microsoft R Open 4.0.2
The enhanced R distribution from Microsoft
Microsoft packages Copyright (C) 2020 Microsoft Corporation

Using the Intel MKL for parallel mathematical computing (using 8 cores).

Default CRAN mirror snapshot taken on 2020-07-16.
See: https://mran.microsoft.com/.

** help
*** installing help indices
** building package indices
Microsoft R Open 4.0.2
The enhanced R distribution from Microsoft
Microsoft packages Copyright (C) 2020 Microsoft Corporation

Using the Intel MKL for parallel mathematical computing (using 8 cores).

Default CRAN mirror snapshot taken on 2020-07-16.
See: https://mran.microsoft.com/.

** testing if installed package can be loaded from temporary location
Microsoft R Open 4.0.2
The enhanced R distribution from Microsoft
Microsoft packages Copyright (C) 2020 Microsoft Corporation

Using the Intel MKL for parallel mathematical computing (using 8 cores).

Default CRAN mirror snapshot taken on 2020-07-16.
See: https://mran.microsoft.com/.

** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Microsoft R Open 4.0.2
The enhanced R distribution from Microsoft
Microsoft packages Copyright (C) 2020 Microsoft Corporation

Using the Intel MKL for parallel mathematical computing (using 8 cores).

Default CRAN mirror snapshot taken on 2020-07-16.
See: https://mran.microsoft.com/.

** testing if installed package keeps a record of temporary installation path
* DONE (rJava)

Error

> library(rJava)
Error: package or namespace load failed for ‘rJava’:
 .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/.../app/R40_Library/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory
@isaac2lord isaac2lord changed the title Cannot Install rJava on R4.0.2 Cannot load rJava library after installation Nov 5, 2021
@isaac2lord isaac2lord changed the title Cannot load rJava library after installation Cannot load rJava | unable to load shared object rJava.so Nov 5, 2021
@s-u
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s-u commented Nov 12, 2021

The error typically means that your R is not configured properly for your JVM location. Since you are using 3rd party distribution of R, please contact Microsoft for support.

In regular R you would use R CMD javareconf to make sure R is configured for your Java. In technical terms, R records the location of Java in $R_HOME/etc/ldpaths so if your R is configured properly you will see Java included in LD_LIBRARY_PATH, e.g.:

> Sys.getenv("LD_LIBRARY_PATH")
[1] "/usr/R/devel/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server"

The path containing libjvm.so must be listed there. If you don't see your JDK there then your R is not properly configured.

@isaac2lord
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Thanks for replying.

I have already run R CMD javareconf before installation, and I think it sets everything up appropriately.

Sys.getenv("LD_LIBRARY_PATH")
[1] "/opt/microsoft/ropen/4.0.2/lib64/R/lib:/lib:/builddir/vendor/build/lib:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.41.x86_64/jre/lib/amd64/server"

I found this response in stackoverflow but not sure if it's relevant to this error or not? This seems to be an RStudio thing, but I get the same error when trying to load rJava at CLI.

@isaac2lord
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I had to stop and start RStudio session after running that R CMD javareconf for things to get completely effective.

sudo systemctl stop rstudio-server
sudo systemctl start rstudio-server

Thanks for the hints @s-u

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