Develop Reference

Installing rJava on a Mac

I'm trying to install the rJava package for Rstudio on a Mac. I use the steps provided by this Github workshop. I ran in trouble with step 2:
#If you are using a Mac machine, an additional step may be needed before loading rJava package
#dyn.load('/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/server/libjvm.dylib')
library("rJava")
This is the R script I used with the console output:
> dyn.load('/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/server/libjvm.dylib')
> library("rJava")
Output:
> dyn.load('/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/server/libjvm.dylib')
Error in dyn.load("/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/server/libjvm.dylib") :
unable to load shared object '/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/server/libjvm.dylib':
dlopen(/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/server/libjvm.dylib, 0x0006): tried: '/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/server/libjvm.dylib' (no such file)
> library("rJava")
Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(jli, FALSE)
error: unable to load shared object '/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/jli/libjli.dylib':
dlopen(/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/jli/libjli.dylib, 0x000A): tried: '/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/jli/libjli.dylib' (mach-o file, but is an incompatible architecture (have (x86_64), need (arm64e)))

openJDK build on solaris 10: Format error: shdr table truncated

I am trying to build openJDK8 in Solaris 10.
Solaris:
uname -a
o/p: SunOS xxxx 5.10 Generic_148889-05 i86pc i386 i86pc
I followed the steps mentioned in https://hg.openjdk.java.net/jdk8u/jdk8u/raw-file/tip/README-builds.html#solaris
Installed necessary packages to build openJDK such as Mercurial, gmake, freetype, cups and xRender from openCSW.
I've downloaded jdk8 from Mercurials and got source.
bash ./configure is success. After that when i run gmake all getting below error.
Making libjvm_db.so
Opening 'libjvm_db.so' for update
No SHF_ALLOC flags needed to be cleared.
Done with 'libjvm_db.so'
Computing CRC for 'libjvm_db.debuginfo'
Opening 'libjvm_db.so' for update
Adding ELF data for new section name
Adding ELF data for debug_info_path value
Saving updates to 'libjvm_db.so'
Done updating 'libjvm_db.so'
/usr/ccs/bin/nm: g1CollectedHeap.o: Format error: shdr table truncated
ld: warning: symbol '__JvmOffsets' has differing types:
(file JvmOffsets.o type=OBJT; file dtrace.o type=FUNC);
ld: warning: symbol 'CodeCache::_heap' has differing types:
(file codeCache.o type=OBJT; file dtrace.o type=FUNC);
ld: warning: symbol 'BufferBlob::__vtbl' has differing types:
(file codeBlob.o type=OBJT; file dtrace.o type=FUNC);
ld: fatal: file g1CollectedHeap.o: Format error: shdr table truncated
ld: fatal: file processing errors. No output written to libjvm.so
gmake[6]: *** [libjvm.so] Error 2
gmake[5]: *** [the_vm] Error 2
gmake[4]: *** [product] Error 2
gmake[3]: *** [generic_build2] Error 2
gmake[2]: *** [product] Error 2
gmake[1]: *** [/export/home/openjdk/build/solaris-x86_64-normal-server-release/hotspot/_hotspot.timestamp] Error 2
gmake: *** [hotspot-only] Error 2
Can anyone point out how to resolve this error.

rJava: non-zero exit status

I have been trying to install rJava using the following commands:
install.packages('rJava',,'http://www.rforge.net/')
or
install.packages('rJava', type = 'source', INSTALL_opts='--merge-multiarch')
but each time I fail due to this error:
WARNING: JRI could NOT be built Set IGNORE=1 if you want to build
rJava anyway. ERROR: configuration failed for package 'rJava'. I have uninstalled and re-installed both version of java on my machine but still no help!
Does anyone has a solution ?
the full description is as below:
install for i386
installing source package 'rJava' ...
** package 'rJava' successfully unpacked and MD5 sums checked Generate Windows-specific files (src/jvm-w32) ... make: Entering directory
'/Users/ahkay/AppData/Local/Temp/RtmpKalUob/R.INSTALL192609e43b16/rJava/src/jvm-w32'
C:/Rtools/mingw_32/bin/dlltool --as C:/Rtools/mingw_32/bin/as
--input-def jvm.def --kill-at --dllname jvm.dll --output-lib libjvm.dll.a C:/Rtools/mingw_32/bin/gcc -O2 -c -o findjava.o
findjava.c C:/Rtools/mingw_32/bin/gcc -s -o findjava.exe findjava.o
make: Leaving directory
'/Users/ahkay/AppData/Local/Temp/RtmpKalUob/R.INSTALL192609e43b16/rJava/src/jvm-w32'
Find Java... ./configure.win: line 15: [: too many arguments
JAVA_HOME=C:/Program Files/Java/jre1.8.0_202
=== Building JRI === configure.win: line 21: [: too many arguments JAVA_HOME=C:/Program Files/Java/jre1.8.0_202
R_HOME=C:/PROGRA~1/R/R-35~1.2 Creating Makefiles ... Configuration
done. make -C src JRI.jar make[1]: Entering directory
'/Users/ahkay/AppData/Local/Temp/RtmpKalUob/R.INSTALL192609e43b16/rJava/jri/src'
C:/Program Files/Java/jre1.8.0_202/bin/javac -d . ../RList.java
../RBool.java ../RVector.java ../RMainLoopCallbacks.java
../RConsoleOutputStream.java ../Mutex.java ../Rengine.java
../REXP.java ../RFactor.java ../package-info.java make[1]: C:/Program:
Command not found make[1]: * [Makefile.all:41:
org/rosuda/JRI/Rengine.class] Error 127 make[1]: Leaving directory
'/Users/ahkay/AppData/Local/Temp/RtmpKalUob/R.INSTALL192609e43b16/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:/Users/ahkay/Documents/R/win-library/3.5/rJava' In R CMD INSTALL In R CMD INSTALL Warning in install.packages : installation
of package ‘rJava’ had non-zero exit status

I have experienced same issue and following approach worked for me in my Mac OS 10.13.6, you can apply minor OS related changes if using in other OS.
OS:
Installing rJava Manually
# curl -#ROL https://www.rforge.net/rJava/snapshot/rJava_0.9-8.tar.gz
# R CMD INSTALL rJava_0.9-8.tar.gz
# su -
Location you have installed R software, you might have different location.
# cd /Library/Frameworks/R.framework/Versions/3.5/Resources/lib
I found that different Java used by R, and forcing by softlink:
#ln -s /Library/Java/JavaVirtualMachines/jdk-10.0.2.jdk/Contents/Home/lib/server/libjvm.dylib libjvm.dylib
Remember, you need to put your JAVA_HOME in the following location in R Studio:
>Sys.setenv(JAVA_HOME = "/Library/Java/JavaVirtualMachines/jdk-10.0.2.jdk/Contents/Home")
Verifying rJava working in R Studio:
>require(rJava)

Build OpenJDK 9 in CentOS5

I was trying to build OpenJDK 9 in Centos 5. I used
sh ./configure --disable-warnings-as-errors
make all
I am getting the following error.
Building target 'all' in configuration 'linux-x86_64-normal-server-release'
/root/jdk9/build/linux-x86_64-normal-server-
release/support/native/java.base/libjava/io_util_md.o: In function
`handleSetLength':
/root/jdk9/jdk/src/java.base/unix/native/libjava/io_util_md.c:228:
undefined reference to `fallocate64'
collect2: ld returned 1 exit status
/usr/bin/objcopy: '/root/jdk9/build/linux-x86_64-normal-server-
release/support/modules_libs/java.base/libjava.so': No such file
gmake[3]: *** [/root/jdk9/build/linux-x86_64-normal-server-
release/support/modules_libs/java.base/libjava.so] Error 1
gmake[2]: *** [java.base-libs] Error 2
ERROR: Build failed for target 'all' in configuration 'linux-x86_64-normal-
server-release' (exit code 2)
=== Output from failing command(s) repeated here ===
* For target support_native_java.base_libjava_BUILD_LIBJAVA_link:
/root/jdk9/build/linux-x86_64-normal-server-
release/support/native/java.base/libjava/io_util_md.o: In function
`handleSetLength':
/root/jdk9/jdk/src/java.base/unix/native/libjava/io_util_md.c:228:
undefined reference to `fallocate64'
collect2: ld returned 1 exit status
* All command lines available in /root/jdk9/build/linux-x86_64-normal-
server-release/make-support/failure-logs.
=== End of repeated output ===
No indication of failed target found.
Hint: Try searching the build log for '] Error'.
Hint: See common/doc/building.html#troubleshooting for assistance.
make[1]: *** [main] Error 2
make: *** [all] Error 2
I also tried other make targets such as make images and make install. But still getting the same error. My GCC version is gcc (GCC) 4.4.7 which I manually installed because Centos 5 by default has an older version.

Building JDK requires at least GCC 5.0 (see Building the JDK: CC).
This seems to be a problem in the glibc version (see redhat-issue, util-linux). So, updating your glibc to the latest version might solve it.
If you don't want to update your system's glibc, here is another alternative:
By looking at the man page of fallocate, we find that the description mentions that posix_fallocate(3) is a portable, POSIX.1-specified version of it, in case the mode parameter has the default value (0). The same applies to fallocate64.
Since all the occurrences of the aforementioned error already use the default mode value, you can replace them with posix_fallocate64() (instead of commenting them out as you mentioned in another comment).
The denoted man page says that:
This default behavior [of fallocate with mode=0] closely resembles the
behavior of the posix_fallocate(3) library function, and is intended
as a method of optimally implementing that function.

Error in RFT - memoryCorruptionDetected

In RFT 8.3 an error occurs:
09:22:09.077 0x1bbb00 j9prt.748 * ** ASSERTION FAILED ** at common/j9memtag.c:145: ((memoryCorruptionDetected))
I tryed set jvm option -Xverify:none and -Xdump:heap, but it's not working. Any ideas?