search for: ljvm

.../bin/javah Java archive tool: /Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/jar Non-system Java on macOS trying to compile and link a JNI program detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/darwin detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm /usr/local/opt/llvm/bin/clang -I/usr/local/Cellar/r/3.4.4/lib/R/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include/darwin -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC...

...: >/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/jar >Non-system Java on macOS > >trying to compile and link a JNI program >detected JNI cpp flags : -I$(JAVA_HOME)/include >-I$(JAVA_HOME)/include/darwin >detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm >/usr/local/opt/llvm/bin/clang >-I/usr/local/Cellar/r/3.4.4/lib/R/include -DNDEBUG >-I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include >-I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include/darwin >-I/usr/local/opt/gettext/include -I/usr/local/opt/ll...

...-12-oracle/bin/jar'* *compiler : '/usr/lib/jvm/java-12-oracle/bin/javac'* *header prep.: '/usr/bin/javah'* *cpp flags : '-I/usr/lib/jvm/java-12-oracle/include -I/usr/lib/jvm/java-12-oracle/include/linux'* *java libs : '-L/usr/lib/jvm/java-12-oracle/lib/server -ljvm -ldl'* *checking whether Java run-time works... ./configure: line 3766: /usr/lib/jvm/java-12-oracle/bin/java: No such file or directory* *no* *configure: error: Java interpreter '/usr/lib/jvm/java-12-oracle/bin/java' does not work* *ERROR: configuration failed for package ?rJava?* ** re...

...x86_64/jre Java compiler : /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar trying to compile and link a JNI program detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm make[2]: Entering directory `/tmp/Rjavareconf.lcq59l' gcc -std=gnu99 -I/home/dmccully/R-3.2.2/include -DNDEBUG -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c confte...

...lMachines/jdk-10.jdk/Contents/Home/bin/jar >> Non-system Java on macOS >> >> trying to compile and link a JNI program >> detected JNI cpp flags : -I$(JAVA_HOME)/include >> -I$(JAVA_HOME)/include/darwin >> detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm >> /usr/local/opt/llvm/bin/clang >> -I/usr/local/Cellar/r/3.4.4/lib/R/include -DNDEBUG >> -I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include >> -I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include/darwin >> -I/usr/local/opt/gettext/in...

.../usr/bin/jar Java library path: $(JAVA_HOME)/lib/i386/client:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386:/usr/java/packages/lib/i386:/lib:/usr/lib JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -L$(JAVA_HOME)/lib/i386 -L$(JAVA_HOME)/../lib/i386 -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm JNI cpp flags : Updating Java configuration in /usr/lib/R Done. > install.packages(c("rJava"), dependencies = T, repos = "http://cran.fhcrc.org") . . . checking whether siglongjmp is declared... yes checking Java support in R... present: interpreter : '/usr/bin/java...

...sun-jdk-1.6.0.20/jre/../include -I/opt/sun-jdk-1.6.0.20/jre/../include/linux' java libs : '-L/opt/sun-jdk-1.6.0.20/jre/lib/amd64/server -L/opt/sun-jdk-1.6.0.20/jre/lib/amd64 -L/opt/sun-jdk-1.6.0.20/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm' checking whether JNI programs can be compiled... yes checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this. ERROR: configuration failed for packa...

...nftest -g -O2 -I/path/to/x86-64-linux/jdk-1.6.0_06/jre/../include conftest.c -L/path/to/x86-64-linux/jdk-1.6.0_06/jre/lib/amd64/server -L/path/to/x86-64-linux/jdk-1.6.0_06/jre/lib/amd64 -L/path/to/x86-64-linux/jdk-1.6.0_06/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm >&5 /path/to/x86-64-linux/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/lib/libc.a: could not read symbols: File format is ambiguous collect2: ld returned 1 exit status It looks like the command above could use /lib64/libc.so.6, but running "R CMD javar...

.../usr/bin/javac > Java headers gen.: /usr/bin/javah > Java archive tool: /usr/bin/jar > > trying to compile and link a JNI program > detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux > detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm > make[2]: Entering directory `/tmp/Rjavareconf.lcq59l' > gcc -std=gnu99 -I/home/dmccully/R-3.2.2/include -DNDEBUG -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre/../include/linux -I/usr/local/include -fpic -g -O2...

...Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux Updating Java configuration in /etc/R Done. The sessionInfo is identical for root I've un-installed and re-installed r-base and r-cran-* I've done a reboot; I've done 'R CMD javareconf' The file...

...iler : '' header prep.: '' cpp flags : '' java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm' configure: error: Java Development Kit (JDK) is missing or not registered in R Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R. ...so i do as suggested: $ sudo R CMD javareconf Java interpreter : /usr/bin/java Java vers...

...ib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux' java libs : '-L/usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/server -L/usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64 -L/usr/lib/jvm/java-6-sun-1.6.0.07/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm:-L/usr/lib32:-L/usr/lib64' checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. Make sure you have Java Development Kit installed and correctly registered in R. If in doubt, re-run "R CMD javareconf" as ro...

...gt;>> Non-system Java on macOS >>>> >>>> trying to compile and link a JNI program >>>> detected JNI cpp flags : -I$(JAVA_HOME)/include >>>> -I$(JAVA_HOME)/include/darwin >>>> detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm >>>> /usr/local/opt/llvm/bin/clang >>>> -I/usr/local/Cellar/r/3.4.4/lib/R/include -DNDEBUG >>>> -I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include >>>> -I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include/darwin >&...

...27-9) on an AMD Phenom Triple-Core The problem arises here: java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm' configure: error: Java Development Kit (JDK) is missing or not registered in R Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R. When I then do that > sudo R CMD javareconf # at terminal I get this: Updating Java con...

...'/usr/bin/javac' header prep.: '/usr/bin/javah' cpp flags : '' java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/i386/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/i386 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm' configure: error: One or more Java configuration variables are not set. Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R. If you don't have root privileges, run R CMD javareconf -e to set all Java-related variables and...

...vac Java headers gen.: /usr/lib/jvm/default-java/bin/javah Java archive tool: /usr/lib/jvm/default-java/bin/jar trying to compile and link a JNI program detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/default-java/ include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -fdebug- prefix-map=/home/jranke/git/r-backports/stretch/r-base-3.4.3=. -fstack- protector-strong -Wformat -Werror=format-security -Wdate-time - D_FORTIFY_...

...;; \ *) \ uname -m \ ;; \ esac ARCH = $(shell $(archExpr) ) JAVA_HOME=/opt/blackdown-jdk-1.4.1/ INCLUDES=-I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux -I/usr/local/lib/R/include LIBS=-L$(JAVA_HOME)/jre/lib/$(ARCH)/client -ljvm # The recommended c compiler flags CFLAGS=-D_REENTRANT -D_GNU_SOURCE all: excelpoi.so excelpoi.so: excelpoi.cpp excelpoi.h $(CXX) -O2 $(CFLAGS) $(INCLUDES) $(LIBS) -shared -fPIC -o $@ $< </Makefile> [[alternative HTML version deleted]]

.../usr/bin/javac > Java headers gen.: /usr/bin/javah > Java archive tool: /usr/bin/jar > > trying to compile and link a JNI program > detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux > detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm > make[2]: Entering directory `/tmp/Rjavareconf.lcq59l' > gcc -std=gnu99 -I/home/dmccully/R-3.2.2/include -DNDEBUG -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64/jre/../include/linux -I/usr/local/include -fpic -g -O2...

...n : 1.5.0 Java home path : /usr/lib/jvm/java-1.5.0-gcj-4.2-1.5.0.0/jre Java compiler : /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar Java library path: /usr/lib/../lib/gcj-4.2-81:/usr/lib/jni JNI linker flags : -L/usr/lib/../lib/gcj-4.2-81 -L/usr/lib/jni -ljvm JNI cpp flags : Updating Java configuration in /etc/R Done. What little I've been able to find on this problem suggests that the blank space beside the cpp flags variable is the key point, but all the notes I found suggest programming solutions outside of my abilities. Are there any simpl...

...n/java' archiver : '/usr/bin/jar' compiler : '/usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../bin/javac' header prep.: '/usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../bin/javah' cpp flags : '' java libs : '-L/usr/lib/../lib/gcj-4.3-90 -L/usr/lib/jni -ljvm' configure: error: One or more Java configuration variables are not set. Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R. If you don't have root privileges, run R CMD javareconf -e to set all Java-related variables and...