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Posted to user@spark.apache.org by "Arif,Mubaraka" <ar...@heb.com> on 2016/09/19 19:29:04 UTC
Java Compatibity Problems when we install rJava
The downloaded source packages are in
�/tmp/RtmpfdQwg8/downloaded_packages�
[I 13:41:00.060 NotebookApp] Saving file at /R_test.ipynb
trying URL 'http://cran.us.r-project.org/src/contrib/rJava_0.9-8.tar.gz'
Content type 'application/x-gzip' length 656615 bytes (641 KB)
==================================================
downloaded 641 KB
* installing *source* package �rJava� ...
** package �rJava� successfully unpacked and MD5 sums checked
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 : '/opt/teradata/jvm64/jdk8/jre/bin/java'
archiver : '/opt/teradata/jvm64/jdk8/bin/jar'
compiler : '/opt/teradata/jvm64/jdk8/bin/javac'
header prep.: '/opt/teradata/jvm64/jdk8/bin/javah'
cpp flags : '-I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux'
java libs : '-L/opt/teradata/jvm64/jdk8/jre/lib/amd64/server -ljvm -ldl'
checking whether Java run-time works... yes
checking whether -Xrs is supported... yes
checking whether JNI programs can be compiled... 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/RtmpU52Epw/R.INSTALL1fd0c64aa2bcd/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 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/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -DNDEBUG -I. -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -fpic -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -c Rglue.c -o Rglue.o
gcc -std=gnu99 -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -DNDEBUG -I. -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -fpic -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -c arrayc.c -o arrayc.o
gcc -std=gnu99 -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -DNDEBUG -I. -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -fpic -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -c callJNI.c -o callJNI.o
gcc -std=gnu99 -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -DNDEBUG -I. -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -fpic -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -c callback.c -o callback.o
gcc -std=gnu99 -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -DNDEBUG -I. -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -fpic -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -c fields.c -o fields.o
gcc -std=gnu99 -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -DNDEBUG -I. -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -fpic -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -c init.c -o init.o
gcc -std=gnu99 -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -DNDEBUG -I. -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -fpic -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -c jri_glue.c -o jri_glue.o
gcc -std=gnu99 -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -DNDEBUG -I. -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -fpic -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -c loader.c -o loader.o
gcc -std=gnu99 -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -DNDEBUG -I. -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -fpic -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -c otables.c -o otables.o
gcc -std=gnu99 -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -DNDEBUG -I. -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -fpic -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -c rJava.c -o rJava.o
gcc -std=gnu99 -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -DNDEBUG -I. -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -fpic -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -c tools.c -o tools.o
gcc -std=gnu99 -shared -L/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/lib -L/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib -lgfortran -o rJava.so Rglue.o arrayc.o callJNI.o callback.o fields.o init.o jri_glue.o loader.o otables.o rJava.o tools.o -L/opt/teradata/jvm64/jdk8/jre/lib/amd64/server -ljvm -ldl -L/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/lib -lR
(cd ../jri && make)
make[1]: Entering directory `/tmp/RtmpU52Epw/R.INSTALL1fd0c64aa2bcd/rJava/jri'
make -C src JRI.jar
make[2]: Entering directory `/tmp/RtmpU52Epw/R.INSTALL1fd0c64aa2bcd/rJava/jri/src'
/opt/teradata/jvm64/jdk8/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java ../RBool.java ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java ../RVector.java ../Rengine.java ../package-info.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
/opt/teradata/jvm64/jdk8/bin/javah -d . -classpath . org.rosuda.JRI.Rengine
gcc -std=gnu99 -c -o Rengine.o Rengine.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -fpic -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include
gcc -std=gnu99 -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -fpic -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include
gcc -std=gnu99 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -fpic -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include
gcc -std=gnu99 -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -fpic -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/include
gcc -std=gnu99 -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -fpic -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux
gcc -std=gnu99 -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -I/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/include -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux -fpic -I/opt/teradata/jvm64/jdk8/include -I/opt/teradata/jvm64/jdk8/include/linux
gcc -std=gnu99 -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -shared -L/opt/teradata/jvm64/jdk8/jre/lib/amd64/server -ljvm -ldl -Wl,--export-dynamic -fopenmp -L/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/lib -lR -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: cannot find -lpcre
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: cannot find -llzma
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: cannot find -lbz2
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: cannot find -licuuc
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: cannot find -licui18n
collect2: ld returned 1 exit status
make[2]: *** [libjri.so] Error 1
make[2]: Leaving directory `/tmp/RtmpU52Epw/R.INSTALL1fd0c64aa2bcd/rJava/jri/src'
make[1]: *** [src/JRI.jar] Error 2
make[1]: Leaving directory `/tmp/RtmpU52Epw/R.INSTALL1fd0c64aa2bcd/rJava/jri'
make: *** [jri] Error 2
ERROR: compilation failed for package �rJava�
* removing �/var/opt/teradata/cloudera/parcels/Anaconda-4.0.0/lib/R/library/rJava�
RE: Java Compatibity Problems when we install rJava
Posted by "Arif,Mubaraka" <ar...@heb.com>.
we are running Juypter in the yarn-client mode for pyspark (python spark). And, we wanted to know if anybody faced such issues while installing rJava on Jupyter notebook.
Also, reaching out for support with cloudera.
thanks,
Muby
________________________________________
From: Sean Owen [sowen@cloudera.com]
Sent: Monday, September 19, 2016 2:31 PM
To: Arif,Mubaraka
Cc: User; Toivola,Sami
Subject: Re: Java Compatibity Problems when we install rJava
This isn't a Spark question, so I don't think this is the right place.
It shows that compilation of rJava failed for lack of some other
shared libraries (not Java-related). I think you'd have to get those
packages installed locally too.
If it ends up being Anaconda specific, you should try Continuum, or if
it looks CDH-related head to Cloudera support.
On Mon, Sep 19, 2016 at 8:29 PM, Arif,Mubaraka <ar...@heb.com> wrote:
> We are trying to install rJava on suse Linux running Cloudera Hadoop CDH
> 5.7.2 with Spark 1.6.
>
> Anaconda 4.0 was installed using the CDH parcel.
>
>
>
> Have setup for Jupyter notebook but there are Java compability problems.
>
>
>
> For Java we are running :
>
>
>
> java version "1.8.0_51"
> Java(TM) SE Runtime Environment (build 1.8.0_51-tdc1-b16)
> Java HotSpot(TM) 64-Bit Server VM (build 25.51-b03, mixed mode)
>
>
>
> We followed the instructions from the blog :
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ibm.com_support_knowledgecenter_SSPT3X-5F3.0.0_com.ibm.swg.im.infosphere.biginsights.install.doc_doc_install-5Finstall-5Fr.html&d=CwIBaQ&c=RI9dKKMRNVHr9NFa7OQiQw&r=dUN85GiSQZVDs0gTK4x1mSiAdXTZ-7F0KzGt2fcse38&m=Lz3LdXM3lDkt_CskgKDNAs2kYGJuhgmloph8m-sND-M&s=J58OWa6hGmo90uWwGXKHLUxIbOGOe5yoHQM0tQOSCX8&e=
>
>
>
> After running we get the output : [as attached in file - rJava_err.txt]
>
>
>
> Any help is greatly appreciated.
>
>
>
> thanks,
>
> Muby
>
>
>
> ---------------------------------------------------------------------
> To unsubscribe e-mail: user-unsubscribe@spark.apache.org
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Re: Java Compatibity Problems when we install rJava
Posted by Sean Owen <so...@cloudera.com>.
This isn't a Spark question, so I don't think this is the right place.
It shows that compilation of rJava failed for lack of some other
shared libraries (not Java-related). I think you'd have to get those
packages installed locally too.
If it ends up being Anaconda specific, you should try Continuum, or if
it looks CDH-related head to Cloudera support.
On Mon, Sep 19, 2016 at 8:29 PM, Arif,Mubaraka <ar...@heb.com> wrote:
> We are trying to install rJava on suse Linux running Cloudera Hadoop CDH
> 5.7.2 with Spark 1.6.
>
> Anaconda 4.0 was installed using the CDH parcel.
>
>
>
> Have setup for Jupyter notebook but there are Java compability problems.
>
>
>
> For Java we are running :
>
>
>
> java version "1.8.0_51"
> Java(TM) SE Runtime Environment (build 1.8.0_51-tdc1-b16)
> Java HotSpot(TM) 64-Bit Server VM (build 25.51-b03, mixed mode)
>
>
>
> We followed the instructions from the blog :
> http://www.ibm.com/support/knowledgecenter/SSPT3X_3.0.0/com.ibm.swg.im.infosphere.biginsights.install.doc/doc/install_install_r.html
>
>
>
> After running we get the output : [as attached in file - rJava_err.txt]
>
>
>
> Any help is greatly appreciated.
>
>
>
> thanks,
>
> Muby
>
>
>
> ---------------------------------------------------------------------
> To unsubscribe e-mail: user-unsubscribe@spark.apache.org
---------------------------------------------------------------------
To unsubscribe e-mail: user-unsubscribe@spark.apache.org