Ubuntu'da rJava 0.9 yüklenemiyor 10.04

Question

Ubuntu 10.04 için CRAN apt repo'undan R 2.13 kullanıyorum ve JGR/rJava gerektiren Deducer'ı yüklemeyi deniyorum, ancak rJava'yı kurmak/yüklemek reddediyor, şikayet ediyor bir JNI uygulaması oluşturamamak. sudo R CMD javareconf'u önerildiği gibi denedim, ancak yalnızca yapılandırmanın kaldırılmasında farklı bir hata oluştu. Ben R: rJava package install failing buldum, o yüzden orada r-cran-rjava yükleme önerileri çalıştı (ama bu 0.8 var ve Deducer/JGR 0.9 yüklemeden ısrar görünüyor) ve boşuna benim $JAVA_HOME, tüm kurcalıyor. Herhangi bir fikir?

$ sudo aptitude install r-cran-rjava 
... 
$ R 

R version 2.13.1 (2011-07-08) 
Copyright (C) 2011 The R Foundation for Statistical Computing 
ISBN 3-900051-07-0 
Platform: x86_64-pc-linux-gnu (64-bit) 

R is free software and comes with ABSOLUTELY NO WARRANTY. 
You are welcome to redistribute it under certain conditions. 
Type 'license()' or 'licence()' for distribution details. 

    Natural language support but running in an English locale 

R is a collaborative project with many contributors. 
Type 'contributors()' for more information and 
'citation()' on how to cite R or R packages in publications. 

Type 'demo()' for some demos, 'help()' for on-line help, or 
'help.start()' for an HTML browser interface to help. 
Type 'q()' to quit R. 

> install.packages(c('JGR','Deducer')) 
Installing package(s) into ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13’ 
(as ‘lib’ is unspecified) 
also installing the dependencies ‘rJava’, ‘JavaGD’, ‘iplots’ 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-1.tar.gz' 
Content type 'application/x-gzip' length 527197 bytes (514 Kb) 
opened URL 
================================================== 
downloaded 514 Kb 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/JavaGD_0.5-4.tar.gz' 
Content type 'application/x-gzip' length 102242 bytes (99 Kb) 
opened URL 
================================================== 
downloaded 99 Kb 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/iplots_1.1-4.tar.gz' 
Content type 'application/x-gzip' length 330323 bytes (322 Kb) 
opened URL 
================================================== 
downloaded 322 Kb 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/JGR_1.7-7.tar.gz' 
Content type 'application/x-gzip' length 536564 bytes (523 Kb) 
opened URL 
================================================== 
downloaded 523 Kb 

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/Deducer_0.4-4.tar.gz' 
Content type 'application/x-gzip' length 5325794 bytes (5.1 Mb) 
opened URL 
================================================== 
downloaded 5.1 Mb 

* installing *source* package ‘rJava’ ... 
checking for gcc... gcc 
checking for C compiler default output file name... a.out 
checking whether the C compiler works... yes 
checking whether we are cross compiling... no 
checking for suffix of executables... 
checking for suffix of object files... o 
c hecking whether we are using the GNU C compiler... yes 
checking whether gcc accepts -g... yes 
checking for gcc option to accept ISO C89... none needed 
checking how to run the C preprocessor... gcc -E 
checking for grep that handles long lines and -e... /bin/grep 
checking for egrep... /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 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 : '/usr/bin/java' 
archiver : '/usr/bin/jar' 
compiler : '/usr/bin/javac' 
header prep.: '/usr/bin/javah' 
cpp flags : '-I/usr/lib/jvm/java-6-openjdk/jre/../include' 
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' 
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 root. 

ERROR: configuration failed for package ‘rJava’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/rJava’ 
* installing *source* package ‘JavaGD’ ... 
checking for gcc... gcc 
checking for C compiler default output file name... a.out 
checking whether the C compiler works... yes 
checking whether we are cross compiling... no 
checking for suffix of executables... 
checking for suffix of object files... o 
checking whether we are using the GNU C compiler... yes 
checking whether gcc accepts -g... yes 
checking for gcc option to accept ISO C89... none needed 
checking how to run the C preprocessor... gcc -E 
checking for grep that handles long lines and -e... /bin/grep 
checking for egrep... /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 
checking for stdlib.h... (cached) yes 
checking for GNU libc compatible malloc... yes 
checking return type of signal handlers... void 
checking for memset... yes 
checking for mkdir... yes 
checking for rmdir... yes 
checking for select... yes 
checking for socket... yes 
checking Java support in R... present: 
interpreter : '/usr/bin/java' 
cpp flags : '-I/usr/lib/jvm/java-6-openjdk/jre/../include' 
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' 
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. 
ERROR: configuration failed for package ‘JavaGD’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/JavaGD’ 
ERROR: dependency ‘rJava’ is not available for package ‘iplots’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/iplots’ 
ERROR: dependencies ‘rJava’, ‘JavaGD’, ‘iplots’ are not available for package ‘JGR’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/JGR’ 
ERROR: dependencies ‘rJava’, ‘JGR’ are not available for package ‘Deducer’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/Deducer’ 

The downloaded packages are in 
     ‘/tmp/RtmpCSITmm/downloaded_packages’ 
Warning messages: 
1: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'rJava' had non-zero exit status 
2: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'JavaGD' had non-zero exit status 
3: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'iplots' had non-zero exit status 
4: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'JGR' had non-zero exit status 
5: In install.packages(c("JGR", "Deducer")) : 
    installation of package 'Deducer' had non-zero exit status 
> 


R version 2.13.1 (2011-07-08) 
Copyright (C) 2011 The R Foundation for Statistical Computing 
ISBN 3-900051-07-0 
Platform: x86_64-pc-linux-gnu (64-bit) 

R is free software and comes with ABSOLUTELY NO WARRANTY. 
You are welcome to redistribute it under certain conditions. 
Type 'license()' or 'licence()' for distribution details. 

    Natural language support but running in an English locale 

R is a collaborative project with many contributors. 
Type 'contributors()' for more information and 
'citation()' on how to cite R or R packages in publications. 

Type 'demo()' for some demos, 'help()' for on-line help, or 
'help.start()' for an HTML browser interface to help. 
Type 'q()' to quit R. 

> install.packages('rJava') 
Installing package(s) into ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13’ 
(as ‘lib’ is unspecified) 
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-1.tar.gz' 
Content type 'application/x-gzip' length 527197 bytes (514 Kb) 
opened URL 
================================================== 
downloaded 514 Kb 

* installing *source* package ‘rJava’ ... 
checking for gcc... gcc 
checking for C compiler default output file name... a.out 
checking whether the C compiler works... yes 
checking whether we are cross compiling... no 
checking for suffix of executables... 
checking for suffix of object files... o 
checking whether we are using the GNU C compiler... yes 
checking whether gcc accepts -g... yes 
checking for gcc option to accept ISO C89... none needed 
checking how to run the C preprocessor... gcc -E 
checking for grep that handles long lines and -e... /bin/grep 
checking for egrep... /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 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 : '/usr/bin/java' 
archiver : '/usr/bin/jar' 
compiler : '/usr/bin/javac' 
header prep.: '/usr/bin/javah' 
cpp flags : '-I/usr/lib/jvm/java-6-openjdk/jre/../include' 
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' 
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 root. 

ERROR: configuration failed for package ‘rJava’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/rJava’ 

The downloaded packages are in 
     ‘/tmp/RtmpTk0ftk/downloaded_packages’ 
Warning message: 
In install.packages("rJava") : 
    installation of package 'rJava' had non-zero exit status 
> 
$ sudo R CMD javareconf 
Java interpreter : /usr/bin/java 
Java version  : 1.6.0_20 
Java home path : /usr/lib/jvm/java-6-openjdk/jre 
Java compiler : /usr/bin/javac 
Java headers gen.: /usr/bin/javah 
Java archive tool: /usr/bin/jar 
Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib 
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm 
JNI cpp flags : 

Updating Java configuration in /etc/R 
Done. 

$ R 

R version 2.13.1 (2011-07-08) 
Copyright (C) 2011 The R Foundation for Statistical Computing 
ISBN 3-900051-07-0 
Platform: x86_64-pc-linux-gnu (64-bit) 

R is free software and comes with ABSOLUTELY NO WARRANTY. 
You are welcome to redistribute it under certain conditions. 
Type 'license()' or 'licence()' for distribution details. 

    Natural language support but running in an English locale 

R is a collaborative project with many contributors. 
Type 'contributors()' for more information and 
'citation()' on how to cite R or R packages in publications. 

Type 'demo()' for some demos, 'help()' for on-line help, or 
'help.start()' for an HTML browser interface to help. 
Type 'q()' to quit R. 

> install.packages('rJava') 
Installing package(s) into ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13’ 
(as ‘lib’ is unspecified) 
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rJava_0.9-1.tar.gz' 
Content type 'application/x-gzip' length 527197 bytes (514 Kb) 
opened URL 
================================================== 
downloaded 514 Kb 

* installing *source* package ‘rJava’ ... 
checking for gcc... gcc 
checking for C compiler default output file name... a.out 
checking whether the C compiler works... yes 
checking whether we are cross compiling... no 
checking for suffix of executables... 
checking for suffix of object files... o 
checking whether we are using the GNU C compiler... yes 
checking whether gcc accepts -g... yes 
checking for gcc option to accept ISO C89... none needed 
checking how to run the C preprocessor... gcc -E 
checking for grep that handles long lines and -e... /bin/grep 
checking for egrep... /bin/grep -E 
checking for ANSI C header files... yes 
c hecking 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 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 : '/usr/bin/java' 
archiver : '/usr/bin/jar' 
compiler : '/usr/bin/javac' 
header prep.: '/usr/bin/javah' 
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: 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 then install rJava. 

ERROR: configuration failed for package ‘rJava’ 
* removing ‘/home/yang/R/x86_64-pc-linux-gnu-library/2.13/rJava’ 

The downloaded packages are in 
     ‘/tmp/RtmpsJBxfe/downloaded_packages’ 
Warning message: 
In install.packages("rJava") : 
    installation of package 'rJava' had non-zero exit status 
> 

Answer 1

Dah uzun değil yazdıktan sonra burada cevap buldu: İşte

olanları daha tam transkript

http://r-interface.blogspot.com/2012/04/install-r-jgr-and-deducer-in-ubuntu.html

Zaten Sun Java yüklü olmasına rağmen, key, javareconf'u çalıştırmadan önce ilk olarak Sun Java'ya geçmek için update-java-alternatives'u çalıştırmaktı:

Answer 2

Burada başka seçenek:

Ar çalıştırmadan önce, do bu

export LD_LIBRARY_PATH=/usr/lib/jvm/java-1.6.0-openjdk/jre/lib/amd64/server 

(yukarıdaki yolu için, belirli libjvm.so ait yedek konum, farklı bir yapılandırma varsa). libjvm.so bulmak için,

sudo updatedb && locate libjvm.so 

Answer 3

bir diğer (nispeten bariz) uyarıyı yapabilirsiniz: Benim yaptığımı ve java6 ve java7 hem yüklemeyin. Bu bir anlaşmazlığa yol açarak yol ve ortam değişkenlerini belirterek 'düzeltemedim'. Her ikisini de kaldırıp java6'yı yeniden yüklemek JGR'nin başarılı bir şekilde kurulmasına yol açtı. (ubuntu altında bu hassas, üzerinde bir Apple G4 powerbook)

Answer 4

DWright right..an alternatif yerine R java yolu

sudo locate libjvm.so 

bulup ldpaths için ir ekleyin başlamak daha her zaman dışa olan

sudo gedit /etc/R/ldpaths 

i.e 
${JAVA_HOME=/usr/java/jdk1.7.0_07/jre}