无法在Ubuntu 10.04上安装rJava 0.9

我使用RAN 2.10从CRAN apt回购Ubuntu 10.04，我试图安装Deducer，它需要JGR/rJava，但rJava拒绝构建/安装，抱怨无法构建JNI应用程序。我按照建议尝试了sudo R CMD javareconf，但这只会导致关于配置未设置的不同错误。我发现R: rJava package install failing，所以我试着在那里安装r-cran-rjava（但这是0.8和Deducer/JGR似乎坚持要安装0.9），并摆弄我的$JAVA_HOME，都无济于事。有任何想法吗？无法在Ubuntu 10.04上安装rJava 0.9

这里是发生了什么事更完整的成绩单：

$ 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 
>

来源

2011-08-20 Yang

它给了你几次相同的建议。有没有理由不听它？在这里，如果你错过了它：“如果有疑问，请以root身份重新运行”R CMD javareconf“。” –

咦？我明确表示，我在原来的问题中这样做了，而且它也在成绩单中...... – Yang

对不起。我所看到的是你引用了一个问题，然后在进行建议的修复之前进行安装。 –

大新，发布后没多久，我发现这里的答案：

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

虽然我已经安装了Sun Java中，关键是运行update-java-alternatives在运行javareconf之前先切换到Sun Java：

sudo update-java-alternatives -s java-6-sun 
sudo R CMD javareconf

来源

2011-08-20 03:05:12 Yang

它应该全部在Debian/Ubuntu中使用，并且在Ubuntu中使用Java SDK在为R和rJava包构建Java配置时进行配置。如果您决定切换到不同的Java后端，则必须进行重新配置。 –

这里的另一种选择：

运行在R之前，这样做

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

（以上路径，您的特定libjvm.so的替补位置，如果你有一个不同的配置）。为了找到libjvm.so，你可以做

sudo updatedb && locate libjvm.so

来源

2011-12-27 05:01:26 DWright

另外一个（相对明显）警告：不要做我所做的和同时安装的Java6和java7。这导致了一个冲突，我无法通过指定路径和环境变量来“修复”。删除并重新安装java6导致成功安装JGR。（这ubuntu下精确，在苹果的PowerBook G4）

来源

2013-02-06 02:41:06

DWright是right..an替代比每次启动R是找到你的java路径

sudo locate libjvm.so

和IR添加到ldpaths时间，而不是将其导出

sudo gedit /etc/R/ldpaths 

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

来源

2013-07-22 02:58:09 CocoOS

无法在Ubuntu 10.04上安装rJava 0.9

回答

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