无法在Ubuntu10.04上安装rJava 0.9
无法在Ubuntu10.04上安装rJava 0.9
提问于 2011-08-20 10:52:25
我使用Ubuntu10.04的CRAN apt repo中的R 2.13，我正在尝试安装Deducer，这需要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，但这只是导致了另一个关于配置未设置的错误。我找到了R: rJava package install failing，所以我尝试了在那里安装r-cran-rjava的建议(但那是0.8，Deducer/JGR似乎坚持要安装0.9)，并摆弄我的$JAVA_HOME，所有这些都没有用。有什么想法吗？
以下是所发生事件的更完整的文字记录：
$ 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
>回答 4
Stack Overflow用户
回答已采纳
发布于 2011-08-20 11:05:13
啊，发帖后不久，我在这里找到了答案：
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，但在运行javareconf之前，关键是要运行update-java-alternatives，以便真正切换到Sun Java：
sudo update-java-alternatives -s java-6-sun
sudo R CMD javareconfStack Overflow用户
发布于 2013-02-06 10:41:06
另一个(相对明显的)警告是:不要像我那样同时安装java6和java7。这导致了一个我无法通过指定路径和环境变量来“修复”的冲突。删除并重新安装java6会导致JGR的成功安装。(这是在ubuntu precise下，在苹果G4 powerbook上)
Stack Overflow用户
发布于 2011-12-27 13:01:26
这里有另一个选择：
在运行R之前，请执行以下操作
export LD_LIBRARY_PATH=/usr/lib/jvm/java-1.6.0-openjdk/jre/lib/amd64/server(对于上面的路径，如果您有不同的配置，请替换为您的特定libjvm.so的位置)。要查找libjvm.so，您可以执行以下操作
sudo updatedb && locate libjvm.so页面原文内容由Stack Overflow提供。腾讯云小微IT领域专用引擎提供翻译支持
原文链接：
https://stackoverflow.com/questions/7129303
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