无法在 Ubuntu 10.04 上安装 rJava 0.9答案

【问题标题】：Can't install rJava 0.9 on Ubuntu 10.04无法在 Ubuntu 10.04 上安装 rJava 0.9
【发布时间】：2011-10-31 01:17:33
【问题描述】：

我使用 Ubuntu 10.04 的 CRAN apt repo 中的 R 2.13，我正在尝试安装 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，但这只会导致有关未设置配置的不同错误。我找到了R: rJava package install failing，所以我尝试了安装r-cran-rjava 的建议（但那是0.8，而Deducer/JGR 似乎坚持安装0.9）并摆弄我的$JAVA_HOME，都无济于事。有什么想法吗？

以下是所发生事件的更完整记录：

$ 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
>

【问题讨论】：

它多次给了你同样的建议。有充分的理由不注意它吗？如果您错过了，这里又是：“如果有疑问，请以 root 身份重新运行“R CMD javareconf”。”
嗯？我在最初的问题中明确表示我是这样做的，而且它也在成绩单中......
对不起。我看到是您引用了一个问题，然后在执行建议的修复之前继续安装。
使用 sudo 和以 root 身份运行并不完全相同。
哇！这真是令人大开眼界！确实，“sudo R CMD javareconf”没有做到这一点——但是“sudo su”和“R CMD javareconf”有所不同！谢谢！

标签： r rjava

【解决方案1】：

DWright 是对的。另一种方法是在每次启动 R 时将其导出为找到您的 java 路径

 sudo locate libjvm.so

并将 ir 添加到 ldpaths

 sudo gedit /etc/R/ldpaths 

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

【讨论】：

【解决方案2】：

另一个（相对明显的）警告：不要像我一样安装java6和java7。这导致了我无法通过指定路径和环境变量来“修复”的冲突。删除两者并重新安装 java6 导致 JGR 成功安装。（这在 ubuntu 下精确，在 Apple G4 powerbook 上）

【讨论】：

【解决方案3】：

Dah，发布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，但关键是在运行 javareconf 之前先运行 update-java-alternatives 以实际切换到 Sun Java：

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

【讨论】：

它应该在 Debian / Ubuntu 中使用 Java SDK 在构建时为 R 和 rJava 包配置的 Java 选项运行。如果您决定切换到不同的 Java 后端，您确实必须重新配置。

【解决方案4】：

这是另一个选择：

在运行 R 之前，请执行此操作

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，请替换您的特定 libjvm.so 的位置）。要找到libjvm.so，你可以这样做

sudo updatedb && locate libjvm.so

【讨论】：