我试图在OpenSUSE 11.3上的R 2.14.1-9.1上安装rJava包.我已经看到了这个问题,但它适用于Ubuntu.我已经安装了Sun JDK并重新配置了系统以使用它.
admin@linux-nb3w:~> java -version
java version "1.6.0_29"
Java(TM) SE Runtime Environment (build 1.6.0_29-b11)
Java HotSpot(TM) Client VM (build 20.4-b02, mixed mode)
admin@linux-nb3w:~>
编辑1:
更新了JDK和JRE.现在运行时出现稍微不同的错误install.packages("rJava"),我得到以下输出错误(发布新错误,粗体以结尾):
> install.packages("rJava")
Installing package(s) into ‘/home/admin/R/i686-pc-linux-gnu-library/2.14’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://ftp.iitm.ac.in/cran/src/contrib/rJava_0.9-3.tar.gz'
Content type 'application/x-gzip' length 537153 bytes (524 Kb)
opened URL
==================================================
downloaded 524 Kb
* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
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 -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 : '/usr/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-1.6.0-sun-1.6.0/jre/../include -I/usr/lib/jvm/java-1.6.0-sun-1.6.0/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-1.6.0-sun-1.6.0/jre/lib/i386/client -L/usr/lib/jvm/java-1.6.0-sun-1.6.0/jre/lib/i386 -L/usr/lib/jvm/java-1.6.0-sun-1.6.0/jre/../lib/i386 -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... yes
checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/admin/R/i686-pc-linux-gnu-library/2.14/rJava’
The downloaded packages are in
‘/tmp/RtmpIFKEha/downloaded_packages’
Warning message:
In install.packages("rJava") :
installation of package ‘rJava’ had non-zero exit status
>
新错误行:
检查JNI数据类型... configure:错误:一个或多个JNI类型与相应的本机类型不同.您可能需要使用非标准编译器标志或不同的编译器来解决此问题.
我确实运行了R CMD javareconfas root.它使cpp标志字段为空.我知道这是失败的原因之一,但不知道如何解决它.
我已经尝试了这个带有dependencies = TRUE选项的安装命令,并且还明确指定了repo(例如repo ="blah blah").没有任何效果.
我不知道如何更新OpenSUSE.但是对于SUSE来说看起来没有简单的方法,不像Ubuntu,这里明确给出了步骤.
任何帮助表示赞赏.
尽管运行正常update-alternatives --config javac,JAVA_HOME但未更新.因此我手动设置:
export JAVA_HOME=/usr/lib/jvm/java-1.6.0-sun-1.6.0.u6
你必须以上面的命令运行root.
然后跑了R CMD javareconf.取得了一些进展,安装超出了先前失败的地方.但它仍然给我以下错误:
Warning: R include directory is empty -- perhaps need to install R-devel.rpm or similar
gcc -std=gnu99 -I/usr/lib/R/include -I. -I/usr/lib/jvm/java-1.6.0-sun-1.6.0/include -I/usr/lib/jvm/java-1.6.0-sun-1.6.0/include/linux -I/usr/local/include -fpic -fomit-frame-pointer -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c Rglue.c -o Rglue.o
In file included from Rglue.c:2:0:
rJava.h:23:15: fatal error: R.h: No such file or directory
compilation terminated.
make: *** [Rglue.o] Error 1
ERROR: compilation failed for package ‘rJava’
* removing ‘/usr/lib/R/library/rJava’
The downloaded packages are in
‘/tmp/Rtmp3zqlgI/downloaded_packages’
Updating HTML index of packages in '.Library'
Making packages.html ... done
Warning message:
In install.packages("rJava") :
installation of package ‘rJava’ had non-zero exit status
>
然后根据错误中的建议,安装R-devel-rpm,如下所示:
zypper install R-patched R-patched-devel
(以上命令运行root)
在此之后,运行R和"install.package("rJava")"工作.
对于一个真正的问题,差不多5个小时的挫折和4个投票......但终于得到了解决!:)