RESOLVED!!

See my solution below, in case this question helps others in the future.

请参阅下面的解决方案,以防这个问题在将来帮助其他人。

Error

As the title described, it it failing for me. The error I'm receiving, when I attempt to install.packages('rJava') from inside R is (with some preceding good checks):

正如标题所描述的那样,它失败了。我收到的错误,当我尝试从R内部安装.packages('rJava')时(有一些先前的好检查):

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 ‘/usr/local/lib/R/3.2/site-library/rJava’

Fix Attempts

I have checked and tried the following resolutions, none of which worked for me:

我检查并尝试了以下决议,其中没有一个对我有用:

sudo R CMD javareconf

sudo R CMD javareconf
more detailed sudo R CMD javareconf

更详细的sudo R CMD javareconf
export JAVA_HOME, however in this case, I did not do the LD_LIBRARY_PATH, as it did not seem relevant to a Mac.

导出JAVA_HOME,但是在这种情况下,我没有执行LD_LIBRARY_PATH,因为它似乎与Mac无关。

No such luck, with any of these attempts.

没有这样的运气,任何这些尝试。

I had previously had rJava (and RJDBC) installed properly.

我以前安装了rJava(和RJDBC)。

[Edit: I later found out, the actual problem was upgrading to OS X 10.11, El Capitan.]

[编辑:我后来发现,实际问题是升级到OS X 10.11,El Capitan。]

Configuration

$ java -version
java version "1.8.0_45"

> R.Version()
$platform
[1] "x86_64-apple-darwin15.0.0"
$version.string
[1] "R version 3.2.2 (2015-08-14)"

Mac OS itself:

Mac OS本身:

System Version: OS X 10.11.1 (15B42)

2 个解决方案

#1

I did not do the LD_LIBRARY_PATH, as it did not seem relevant to a Mac

我没有做LD_LIBRARY_PATH,因为它似乎与Mac无关

Yes, but a Mac has DYLD_LIBRARY_PATH. If you link with -ljvm you have to have the directory containing libjvm.dylib in DYLD_LIBRARY_PATH.

是的,但Mac有DYLD_LIBRARY_PATH。如果链接-ljvm,则必须在DYLD_LIBRARY_PATH中包含libjvm.dylib的目录。

That said, I found it more convenient to link JNI programs with -ljli (in lib/jli), because the programs linked with -ljvm will open a prompt to install Apple's own Java runtime when the system doesn't have it (at least they did on my and our customers' systems some while ago).

也就是说,我发现使用-ljli(在lib / jli中)链接JNI程序更方便,因为与-ljvm链接的程序会在系统没有它时打开安装Apple自己的Java运行库的提示(至少他们之前在我和我们客户的系统上做过。

Edit: here's a link to the dyld documentation

编辑:这是dyld文档的链接

#2

I finally resolved this, via a solution I found here.

我终于通过我在这里找到的解决方案解决了这个问题。

The new Mac OS X (10.11, El Capitan) has trouble with env variables.

新的Mac OS X(10.11,El Capitan)在env变量方面存在问题。

The newest dev flavor of rJava manages to handle things correctly. Here is what I did to resolve it:

rJava的最新开发风格设法正确处理事情。以下是我解决它的方法:

Download version 0.9-8 (rJava_0.9-8.tar.gz) from here

从这里下载0.9-8版本(rJava_0.9-8.tar.gz)

Install it from the downloaded source:

从下载的源安装它:

$ R CMD INSTALL ~/Downloads/rJava_0.9-8.tar.gz

$ R CMD INSTALL~ / Downloads / rJava_0.9-8.tar.gz

(Or wherever you put it)

(或者无论你把它放在哪里)

That's all it took!

这就是全部!

#1