java - 如何在 Amazon Linux 上安装 dplyr-snowflakedb 和 rJava？

Question

这里的目标是安装 dplyr-snowflakedb R在 AWS Linux 机器上打包。问题在于rJava包不会安装，它失败并显示以下错误消息:

“installation of package ‘rJava’ had non-zero exit status”

dplyr.snowflakedb包提出以下建议:

The rJava package needs to be installed and working with Java 8 to support the SnowflakeDB JDBC requirements. This may require:

• installing Java 8

• running R CMD javareconf so R uses the Java 8 for its JAVA_HOME

• installing rJava from source so it can be linked against Java 8

尽管尝试了这些策略，rJava 仍然无法安装在 AWS linux 上。

AWS linux 实例运行的是 Java 8:

conda activate ~/anaconda3/envs/R
(R) [ec2-user@ip-xx-xx-xx-xx ~]$ java -version

>>> openjdk version "1.8.0_152-release"
>>> OpenJDK Runtime Environment (build 1.8.0_152-release-1056-b12)
>>> OpenJDK 64-Bit Server VM (build 25.152-b12, mixed mode)

R CMD javareconf命令被执行:

Java interpreter : /home/ec2-user/anaconda3/envs/JupyterSystemEnv/jre/bin/java
Java version     : 1.8.0_152-release
Java home path   : /home/ec2-user/anaconda3/envs/JupyterSystemEnv
Java compiler    : /home/ec2-user/anaconda3/envs/JupyterSystemEnv/bin/javac
Java headers gen.: /home/ec2-user/anaconda3/envs/JupyterSystemEnv/bin/javah
Java archive tool: /home/ec2-user/anaconda3/envs/JupyterSystemEnv/bin/jar

trying to compile and link a JNI program 
detected JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
x86_64-conda_cos6-linux-gnu-cc -I"/home/ec2-user/anaconda3/envs/R/lib/R/include" -DNDEBUG -I/home/ec2-user/anaconda3/envs/JupyterSystemEnv/include -I/home/ec2-user/anaconda3/envs/JupyterSystemEnv/include/linux  -DNDEBUG -D_FORTIFY_SOURCE=2 -O2  -I/home/ec2-user/anaconda3/envs/R/include -Wl,-rpath-link,/home/ec2-user/anaconda3/envs/R/lib  -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/ec2-user/anaconda3/envs/R/include -fdebug-prefix-map=/tmp/build/80754af9/r-base_1570124924484/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/ec2-user/anaconda3/envs/R=/usr/local/src/conda-prefix  -c conftest.c -o conftest.o
x86_64-conda_cos6-linux-gnu-cc -shared -L/home/ec2-user/anaconda3/envs/R/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/ec2-user/anaconda3/envs/R/lib -Wl,-rpath-link,/home/ec2-user/anaconda3/envs/R/lib -L/home/ec2-user/anaconda3/envs/R/lib -Wl,-rpath-link,/home/ec2-user/anaconda3/envs/R/lib -o conftest.so conftest.o -L/home/ec2-user/anaconda3/envs/JupyterSystemEnv/jre/lib/amd64/server -ljvm -L/home/ec2-user/anaconda3/envs/R/lib/R/lib -lR


JAVA_HOME        : /home/ec2-user/anaconda3/envs/JupyterSystemEnv
Java library path: /home/ec2-user/anaconda3/envs/JupyterSystemEnv/jre/lib/amd64/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
Updating Java configuration in /home/ec2-user/anaconda3/envs/R/lib/R
Done.

不清楚如何安装 rJava从源代码或将其链接到 Java 8。

这个相关问题: Can't install rJava on ubuntu system建议运行以下命令:

sudo apt-get install r-cran-rjava

但是 AWS Linux 不使用 apt-get ，它使用 yum , 和 yum 的等效命令找不到包:

sudo yum install r-cran-rjava
>>> No package r-cran-rjava available.

也许问题是 JAVA_HOME 设置为 JupyterSystemEnv而不是 R环境？

Answer 1

确保不仅安装 JRE，还安装 JDK:
sudo yum install java-1.8.0-openjdksudo yum install java-1.8.0-openjdk-devel

配置:sudo R CMD javareconf

在 R 中安装 rJava:install.packages("rJava")

一旦您安装了 rJava 并验证它使用的是 Java 8，您就可以安装 dplyr 和依赖项。install.packages(c("RJDBC", "DBI", "dplyr"))

安装 dplyr.snowflakedbinstall.packages("devtools")devtools::install_github("snowflakedb/dplyr-snowflakedb")

如果您在安装 devtools 时遇到问题，请尝试安装依赖项或尝试另一个 repo:

install.packages("devtools", dependencies=TRUE)

install.packages('devtools',dependencies=TRUE,
repos='https://stat.ethz.ch/CRAN/')