R-Project：xlsx 软件包安装失败（由于 java 问题）

java xlsx r rjava

2022-09-04 01:57:14

我试图安装xlsx软件包，不幸的是，Java有一个问题，我无法解决。

请在下面找到尝试安装软件包xlsx时产生的输出。

下面是输出：

R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-redhat-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("xlsx")
Installing package into ‘/home/tamaspavlicek/R/x86_64-redhat-linux-gnu-library/3.1’
(as ‘lib’ is unspecified)
also installing the dependencies ‘rJava’, ‘xlsxjars’

trying URL 'contrib/rJava_0.9-6.tar.gz'
Content type 'application/x-gzip' length 567515 bytes (554 Kb)
opened URL
==================================================
downloaded 554 Kb

trying URL 'contrib/xlsxjars_0.6.1.tar.gz'
Content type 'application/x-gzip' length 9477071 bytes (9.0 Mb)
opened URL
==================================================
downloaded 9.0 Mb

trying URL 'contrib/xlsx_0.5.7.tar.gz'
Content type 'application/x-gzip' length 312839 bytes (305 Kb)
opened URL
==================================================
downloaded 305 Kb

* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -m64 -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -m64 -std=gnu99 accepts -g... yes
checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -m64 -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 -m64 -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 : '/bin/java'
archiver    : '/bin/jar'
compiler    : '/bin/javac'
header prep.: '/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/../include/linux'
java libs   : '-L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/lib/amd64/server -ljvm'
checking whether Java run-time works... 
Error: Could not find or load main class getsp
no
configure: error: Java interpreter '/bin/java' does not work
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/tamaspavlicek/R/x86_64-redhat-linux-gnu-library/3.1/rJava’
Warning in install.packages :
  installation of package ‘rJava’ had non-zero exit status
ERROR: dependency ‘rJava’ is not available for package ‘xlsxjars’
* removing ‘/home/tamaspavlicek/R/x86_64-redhat-linux-gnu-library/3.1/xlsxjars’
Warning in install.packages :
  installation of package ‘xlsxjars’ had non-zero exit status
ERROR: dependencies ‘rJava’, ‘xlsxjars’ are not available for package ‘xlsx’
* removing ‘/home/tamaspavlicek/R/x86_64-redhat-linux-gnu-library/3.1/xlsx’
Warning in install.packages :
  installation of package ‘xlsx’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/Rtmpj1UG8a/downloaded_packages’

安装了 Java：

java -version 给出了以下输出：

java version "1.7.0_71"
OpenJDK Runtime Environment (fedora-2.5.3.0.fc20-x86_64 u71-b14)
OpenJDK 64-Bit Server VM (build 24.65-b04, mixed mode)

“sudo R CMD javareconf” 导致：

Java interpreter : /bin/java
Java version     : 1.7.0_71
Java home path   : /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre
Java compiler    : /bin/javac
Java headers gen.: /bin/javah
Java archive tool: /bin/jar

trying to compile and link a JNI progam 
detected JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/../include/linux -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -c conftest.c -o conftest.o
gcc -m64 -std=gnu99 -shared -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/lib/amd64/server -ljvm -L/usr/lib64/R/lib -lR


JAVA_HOME        : /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre
Java library path: $(JAVA_HOME)/lib/amd64/server
JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
Updating Java configuration in /usr/lib64/R
Done.

尽管如此，install.packages（'rJava'）会导致：

checking Java support in R... present:
interpreter : '/bin/java'
archiver    : '/bin/jar'
compiler    : '/bin/javac'
header prep.: '/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/../include/linux'
java libs   : '-L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/lib/amd64/server -ljvm'
checking whether Java run-time works... 
Error: Could not find or load main class getsp
no
configure: error: Java interpreter '/bin/java' does not work
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/tamaspavlicek/R/x86_64-redhat-linux-gnu-library/3.1/rJava’
Warning in install.packages :
  installation of package ‘rJava’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/Rtmpnl17m7/downloaded_packages’

我不知道如何解决这个java问题。我使用RStudio和Fedora。非常感谢您的帮助。

谢谢

塔马斯

答案 1

如果您安装了 Java，请尝试从命令行重置 R 的 Java 配置

sudo R CMD javareconf

然后再次尝试安装（您可以先重新启动 RStudio）rJava

install.packages('rJava')

如果这仍然不能解决你的问题，错误表明R无法加载getsp.：

checking whether Java run-time works... 
Error: Could not find or load main class getsp

首先验证 getsp 是否可访问。

locate getsp

输出可能包含多个项目，但您应该找到如下内容：

/usr/share/R/share/java/getsp.class

然后，我们希望它是可访问的，因此将其导出，以便R可以找到它：

export CLASSPATH=/usr/share/R/share/java

在同一窗口中，启动另一个 R 会话，然后再次尝试安装。rJava

另一件要休息的事情是JAVA_HOME并重新运行javareconf

export JAVA_HOME=/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre
export PATH=$PATH:$JAVA_HOME/bin
sudo R CMD javareconf

还建议在rJava问题中使用它，因为它可能会导致其他问题。在尝试更改JAVA_HOME并再次重置之前，如果这仍然不能解决问题，则可能应该执行此操作。unset CLASSPATH

编辑

鉴于这个问题在很长一段时间内一直没有得到“解答”，我想我也应该添加我的建议，只使用不使用Java的readxl包。它的安装要容易得多，并且是整洁的一部分。只是对于那些尝试使用excel文件的人的一般建议。

答案 2

好吧，我终于通过将“JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.25.x86_64/jre/”添加到我的主文件夹中的.bashrc来管理它。

谢谢你的帮助，cdeterman。

最佳塔马斯