Ubuntu安装xlsx包时遇到ERROR: configuration failed for package ‘rJava’

Ubuntu安装xlsx包时遇到ERROR: configuration failed for package ‘rJava’

环境描述

环境：Ubuntu子系统

R：4.1.2

在R中安装xlsx包

> install.packages("xlsx", repos = "/")
将程序包安装入‘/usr/local/lib/R/site-library’
(因为‘lib’没有被指定)
还安装相依关系‘rJava’, ‘xlsxjars’试开URL’.'
Content type 'application/octet-stream' length 1047062 bytes (1022 KB)
==================================================
downloaded 1022 KB试开URL’.6.'
Content type 'application/octet-stream' length 9477071 bytes (9.0 MB)
==================================================
downloaded 9.0 MB试开URL’.6.'
Content type 'application/octet-stream' length 489493 bytes (478 KB)
==================================================
downloaded 478 KB* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
** using staged installation
checking  gcc -std=gnu99 -std=gnu11
checking whether the C  yes
checking for C compiler default output  a.out
checking for suffix  
checking whether we are  no
checking for suffix of  o
checking whether we are using the GNU  yes
checking whether gcc -std=gnu99 -std=gnu11 accepts -g... yes
checking for gcc -std=gnu99 -std=gnu11 option to accept  none needed
checking how to run the  gcc -std=gnu99 -std=gnu11 -E
checking for grep that handles long lines and -e... /bin/grep
checking  /bin/grep -E
checking for ANSI C  yes
checking for sys/wait.h that is POSIX. yes
checking for sys/ yes
checking for sys/ yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  (cached) yes
checking sys/time. yes
checking sys/time. yes
checking for sys/ yes
checking for  (cached) yes
checking for an ANSI  yes
checking whether time.h and sys/time.h may both  yes
configure: checking whether gcc -std=gnu99 -std=gnu11 supports 
yes
checking whether setjmp.h is POSIX. yes
checking whether sigsetjmp  yes
checking whether siglongjmp  yes
checking Java support  present:
interpreter : '/usr/lib/jvm/default-java/bin/java'
archiver    : '/usr/lib/jvm/default-java/bin/jar'
compiler    : '/usr/lib/jvm/default-java/bin/javac'
header prep.: ''
cpp flags   : '-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux'
java libs   : '-L/usr/lib/jvm/default-java/lib/server -ljvm'
checking whether Java  ./configure: line 3796: /usr/lib/jvm/default-java/bin/java: No such file or directory
no
configure: error: Java interpreter '/usr/lib/jvm/default-java/bin/java' does not work
ERROR: configuration failed for package ‘rJava’
* removing ‘/usr/local/lib/R/site-library/rJava’
ERROR: dependency ‘rJava’ is not available for package ‘xlsxjars’
* removing ‘/usr/local/lib/R/site-library/xlsxjars’
ERROR: dependencies ‘rJava’, ‘xlsxjars’ are not available for package ‘xlsx’
* removing ‘/usr/local/lib/R/site-library/xlsx’The downloaded source packages are in‘/tmp/Rtmp4CEfZK/downloaded_packages’
Warning messages:
1: In install.packages("xlsx", repos = "/") :installation of package ‘rJava’ had non-zero exit status
2: In install.packages("xlsx", repos = "/") :installation of package ‘xlsxjars’ had non-zero exit status
3: In install.packages("xlsx", repos = "/") :installation of package ‘xlsx’ had non-zero exit status

再次安装xlsx包

install.packages("xlsx", repos = "/")
将程序包安装入‘/usr/local/lib/R/site-library’
(因为‘lib’没有被指定)
还安装相依关系‘rJava’, ‘xlsxjars’试开URL’.'
Content type 'application/octet-stream' length 1047062 bytes (1022 KB)
==================================================
downloaded 1022 KB试开URL’.6.'
Content type 'application/octet-stream' length 9477071 bytes (9.0 MB)
==================================================
downloaded 9.0 MB试开URL’.6.'
Content type 'application/octet-stream' length 489493 bytes (478 KB)
==================================================
downloaded 478 KB* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
** using staged installation
checking  gcc -std=gnu99 -std=gnu11
checking whether the C  yes
checking for C compiler default output  a.out
checking for suffix  
checking whether we are  no
checking for suffix of  o
checking whether we are using the GNU  yes
checking whether gcc -std=gnu99 -std=gnu11 accepts -g... yes
checking for gcc -std=gnu99 -std=gnu11 option to accept  none needed
checking how to run the  gcc -std=gnu99 -std=gnu11 -E
checking for grep that handles long lines and -e... /bin/grep
checking  /bin/grep -E
checking for ANSI C  yes
checking for sys/wait.h that is POSIX. yes
checking for sys/ yes
checking for sys/ yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  (cached) yes
checking sys/time. yes
checking sys/time. yes
checking for sys/ yes
checking for  (cached) yes
checking for an ANSI  yes
checking whether time.h and sys/time.h may both  yes
configure: checking whether gcc -std=gnu99 -std=gnu11 supports 
yes
checking whether setjmp.h is POSIX. yes
checking whether sigsetjmp  yes
checking whether siglongjmp  yes
checking Java support  present:
interpreter : '/usr/bin/java'
archiver    : ''
compiler    : ''
header prep.: ''
cpp flags   : ''
java libs   : ''
configure: error: Java Development Kit (JDK) is missing or not registered in R
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 ‘/usr/local/lib/R/site-library/rJava’
ERROR: dependency ‘rJava’ is not available for package ‘xlsxjars’
* removing ‘/usr/local/lib/R/site-library/xlsxjars’
ERROR: dependencies ‘rJava’, ‘xlsxjars’ are not available for package ‘xlsx’
* removing ‘/usr/local/lib/R/site-library/xlsx’The downloaded source packages are in‘/tmp/Rtmp4CEfZK/downloaded_packages’
Warning messages:
1: In install.packages("xlsx", repos = "/") :installation of package ‘rJava’ had non-zero exit status
2: In install.packages("xlsx", repos = "/") :installation of package ‘xlsxjars’ had non-zero exit status
3: In install.packages("xlsx", repos = "/") :installation of package ‘xlsx’ had non-zero exit status

错误提示重要信息

ERROR: configuration failed for package ‘rJava’

configure: error: Java Development Kit (JDK) is missing or not registered in R
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.
 

从错误提示中可以看出是java的问题

因此检查java的问题: java -version

root@DKQNI3:~# java -version
openjdk version "11.0.16" 2022-07-19
OpenJDK Runtime Environment (build 11.0.16+8-post-Ubuntu-0ubuntu118.04)
OpenJDK 64-Bit Server VM (build 11.0.16+8-post-Ubuntu-0ubuntu118.04, mixed mode, sharing)root@DKQNI3:~# R CMD javareconf
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/bin/java
Java version     : 11.0.16
Java home path   : /usr/lib/jvm/java-11-openjdk-amd64
Java compiler    : not present
Java headers gen.: 
Java archive tool: trying to compile and link a JNI program 
detected JNI cpp flags    : 
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
conftest.c:1:10: fatal error: jni.h: No such file or directory#include <jni.h>^~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:168: recipe for target 'conftest.o' failed
make: *** [conftest.o] Error 1
Unable to compile a JNI programJAVA_HOME        : /usr/lib/jvm/java-11-openjdk-amd64
Java library path: 
JNI cpp flags    : 
JNI linker flags : 
Updating Java configuration in /usr/lib/R
Done.

安装相关依赖包

root@DKQNI3:~# apt-get install default-jdk
正在读取软件包列表... 完成
正在分析软件包的依赖关系树       
正在读取状态信息... 完成       
将会同时安装下列软件：default-jdk-headless default-jre default-jre-headless fonts-dejavu-extra libatk-wrapper-javalibatk-wrapper-java-jni libgif7 libice-dev libsm-dev libxt-dev openjdk-11-jdkopenjdk-11-jdk-headless openjdk-11-jre
建议安装：libice-doc libsm-doc libxt-doc openjdk-11-demo openjdk-11-source visualvm
下列【新】软件包将被安装：default-jdk default-jdk-headless default-jre default-jre-headless fonts-dejavu-extralibatk-wrapper-java libatk-wrapper-java-jni libgif7 libice-dev libsm-dev libxt-devopenjdk-11-jdk openjdk-11-jdk-headless openjdk-11-jre
升级了 0 个软件包，新安装了 14 个软件包，要卸载 0 个软件包，有 0 个软件包未被升级。
需要下载 225 MB/225 MB 的归档。
解压缩后会消耗 242 MB 的额外空间。
您希望继续执行吗？ [Y/n] Y

再次执行root@xx:~# R CMD javareconf

root@DKQNI3:~# R CMD javareconf
Java interpreter : /usr/lib/jvm/default-java/bin/java
Java version     : 11.0.16
Java home path   : /usr/lib/jvm/default-java
Java compiler    : /usr/lib/jvm/default-java/bin/javac
Java headers gen.: 
Java archive tool: /usr/lib/jvm/default-java/bin/jartrying 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)/lib/server -ljvm
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -std=gnu11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/lib/server -ljvm -L/usr/lib/R/lib -lRJAVA_HOME        : /usr/lib/jvm/default-java
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /usr/lib/R
Done.

root@DKQNI3:~# R CMD javareconf -e
Java interpreter : /usr/lib/jvm/default-java/bin/java
Java version     : 11.0.16
Java home path   : /usr/lib/jvm/default-java
Java compiler    : /usr/lib/jvm/default-java/bin/javac
Java headers gen.: 
Java archive tool: /usr/lib/jvm/default-java/bin/jartrying 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)/lib/server -ljvm
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -std=gnu11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/lib/server -ljvm -L/usr/lib/R/lib -lRThe following Java variables have been exported:
JAVA_HOME JAVA JAVAC JAVAH JAR JAVA_LIBS JAVA_CPPFLAGS JAVA_LD_LIBRARY_PATH
Running: /bin/bash

重新安装rJava

> install.packages("rJava", repos = "/")
将程序包安装入‘/usr/local/lib/R/site-library’
(因为‘lib’没有被指定)
试开URL’.'
Content type 'application/octet-stream' length 1047062 bytes (1022 KB)
==================================================
downloaded 1022 KB* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
** using staged installation
checking  gcc -std=gnu99 -std=gnu11
checking whether the C  yes
checking for C compiler default output  a.out
checking for suffix  
checking whether we are  no
checking for suffix of  o
checking whether we are using the GNU  yes
checking whether gcc -std=gnu99 -std=gnu11 accepts -g... yes
checking for gcc -std=gnu99 -std=gnu11 option to accept  none needed
checking how to run the  gcc -std=gnu99 -std=gnu11 -E
checking for grep that handles long lines and -e... /bin/grep
checking  /bin/grep -E
checking for ANSI C  yes
checking for sys/wait.h that is POSIX. yes
checking for sys/ yes
checking for sys/ yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  (cached) yes
checking sys/time. yes
checking sys/time. yes
checking for sys/ yes
checking for  (cached) yes
checking for an ANSI  yes
checking whether time.h and sys/time.h may both  yes
configure: checking whether gcc -std=gnu99 -std=gnu11 supports 
yes
checking whether setjmp.h is POSIX. yes
checking whether sigsetjmp  yes
checking whether siglongjmp  yes
checking Java support  present:
interpreter : '/usr/lib/jvm/default-java/bin/java'
archiver    : '/usr/lib/jvm/default-java/bin/jar'
compiler    : '/usr/lib/jvm/default-java/bin/javac'
header prep.: ''
cpp flags   : '-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux'
java libs   : '-L/usr/lib/jvm/default-java/lib/server -ljvm'
checking whether Java  yes
checking whether -Xrs  yes
checking whether -Xrs will  yes
checking whether JVM will be  no
checking whether JNI programs can  yes
checking whether JNI  yes
checking JNI  ok
checking whether JRI should be compiled (autodetect)... yes
checking whether debugging output should  no
checking whether memory profiling  no
checking whether threads support  no
checking whether callbacks support  no
checking whether JNI cache support  no
checking whether headless init  no
checking whether JRI  yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
=== configuring in jri (/tmp/Rtmpx8fPnF/R.INSTALL9d76b771f72/rJava/jri)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local'  --cache-file=/dev/null --srcdir=.
checking build  x86_64-pc-linux-gnu
checking host  x86_64-pc-linux-gnu
checking  gcc -std=gnu99 -std=gnu11
checking whether the C  yes
checking for C compiler default output  a.out
checking for suffix  
checking whether we are  no
checking for suffix of  o
checking whether the compiler supports  yes
checking whether gcc -std=gnu99 -std=gnu11 accepts -g... yes
checking for gcc -std=gnu99 -std=gnu11 option to enable  none needed
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for  yes
checking for sys/ yes
checking for sys/ yes
checking for  yes
checking for sys/ yes
checking for sys/ (cached) yes
checking for sys/ yes
checking  11.0.16
checking Java compatibility version (integer)... 11
checking whether   no
checking whether javah was replaced by javac -h... yes
checking for   -h . -target 1.6 -source 1.6
checking whether Java  checking whether JNI programs can  yes
checking whether JNI programs can  yes
checking JNI  ok
checking whether Rinterface.h exports R_ yes
checking whether Rinterface.h exports  yes
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating Makefile
config.status: creating run
config.status: creating src/config.h
** libs
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rglue.c -o Rglue.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c arrayc.c -o arrayc.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c callJNI.c -o callJNI.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c callback.c -o callback.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fields.c -o fields.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c jri_glue.c -o jri_glue.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c loader.c -o loader.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c otables.c -o otables.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rJava.c -o rJava.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c registration.c -o registration.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tools.c -o tools.o
gcc -std=gnu99 -std=gnu11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o rJava.so Rglue.o arrayc.o callJNI.o callback.o fields.o init.o jri_glue.o loader.o otables.o rJava.o registration.o tools.o -L/usr/lib/jvm/default-java/lib/server -ljvm -L/usr/lib/R/lib -lR
(cd ../jri && make)
make[1]: Entering directory '/tmp/Rtmpx8fPnF/R.INSTALL9d76b771f72/rJava/jri'
make -C src JRI.jar
make[2]: Entering directory '/tmp/Rtmpx8fPnF/R.INSTALL9d76b771f72/rJava/jri/src'
/usr/lib/jvm/default-java/bin/javac -h . -target 1.6 -source 1.6  -d . ../package-info.java ../RFactor.java ../REXP.java ../Rengine.java ../Mutex.java ../RConsoleOutputStream.java ../RMainLoopCallbacks.java ../RVector.java ../RBool.java ../RList.java
warning: [options] bootstrap class path not set in conjunction with -source 6
warning: [options] source value 6 is obsolete and will be removed in a future release
warning: [options] target value 1.6 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
4 warnings
if [ -n "" ]; then  -d . -classpath . suda.JRI.Rengine; fi
gcc -std=gnu99 -std=gnu11 -c -o Rengine.o Rengine.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux  -fpic -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -I/usr/share/R/include -I/usr/share/R/include 
gcc -std=gnu99 -std=gnu11 -c -o jri.o jri.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux  -fpic -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -I/usr/share/R/include -I/usr/share/R/include 
gcc -std=gnu99 -std=gnu11 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux  -fpic -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -I/usr/share/R/include -I/usr/share/R/include 
gcc -std=gnu99 -std=gnu11 -c -o Rinit.o Rinit.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux  -fpic -I/usr/share/R/include -I/usr/share/R/include 
gcc -std=gnu99 -std=gnu11 -c -o globals.o globals.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux  -fpic -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux 
gcc -std=gnu99 -std=gnu11 -c -o rjava.o rjava.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux  -fpic -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux 
gcc -std=gnu99 -std=gnu11 -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o  -shared -L/usr/lib/jvm/default-java/lib/server -ljvm -Wl,--export-dynamic -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n 
/usr/lib/jvm/default-java/bin/javac -h . -target 1.6 -source 1.6  -d . ../package-info.java ../RFactor.java ../REXP.java ../RList.java ../Mutex.java ../RVector.java ../RBool.java ../RConsoleOutputStream.java ../RMainLoopCallbacks.java ../Rengine.java
warning: [options] bootstrap class path not set in conjunction with -source 6
warning: [options] source value 6 is obsolete and will be removed in a future release
warning: [options] target value 1.6 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
4 warnings
/usr/lib/jvm/default-java/bin/jar fc JRI.jar org libjri.so
make[2]: Leaving directory '/tmp/Rtmpx8fPnF/R.INSTALL9d76b771f72/rJava/jri/src'
rm -f libjri.so
cp src/libjri.so libjri.so
/usr/lib/jvm/default-java/bin/javac -h . -target 1.6 -source 1.6 -classpath src/JRI.jar -d examples examples/rtest.java
warning: [options] bootstrap class path not set in conjunction with -source 6
warning: [options] source value 6 is obsolete and will be removed in a future release
warning: [options] target value 1.6 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
Note: examples/rtest.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
4 warnings
/usr/lib/jvm/default-java/bin/javac -h . -target 1.6 -source 1.6 -classpath src/JRI.jar -d examples examples/rtest2.java
warning: [options] bootstrap class path not set in conjunction with -source 6
warning: [options] source value 6 is obsolete and will be removed in a future release
warning: [options] target value 1.6 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
Note: examples/rtest2.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
4 warnings
make[1]: Leaving directory '/tmp/Rtmpx8fPnF/R.INSTALL9d76b771f72/rJava/jri'
installing via 'install.libs.R' to /usr/local/lib/R/site-library/00LOCK-rJava/00new/rJava
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rJava)The downloaded source packages are in‘/tmp/Rtmp4CEfZK/downloaded_packages’

rJava安装后重新安装xlsx

> install.packages("xlsx", repos = "/")
将程序包安装入‘/usr/local/lib/R/site-library’
(因为‘lib’没有被指定)
还安装相依关系‘xlsxjars’试开URL’.6.'
Content type 'application/octet-stream' length 9477071 bytes (9.0 MB)
==================================================
downloaded 9.0 MB试开URL’.6.'
Content type 'application/octet-stream' length 489493 bytes (478 KB)
==================================================
downloaded 478 KB* installing *source* package ‘xlsxjars’ ...
** package ‘xlsxjars’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xlsxjars)
* installing *source* package ‘xlsx’ ...
** package ‘xlsx’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xlsx)The downloaded source packages are in‘/tmp/Rtmp4CEfZK/downloaded_packages’