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 = "https://mirrors.ustc.edu.cn/CRAN/")
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’https://mirrors.ustc.edu.cn/CRAN/src/contrib/rJava_1.0-6.tar.gz'
Content type 'application/octet-stream' length 1047062 bytes (1022 KB)
==================================================
downloaded 1022 KB
试开URL’https://mirrors.ustc.edu.cn/CRAN/src/contrib/xlsxjars_0.6.1.tar.gz'
Content type 'application/octet-stream' length 9477071 bytes (9.0 MB)
==================================================
downloaded 9.0 MB
试开URL’https://mirrors.ustc.edu.cn/CRAN/src/contrib/xlsx_0.6.5.tar.gz'
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 for gcc... gcc -std=gnu99 -std=gnu11
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 -std=gnu99 -std=gnu11 accepts -g... yes
checking for gcc -std=gnu99 -std=gnu11 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -std=gnu11 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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 -std=gnu11 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/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 run-time works... ./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 = "https://mirrors.ustc.edu.cn/CRAN/") :
installation of package ‘rJava’ had non-zero exit status
2: In install.packages("xlsx", repos = "https://mirrors.ustc.edu.cn/CRAN/") :
installation of package ‘xlsxjars’ had non-zero exit status
3: In install.packages("xlsx", repos = "https://mirrors.ustc.edu.cn/CRAN/") :
installation of package ‘xlsx’ had non-zero exit status
再次安装xlsx包
install.packages("xlsx", repos = "https://mirrors.ustc.edu.cn/CRAN/")
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’https://mirrors.ustc.edu.cn/CRAN/src/contrib/rJava_1.0-6.tar.gz'
Content type 'application/octet-stream' length 1047062 bytes (1022 KB)
==================================================
downloaded 1022 KB
试开URL’https://mirrors.ustc.edu.cn/CRAN/src/contrib/xlsxjars_0.6.1.tar.gz'
Content type 'application/octet-stream' length 9477071 bytes (9.0 MB)
==================================================
downloaded 9.0 MB
试开URL’https://mirrors.ustc.edu.cn/CRAN/src/contrib/xlsx_0.6.5.tar.gz'
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 for gcc... gcc -std=gnu99 -std=gnu11
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 -std=gnu99 -std=gnu11 accepts -g... yes
checking for gcc -std=gnu99 -std=gnu11 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -std=gnu11 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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 -std=gnu11 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 : ''
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 = "https://mirrors.ustc.edu.cn/CRAN/") :
installation of package ‘rJava’ had non-zero exit status
2: In install.packages("xlsx", repos = "https://mirrors.ustc.edu.cn/CRAN/") :
installation of package ‘xlsxjars’ had non-zero exit status
3: In install.packages("xlsx", repos = "https://mirrors.ustc.edu.cn/CRAN/") :
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$(JAVA_HOME)/lib/server -ljvm
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-J7pprH/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o
conftest.c:1:10: fatal error: jni.h: No such file or directory
#include <jni.h>
^~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:168: recipe for target 'conftest.o' failed
make: *** [conftest.o] Error 1
Unable to compile a JNI program
JAVA_HOME : /usr/lib/jvm/java-11-openjdk-amd64
Java library path:
JNI cpp flags :
JNI linker flags :
Updating Java configuration in /usr/lib/R
Done.
安装相关依赖包
root@DKQNI3:~# apt-get install default-jdk
正在读取软件包列表... 完成
正在分析软件包的依赖关系树
正在读取状态信息... 完成
将会同时安装下列软件：
default-jdk-headless default-jre default-jre-headless fonts-dejavu-extra libatk-wrapper-java
libatk-wrapper-java-jni libgif7 libice-dev libsm-dev libxt-dev openjdk-11-jdk
openjdk-11-jdk-headless openjdk-11-jre
建议安装：
libice-doc libsm-doc libxt-doc openjdk-11-demo openjdk-11-source visualvm
下列【新】软件包将被安装：
default-jdk default-jdk-headless default-jre default-jre-headless fonts-dejavu-extra
libatk-wrapper-java libatk-wrapper-java-jni libgif7 libice-dev libsm-dev libxt-dev
openjdk-11-jdk openjdk-11-jdk-headless openjdk-11-jre
升级了 0 个软件包，新安装了 14 个软件包，要卸载 0 个软件包，有 0 个软件包未被升级。
需要下载 225 MB/225 MB 的归档。
解压缩后会消耗 242 MB 的额外空间。
您希望继续执行吗？ [Y/n] Y
再次执行root@xx:~# R CMD javareconf
root@DKQNI3:~# R CMD javareconf
Java interpreter : /usr/lib/jvm/default-java/bin/java
Java version : 11.0.16
Java home path : /usr/lib/jvm/default-java
Java compiler : /usr/lib/jvm/default-java/bin/javac
Java headers gen.:
Java archive tool: /usr/lib/jvm/default-java/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/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 -lR
JAVA_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/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)/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 -lR
The 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 = "https://mirrors.ustc.edu.cn/CRAN/")
将程序包安装入‘/usr/local/lib/R/site-library’
(因为‘lib’没有被指定)
试开URL’https://mirrors.ustc.edu.cn/CRAN/src/contrib/rJava_1.0-6.tar.gz'
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 for gcc... gcc -std=gnu99 -std=gnu11
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 -std=gnu99 -std=gnu11 accepts -g... yes
checking for gcc -std=gnu99 -std=gnu11 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -std=gnu11 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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 -std=gnu11 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/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 run-time works... yes
checking whether -Xrs is supported... yes
checking whether -Xrs will be used... yes
checking whether JVM will be loaded dynamically... no
checking whether JNI programs can be compiled... yes
checking whether JNI programs run... yes
checking JNI data types... ok
checking whether JRI should be compiled (autodetect)... yes
checking whether debugging output should be enabled... no
checking whether memory profiling is desired... no
checking whether threads support is requested... no
checking whether callbacks support is requested... no
checking whether JNI cache support is requested... no
checking whether headless init is enabled... no
checking whether JRI is requested... 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 system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gcc... gcc -std=gnu99 -std=gnu11
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 the compiler supports GNU C... yes
checking whether gcc -std=gnu99 -std=gnu11 accepts -g... yes
checking for gcc -std=gnu99 -std=gnu11 option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/time.h... yes
checking for sys/types.h... (cached) yes
checking for sys/select.h... yes
checking Java version... 11.0.16
checking Java compatibility version (integer)... 11
checking whether actually works... no
checking whether javah was replaced by javac -h... yes
checking for target flags... -h . -target 1.6 -source 1.6
checking whether Java interpreter works... checking whether JNI programs can be compiled... yes
checking whether JNI programs can be run... yes
checking JNI data types... ok
checking whether Rinterface.h exports R_CStackXXX variables... yes
checking whether Rinterface.h exports R_SignalHandlers... 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 . org.rosuda.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 = "https://mirrors.ustc.edu.cn/CRAN/")
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’https://mirrors.ustc.edu.cn/CRAN/src/contrib/xlsxjars_0.6.1.tar.gz'
Content type 'application/octet-stream' length 9477071 bytes (9.0 MB)
==================================================
downloaded 9.0 MB
试开URL’https://mirrors.ustc.edu.cn/CRAN/src/contrib/xlsx_0.6.5.tar.gz'
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’
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