在 Linux Mint 19.3 Mate 中安裝 rJava 的問題

Question

我的 Linux Mint 19.3 Mate 機器上安裝了 R 3.6.2。

第一次安裝出錯后，我安裝了default-jdk並運行了sudo R CMD javareconf ，但仍然沒有安裝 rJava。

我在下面提供了控制台消息。

Installing package into ‘/home/bishwarup/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/rJava_0.9-11.tar.gz'
Content type 'application/x-gzip' length 675188 bytes (659 KB)
==================================================
downloaded 659 KB

* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc -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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -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 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 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/Rtmp3jWceP/R.INSTALL1801349f8b16/rJava/jri)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local'  --cache-file=/dev/null --srcdir=.
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
'config' variable 'CPP' is deprecated
checking for gcc... gcc -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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -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 Java version... 11.0.6
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 -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-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rglue.c -o Rglue.o
gcc -std=gnu99 -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-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c arrayc.c -o arrayc.o
gcc -std=gnu99 -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-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c callJNI.c -o callJNI.o
gcc -std=gnu99 -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-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c callback.c -o callback.o
gcc -std=gnu99 -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-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fields.c -o fields.o
gcc -std=gnu99 -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-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -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-t3diwe/r-base-3.6.2=. -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 -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-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c loader.c -o loader.o
gcc -std=gnu99 -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-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c otables.c -o otables.o
gcc -std=gnu99 -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-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rJava.c -o rJava.o
gcc -std=gnu99 -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-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tools.c -o tools.o
gcc -std=gnu99 -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 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/Rtmp3jWceP/R.INSTALL1801349f8b16/rJava/jri'
make -C src JRI.jar
make[2]: Entering directory '/tmp/Rtmp3jWceP/R.INSTALL1801349f8b16/rJava/jri/src'
/usr/lib/jvm/default-java/bin/javac -h . -target 1.6 -source 1.6 -d . ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../Mutex.java ../package-info.java ../RMainLoopCallbacks.java ../RVector.java ../RBool.java ../RList.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
if [ -n "" ]; then  -d . -classpath . org.rosuda.JRI.Rengine; fi
gcc -std=gnu99 -c -o Rengine.o Rengine.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -c -o jri.o jri.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -c -o Rinit.o Rinit.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -c -o globals.o globals.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -c -o rjava.o rjava.c -g -Iinclude  -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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
rjava.c: In function ‘RJava_request_lock’:
rjava.c:22:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(ipcout, buf, sizeof(ptrlong));
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rjava.c: In function ‘RJava_clear_lock’:
rjava.c:30:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(ipcout, buf, sizeof(ptrlong));
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rjava.c: In function ‘RJava_request_callback’:
rjava.c:39:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(ipcout, buf, sizeof(ptrlong) * 3);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rjava.c: In function ‘RJava_init_ctrl’:
rjava.c:51:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(ipcout, buf, sizeof(ptrlong));
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rjava.c:52:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(resin, buf, sizeof(ptrlong) * 2);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu99 -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 -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
/usr/bin/ld: cannot find -lpcre2-8
/usr/bin/ld: cannot find -lbz2
collect2: error: ld returned 1 exit status
Makefile.all:35: recipe for target 'libjri.so' failed
make[2]: Leaving directory '/tmp/Rtmp3jWceP/R.INSTALL1801349f8b16/rJava/jri/src'
make[2]: *** [libjri.so] Error 1
Makefile.all:19: recipe for target 'src/JRI.jar' failed
make[1]: Leaving directory '/tmp/Rtmp3jWceP/R.INSTALL1801349f8b16/rJava/jri'
make[1]: *** [src/JRI.jar] Error 2
Makevars:14: recipe for target 'jri' failed
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/home/bishwarup/R/x86_64-pc-linux-gnu-library/3.6/rJava’
Warning in install.packages :
  installation of package ‘rJava’ had non-zero exit status

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

我正在嘗試使用 R 構建 MaxEnt 模型，它是一個 .jar 文件。 因此，我需要能夠安裝 rJava。 請幫我解決這個問題。

編輯：

當我在終端中運行java -version時，會顯示以下輸出：

openjdk version "11.0.6" 2020-01-14
OpenJDK Runtime Environment (build 11.0.6+10-post-Ubuntu-1ubuntu118.04.1)
OpenJDK 64-Bit Server VM (build 11.0.6+10-post-Ubuntu-1ubuntu118.04.1, mixed mode, sharing)

Answer 1

以下是您的問題：

/usr/bin/ld: 找不到 -lpcre2-8 /usr/bin/ld: 找不到 -lbz2

鏈接器 (ld) 找不到這些庫。 我在 Ubuntu 上只有 lpcre2-8 有類似的問題。 我通過安裝解決了我的問題：

須藤 apt-get 安裝 libpcre2-dev

我想 bz2 的第二個錯誤將通過以下方式修復：

須藤 apt-get 安裝 libbz2-dev

希望有幫助