我无法安装 rJava（见下面的日志）。我搜索了 Google，并尝试通过安装以下软件包来解决这个问题，但无济于事：
- libxml2-dev
- libcairo2-dev
- libsqlite-dev
- libmariadbd-dev
- libmariadb-客户端-lgpl-dev
- libpq-dev
- 默认 jdk
- libicu-dev
- libbz2-dev
- liblzma-dev
我R CMD javareconf在尝试安装 rJava 之前运行并得到以下输出：
Java interpreter : /usr/lib/jvm/default-java/bin/java
Java version : 11.0.4
Java home path : /usr/lib/jvm/default-java
Java compiler : /usr/lib/jvm/default-java/bin/javac
Java headers gen.: /usr/bin/javah
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 -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-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o
gcc -std=gnu99 -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.
然后，当我尝试安装 rJava 时，我得到：
> install.packages('rJava')
Installing package into ‘/usr/local/lib/R/site-library’
(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.: '/usr/bin/javah'
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/RtmpzTj1AJ/R.INSTALL1667eb1d2f2/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
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... 11.0.4
checking Java compatibility version (integer)... 11
checking whether /usr/bin/javah actually works... yes
checking for target flags... -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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/RtmpzTj1AJ/R.INSTALL1667eb1d2f2/rJava/jri'
make -C src JRI.jar
make[2]: Entering directory '/tmp/RtmpzTj1AJ/R.INSTALL1667eb1d2f2/rJava/jri/src'
/usr/lib/jvm/default-java/bin/javac -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 "/usr/bin/javah" ]; then /usr/bin/javah -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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-uuRxut/r-base-3.6.1=. -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
collect2: error: ld returned 1 exit status
Makefile.all:35: recipe for target 'libjri.so' failed
make[2]: *** [libjri.so] Error 1
make[2]: Leaving directory '/tmp/RtmpzTj1AJ/R.INSTALL1667eb1d2f2/rJava/jri/src'
Makefile.all:19: recipe for target 'src/JRI.jar' failed
make[1]: *** [src/JRI.jar] Error 2
make[1]: Leaving directory '/tmp/RtmpzTj1AJ/R.INSTALL1667eb1d2f2/rJava/jri'
Makevars:14: recipe for target 'jri' failed
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/usr/local/lib/R/site-library/rJava’
The downloaded source packages are in
‘/tmp/RtmpPyjqqk/downloaded_packages’
Warning message:
In install.packages("rJava") :
installation of package ‘rJava’ had non-zero exit status
关于我还应该尝试什么，还有什么想法吗？
答案1
我通过将 R 从 3.6 降级到 3.4 解决了该问题。我尝试通过 aptitude 安装 rJava 时发现了此解决方案。我找不到任何文档说明 rJava 与 R 3.6 不兼容，并且我在 Mac 上将 rJava 与 R 3.5 一起安装，因此这似乎不是一个理想的解决方案，但它足以满足我当前的需求。
$ sudo aptitude install r-cran-rjava
The following NEW packages will be installed:
r-cran-rjava{b}
0 packages upgraded, 1 newly installed, 0 to remove and 19 not upgraded.
Need to get 557 kB of archives. After unpacking 1704 kB will be used.
The following packages have unmet dependencies:
r-cran-rjava : Depends: r-api-3.4 which is a virtual package, provided by:
- r-base-core (3.4.4-1ubuntu1), but 3.6.1-3bionic is installed
The following actions will resolve these dependencies:
Keep the following packages at their current version:
1) r-cran-rjava [Not Installed]
Accept this solution? [Y/n/q/?] n
The following actions will resolve these dependencies:
Downgrade the following packages:
1) r-base [3.6.1-3bionic (now) -> 3.4.4-1ubuntu1 (bionic)]
2) r-base-core [3.6.1-3bionic (now) -> 3.4.4-1ubuntu1 (bionic)]
3) r-cran-boot [1.3-23-2bionic0 (now) -> 1.3-20-1.1 (bionic)]
4) r-cran-class [7.3-15-1bionic0 (now) -> 7.3-14-2build1 (bionic)]
5) r-cran-cluster [2.1.0-2bionic0 (now) -> 2.0.6-2build1 (bionic)]
6) r-cran-codetools [0.2-16-1bionic0 (now) -> 0.2-15-1.1 (bionic)]
7) r-cran-foreign [0.8.72-1bionic0 (now) -> 0.8.69-1build1 (bionic)]
8) r-cran-kernsmooth [2.23-15-3cranArtful0~ubuntu18.04.1~ppa1 (now) -> 2.23-15-3build1 (bionic)]
9) r-cran-mass [7.3-51.4-2bionic0 (now) -> 7.3-49-1 (bionic)]
10) r-cran-matrix [1.2-17-2bionic0 (now) -> 1.2-12-1 (bionic)]
11) r-cran-nlme [3.1.141-1bionic0 (now) -> 3.1.131-3build1 (bionic)]
12) r-cran-nnet [7.3-12-2cranArtful0~ubuntu18.04.1~ppa1 (now) -> 7.3-12-2build1 (bionic)]
13) r-cran-rpart [4.1-15-2bionic0 (now) -> 4.1-13-1 (bionic)]
14) r-cran-spatial [7.3-11-2cranArtful0~ubuntu18.04.1~ppa1 (now) -> 7.3-11-2build1 (bionic)]
15) r-cran-survival [2.44-1.1-2bionic0 (now) -> 2.41-3-2build1 (bionic)]
16) r-recommended [3.6.1-3bionic (now) -> 3.4.4-1ubuntu1 (bionic)]
答案2
在 18.04 和 [R] 版本 3.6 上，我
sudo apt-get install libpcre2-dev
按照此线程中的说明进行了以下操作https://stackoverflow.com/questions/59969845/problems-with-installation-of-rjava-in-linux-mint-19-3-mate
rJava 已成功安装。