elias-jhsph / rocker-flask Goto Github PK

https://stackoverflow.com/questions/51256462/r-cannot-install-rjava-what-is-r-api-3-4

https://askubuntu.com/questions/1168264/problem-installing-rjava-with-r-3-6-on-ubuntu-18-04

sudo apt-get install -y default-jre
sudo apt-get install -y default-jdk
sudo R CMD javareconf

RJava fails to install both in R prompt and in the terminal

Ubuntu 18.04, R v4.1

Following the reccommended installation instructions

sudo apt-get install -y default-jre
sudo apt-get install -y default-jdk
sudo R CMD javareconf

sudo apt-get install r-cran-rjava

Throws an error asking for dependency r-api-3.4

With R prompt install

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_1.0-4.tar.gz'
Content type 'application/x-gzip' length 672236 bytes (656 KB)
==================================================
downloaded 656 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 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/RtmpkFh0cn/R.INSTALL13125146540f/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... 11.0.11
  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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c registration.c -o registration.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-vB4ZXq/r-base-4.1.0=. -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 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/RtmpkFh0cn/R.INSTALL13125146540f/rJava/jri'
  make -C src JRI.jar
  make[2]: Entering directory '/tmp/RtmpkFh0cn/R.INSTALL13125146540f/rJava/jri/src'
  /usr/lib/jvm/default-java/bin/javac -h . -target 1.6 -source 1.6 -d . ../RConsoleOutputStream.java ../RFactor.java ../REXP.java ../Rengine.java ../RList.java ../Mutex.java ../package-info.java ../RMainLoopCallbacks.java ../RVector.java ../RBool.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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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-vB4ZXq/r-base-4.1.0=. -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 -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/bin/ld: cannot find -lpcre2-8
  /usr/bin/ld: cannot find -llzma
  /usr/bin/ld: cannot find -lbz2
  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/RtmpkFh0cn/R.INSTALL13125146540f/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/RtmpkFh0cn/R.INSTALL13125146540f/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/RtmpFgub8P/downloaded_packages’
Warning message:
In install.packages("rJava") :
installation of package ‘rJava’ had non-zero exit status

And for the terminal install

sudo apt-get install r-cran-rjava
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
r-cran-rjava : Depends: r-api-3.4
E: Unable to correct problems, you have held broken packages.