I have reactivated my dormant Amazon EC2 microinstance with Ubuntu 16.04.LTS and RStudio (see sessionInfo() output below) running (thanks to AMI by Louis Aslett). After ssh-ing to the AWS instance first I've run sudo apt-get update.
When I tried installing some packages (e.g xlsx and others) in R Studio (I've got an error because of missing Java, which seems to be a common problem). I followed advices to 1) install dependencies (for e.g. xlsx like rJava, and xlsxjars) separately; 2) apt-get install r-cran-rjava as suggested here. Then checking the installed java -version showed
openjdk version "1.8.0_131"
OpenJDK Runtime Environment (build 1.8.0_131-8u131-b11-0ubuntu1.16.04.2-b11)
OpenJDK 64-Bit Server VM (build 25.131-b11, mixed mode)
Similar problems were proposed "rJava load error in RStudio/R after “upgrading” to OSX Yosemite" and here "error: unable to load installed packages...", where the solution seemed to be linking the path of java to R export LD_LIBRARY_PATH=$JAVA_LD_LIBRARY_PATH or setting R's env. variables Sys.setenv(JAVA_HOME='/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server').
However, running R CMD javareconf -e revealed (I suppose) some deeper issues (see Image) &/or snippet:
R CMD javareconf -e
Java interpreter : /usr/lib/jvm/default-java/jre/bin/java
Java version : 1.8.0_131
Java home path : /usr/lib/jvm/default-java
Java compiler : not present
Java headers gen.:
Java archive tool:
trying to compile and link a JNI program
detected JNI cpp flags :
detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o
conftest.c:1:17: fatal error: jni.h: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:132: recipe for target 'conftest.o' failed
make: *** [conftest.o] Error 1
Unable to compile a JNI program
The following Java variables have been exported:
JAVA_HOME JAVA JAVAC JAVAH JAR JAVA_LIBS JAVA_CPPFLAGS JAVA_LD_LIBRARY_PATH
Running: /bin/bashwith Java compiler: not present and
conftest.c:1:17: fatal error: jni.h: No such file or directory compilation terminated. /usr/lib/R/etc/Makeconf:132: recipe for target 'conftest.o' failed
Then I've found a question "how to make jni.h be found?": here the best solution suggested gcc -I/usr/lib/jvm/jdk1.7.0_07/include
Checking the same directory cd /usr/lib/jvm/ and listing its content ls --all showed:
.default-java
.java-1.8.0-openjdk-amd64.jinfo
..java-1.8.0-openjdk-amd64 java-8-openjdk-amd64
Running, gcc -I/usr/lib/jvm/java-1.8.0-openjdk-amd64/include resulted in: gcc: fatal error: no input files
Additionally, I have tried sudo apt-get install openjdk-X-jdk (it was among the suggested answers "how to make jni.h be found?") but probably the package does not exist anymore "Unable to locate package openjdk-X-jdk".
Unfortunately, I am stuck and not skilled enough to implement other (seemingly more complicated solutions). I would really appreciate some help/input.
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel compiler stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] openxlsx_4.0.17 qdapTools_1.3.1 qdapRegex_0.7.2
[4] qdapDictionaries_1.0.6 stringr_1.1.0 stringi_1.1.2
[7] dplyr_0.5.0 tm_0.7-1 NLP_0.1-10
[10] scales_0.4.0 RColorBrewer_1.1-2 ParallelForest_1.1.0
[13] doMC_1.3.4 iterators_1.0.8 foreach_1.4.3
[16] boot_1.3-18 reshape2_1.4.1 glmm_1.1.1
[19] Matrix_1.2-6 mvtnorm_1.0-5 trust_0.1-7
[22] ggplot2_2.1.0 shiny_0.13.2
loaded via a namespace (and not attached):
[1] gtools_3.5.0 slam_0.1-40 lattice_0.20-33
[4] colorspace_1.2-7 htmltools_0.3.5 chron_2.3-50
[7] XML_3.98-1.7 DBI_0.5-1 plyr_1.8.4
[10] munsell_0.4.3 gtable_0.2.0 codetools_0.2-14
[13] httpuv_1.3.3 gender_0.5.1 Rcpp_0.12.7
[16] xtable_1.8-2 gdata_2.17.0 mime_0.5
[19] gridExtra_2.2.1 digest_0.6.10 grid_3.3.1
[22] tools_3.3.1 bitops_1.0-6 magrittr_1.5
[25] RCurl_1.95-4.8 tibble_1.2 data.table_1.10.4
[28] assertthat_0.1 R6_2.2.0 igraph_1.0.1 You need to install JDK. Take a look here as well.
where I describe how to play with R, Java and rJava package. Even though description is macOS based, it should work with Linux as well. It's quite general approach.
Your issue is related to the fact you are using JRE instead of JDK. JNI headers are missing there.