is xlsx compatible with Java/16 ?

[eylenth]

Hi

I'm trying to install xlsx with Java/16, but I'm getting the following error message:

Error: package or namespace load failed for xlsx:
 .onLoad failed in loadNamespace() for 'xlsx', details:
  call: .jnew("org/apache/poi/xssf/usermodel/XSSFWorkbook")
  error: java.lang.UnsatisfiedLinkError: $install_dir/Java/16.0.1/lib/libnio.so: $install_dir/Java/16.0.1/lib/libnio.so: undefined symbol: ipv4_available

is xlsx not compatible with Java/16 ?

[colearendt]

Interesting! I'm not sure! I will give this a check.

It's worth noting that you should be able to test the new version of embedded Java bits if you run:

remotes::install_github("colearendt/xlsx@bump-poi")

If this is indeed an "old version of the Apache POI library" issue, that should resolve it. However, I do not yet have all the kinks sorted out of that branch yet, so some functionality does not work.

I would be curious to hear what you find though!

[eylenth]

I'm getting the following error message when I try to install the bump-poi version:

Installing package into ‘$install_dir/R-bundle-extra/4.0.3-foss-2020b-R-4.0.3’
(as ‘lib’ is unspecified)
* installing *source* package ‘xlsx’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in .jcheck() : No running JVM detected. Maybe .jinit() would help.
Error: unable to load R code in package ‘xlsx’
Execution halted
ERROR: lazy loading failed for package ‘xlsx’
* removing $install_dir/R-bundle-extra/4.0.3-foss-2020b-R-4.0.3/xlsx’
Error: Failed to install 'xlsx' from GitHub:
  (converted from warning) installation of package ‘/tmp/Rtmp2hQPu2/file298fd4b653d78/xlsx_0.6.5.9100.tar.gz’ had non-zero exit status
> .jinit()
Error in .jinit() : could not find function ".jinit"
> .jcheck()
Error in .jcheck() : could not find function ".jcheck"

[colearendt]

Apologies for the late reply here. It sounds like some progress here though!

So the .jinit() function is in the rJava package. Maybe try:

rJava::.jInit()
# or
library(rJava)
.jinit()

[eylenth]

I'm getting the following output:

> rJava::.jInit()
Error: '.jInit' is not an exported object from 'namespace:rJava'
> library(rJava)
> .jinit()
[1] 0

then I tried to install the xlsx bump-poi version again, but I'm getting the same error message

[colearendt]

(Sorry for the typo on the first .jinit(). Probably auto-correct got me). The "no running jvm detected" message? Maybe try this?

library(rJava)
.jinit()
.jcheck()
.jstrVal('hello')

Something weird is going on in your JVM, it seems like!

[eylenth]

I'm getting the following output:

> library(rJava)
> .jinit()
> .jcheck()
> .jstrVal('hello')
[1] "hello"
> 

[colearendt]

Weeeird! So now that looks totally normal!! Ok, so I did a bit of testing and this looks like it works (even w/ the CRAN release of xlsx) in a vanilla container. Can you share the output of R CMD javareconf?:

# R CMD javareconf
Java interpreter : /opt/java/openjdk/bin/java
Java version     : 16.0.1
Java home path   : /opt/java/openjdk
Java compiler    : /opt/java/openjdk/bin/javac
Java headers gen.:
Java archive tool: /opt/java/openjdk/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"/opt/R/4.0.5/lib/R/include" -DNDEBUG -I/opt/java/openjdk/include -I/opt/java/openjdk/include/linux  -I/usr/local/include   -fpic  -g -O2  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/opt/R/4.0.5/lib/R/lib -L/usr/local/lib -o conftest.so conftest.o -L/opt/java/openjdk/lib/server -ljvm -L/opt/R/4.0.5/lib/R/lib -lR


JAVA_HOME        : /opt/java/openjdk
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 /opt/R/4.0.5/lib/R
Done.

If you're on linux, you could also try:

find / -name 'libnio.so'
# /opt/java/openjdk/lib/libnio.so
ldd $( find / -name 'libnio.so' )
# ldd: warning: you do not have execution permission for `/opt/java/openjdk/lib/libnio.so'
#       linux-vdso.so.1 =>  (0x00007fff7a8d0000)
#       libjava.so => /opt/java/openjdk/lib/libjava.so (0x00007f9ef1f95000)
#       libnet.so => /opt/java/openjdk/lib/libnet.so (0x00007f9ef1d7f000)
#       libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f9ef1b63000)
#       libdl.so.2 => /lib64/libdl.so.2 (0x00007f9ef195f000)
#       libc.so.6 => /lib64/libc.so.6 (0x00007f9ef1591000)
#       /lib64/ld-linux-x86-64.so.2 (0x00007f9ef23cf000)
#       libjvm.so => not found
#       libjvm.so => not found

I'm wondering if there is something weird in your Java install (i.e. why that ipv4_address variable is missing)

The container I'm using, in case it is helpful:

Dockerfile

FROM adoptopenjdk/openjdk16:jdk-16.0.1_9-centos

ARG R_VERSION=4.0.5
RUN yum install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm && \
  curl -O https://cdn.rstudio.com/r/centos-7/pkgs/R-${R_VERSION}-1-1.x86_64.rpm && \
  yum install -y R-${R_VERSION}-1-1.x86_64.rpm && \
  /opt/R/${R_VERSION}/bin/R --version && \
  ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R && \
  ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript

Then:

docker build -f Dockerfile -t java-r .
docker run -it --rm java-r bash
R CMD javareconf
R -e 'install.packages("xlsx", repos = "https://cran.rstudio.com"); library(xlsx); xlsx::createWorkbook()'
# works fine

It's worth noting that Java weirdness is one reason that many people bail on xlsx (and rJava in general) 😞 R CMD javareconf is probably the most common fix, but it looks like your java install may have an issue.

[eylenth]

R CMD javareconf didn't work as well..

Maybe I have to rebuild the whole R module with Java 16 (or 17)
But I will do that another time. that R module is quite large with a lot of dependencies which requires some time to rebuild

I will close this ticket for now, and I will create a new one if needed