Develop Reference

How to fix an error : 'Could not load library 'toscomm': no toscomm in java.library.path'?

I am getting familiar with Tiny OS enviroment, currently I am at lesson 4 "Mote-PC serial communication and SerialForwarder"
and I am stuck with the part where I have to listen to serial port for any incoming data. I am trying to implement a simple example where I need to use TestSerial script to listen for any incoming messages however when I run
java TestSerial -comm serial#/dev/ttyUSB0:iris
my output looks like that:
Error loading the TinyOS JNI libraries the conventional way!
Attempting to load library 'toscomm'
Could not load library 'toscomm': no toscomm in java.library.path
----------
java.lang.UnsatisfiedLinkError: no toscomm in java.library.path
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1865)
at java.lang.Runtime.loadLibrary0(Runtime.java:870)
at java.lang.System.loadLibrary(System.java:1119)
at net.tinyos.util.TOSLibraryLoader.load(TOSLibraryLoader.java:85)
at net.tinyos.comm.TOSCommJNI.<clinit>(TOSCommJNI.java:14)
at net.tinyos.comm.NativeSerial.getTOSCommMap(NativeSerial.java:207)
at net.tinyos.comm.TOSSerial.<init>(TOSSerial.java:277)
at net.tinyos.packet.SerialByteSource.openStreams(SerialByteSource.java:67)
at net.tinyos.packet.StreamByteSource.open(StreamByteSource.java:61)
at net.tinyos.packet.Packetizer.openSource(Packetizer.java:149)
at net.tinyos.packet.AbstractSource.open(AbstractSource.java:78)
at net.tinyos.packet.Packetizer.open(Packetizer.java:142)
at net.tinyos.packet.PhoenixSource.run(PhoenixSource.java:178)
----------
In order to load the library 'toscomm' Java tries to locate the file 'libtoscomm.so' in one of the following paths:
/usr/java/packages/lib/i386:/lib:/usr/lib
The operating system is 'Linux' (i386)
Trying to locate the file 'linux_x86_toscomm.lib' in the classpath
Temporary file created: '/tmp/toscomm3780740783398787473.lib'
Library copied successfully. Let's load it.
Library loaded successfully
serial#/dev/ttyUSB0:57600: resynchronising
Sending packet 0
Sending packet 1
instead of having
Sending packet 1
Received packet sequence number 4
Sending packet 2
Received packet sequence number 5
as it described in tutorial
I am concerned about the warnings I get when I run this script, particularly this one
Attempting to load library 'toscomm'
Could not load library 'toscomm': no toscomm in java.library.path
According to tutorial, this error can be resolved by running
sudo tos-install-jni,
however when I type this, I get the error that tos command not found.
I tried to go to tinyos-2.x/tools/tinyos/java. directory and typed sudo make
and sudo make install, nevertheless that did not work either giving me the following error:
make[1]: Entering directory '/home/wsn/tinyos-main/tools'
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ./configure --no-create --no-recursion
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for ranlib... ranlib
checking for a Python3 interpreter with version >= 3.0... python3
checking for python3... /bin/python3
checking for python3 version...
checking for python3 platform... linux
checking for python3 script directory... ${prefix}/lib/python3.4/site-packages
checking for python3 extension module directory... /lib/python/site-packages
checking for a Python interpreter with version >= 2.5... python2
checking for python2... /bin/python2
checking for python2 version... 2.7
checking for python2 platform... linux2
checking for python2 script directory... ${prefix}/lib/python2.7/site-packages
checking for python2 extension module directory... (cached) /lib/python/site-packages
checking for perl... /bin/perl
checking for python2... /bin/python2
checking for python3... /bin/python3
checking for python2.7-config... /bin/python2.7-config
checking for dot... no
configure: I can't find dot. dot is required for documentation.
checking for nescc... /bin/nescc
checking for cygwin... no
checking for JDK location... configure: error: java not found
Makefile:377: recipe for target 'config.status' failed
make[1]: *** [config.status] Error 1
make[1]: Leaving directory '/home/wsn/tinyos-main/tools'
Makefile:374: recipe for target '../../config.status' failed
make: *** [../../config.status] Error 2
When I try to run the same command for BaseStation script, the program gives the same warning and just gets frozen at this point:
serial#/dev/ttyUSB0:57600: resynchronising
So I don't even see any packets sent or received!
I am not sure what is the problem here, please help.
I am using Virtual Machine with Fedora OS
I am trying to run the program on mib520 platform and I use iris motes
my java version
openjdk version "1.8.0_31"
OpenJDK Runtime Environment (build 1.8.0_31-b13)
OpenJDK Server VM (build 25.31-b07, mixed mode)

I do not think your issue is with toscomm, as long as the library ends up being loaded successfully you should not be getting any issues. I always used to get the same exception that you are seeing being thrown over there everytime I used the serial but never bothered to fix it as it didn't really hamper the operation of the serial port.
In the end, I got rid of the exception by copying libtoscomm from the {TOS_ROOT}/tools/tinyos/java/serial/ directory to one of the directories that TinyOS is looking for libraries in. In your case you would put a copy of the libtoscomm file in one of the directories /usr/java/packages/lib/i386 , /lib or /usr/lib.
You can try doing that and seeing if that resolves the exception issue for you.
What I suspect might be causing your issue is that you do not have TestSerialAppC loaded onto you mote and connected to the serial port. Have you made sure the mote is connected to the serial port?
I loaded ran the application on a mote and got the output below, so the issue is not with TestSerialAppC
serial#/dev/tty.usbserial-FTYRYAHT:115200: resynchronising
Sending packet 0
Received packet sequence number 3
Sending packet 1
Received packet sequence number 4
Sending packet 2

CMake could not find JNI

I created a new Android Studio Project with C++ support and did not add anything to it. The project builds, compiles and runs with CMake. I then added the following two lines of code to CMakeLists.txt at the bottom of the file and I get a CMake build error.
find_package(Java COMPONENTS Development) # Line 47
find_package(JNI REQUIRED) # Line 48
And this is the error I get when building the project
-- Found Java: /usr/lib/jvm/java-10-oracle/bin/java (found version "10.0.1") found components: Development
-- Configuring incomplete, errors occurred!
CMake Error at /home/xxxxx/Android/Sdk/cmake/3.6.4111459/share/cmake-3.6/Modules/FindPackageHandleStandardArgs.cmake:148 (message):
Could NOT find JNI (missing: JAVA_AWT_LIBRARY JAVA_JVM_LIBRARY
See also "/home/xxxxx/AndroidStudioProjects/MyApplication/app/.externalNativeBuild/cmake/release/x86_64/CMakeFiles/CMakeOutput.log".
JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH)
Call Stack (most recent call first):
/home/xxxxxx/Android/Sdk/cmake/3.6.4111459/share/cmake-3.6/Modules/FindPackageHandleStandardArgs.cmake:388 (_FPHSA_FAILURE_MESSAGE)
/home/xxxxxx/Android/Sdk/cmake/3.6.4111459/share/cmake-3.6/Modules/FindJNI.cmake:314 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
CMakeLists.txt:48 (find_package)
External native generate JSON release: JSON generation completed with problems
CMake runs when being called form the command line, but fails inside Android Studio for some reason and I am not sure why.
EDIT 1
Here is the CMakeOutput.log file
EDIT 2
This is all that is in CMakeLists.txt file. It compiles in cmd with the command cmake.
cmake_minimum_required(VERSION 3.4.1)
find_package(Java COMPONENTS Development)
find_package(JNI REQUIRED)
This is the cmd output
E:\Users\xxxxx\AndroidStudioProjects\MyApplication\app\build>cmake ..
-- Configuring done
-- Generating done
-- Build files have been written to: E:/Users/xxxxx/AndroidStudioProjects/MyApplication/app/build
When I try to add it compile it in Android Studio using gradle I get the following error on Windows 10 pro 64 bit
Microsoft Windows [Version 10.0.17134.112]
(c) 2018 Microsoft Corporation. All rights reserved.
E:\Users\xxxxx\AndroidStudioProjects\MyApplication>gradlew build --stacktrace
> Task :app:generateJsonModelDebug
External native generate JSON debug: starting JSON generation
External native generate JSON debug: using platform version 24 for ABI ARMEABI_V7A and min SDK version 24
External native generate JSON debug: noticing that build file 'E:\Users\xxxxx\AndroidStudioProjects\MyApplication\app\CMakeLists.txt' is out of date with respect to E:\Users\xxxxx\AndroidStudioProjects\MyApplication\app\.extern
alNativeBuild\cmake\debug\armeabi-v7a\android_gradle_build.json
External native generate JSON debug: rebuilding JSON E:\Users\xxxxx\AndroidStudioProjects\MyApplication\app\.externalNativeBuild\cmake\debug\armeabi-v7a\android_gradle_build.json due to:
External native generate JSON debug: - a dependent build file changed
External native generate JSON debug: keeping json folder 'E:\Users\xxxxx\AndroidStudioProjects\MyApplication\app\.externalNativeBuild\cmake\debug\armeabi-v7a' but regenerating project
External native generate JSON debug: executing cmake Executable : E:\Android\SDK\cmake\3.6.4111459\bin\cmake.exe
arguments :
-HE:\Users\xxxxx\AndroidStudioProjects\MyApplication\app
-BE:\Users\xxxxx\AndroidStudioProjects\MyApplication\app\.externalNativeBuild\cmake\debug\armeabi-v7a
-DANDROID_ABI=armeabi-v7a
-DANDROID_PLATFORM=android-24
-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=E:\Users\xxxxx\AndroidStudioProjects\MyApplication\app\build\intermediates\cmake\debug\obj\armeabi-v7a
-DCMAKE_BUILD_TYPE=Debug
-DANDROID_NDK=E:\Android\SDK\ndk-bundle
-DCMAKE_CXX_FLAGS=
-DCMAKE_TOOLCHAIN_FILE=E:\Android\SDK\ndk-bundle\build\cmake\android.toolchain.cmake
-DCMAKE_MAKE_PROGRAM=E:\Android\SDK\cmake\3.6.4111459\bin\ninja.exe
-GAndroid Gradle - Ninja
jvmArgs :
CMake Error at E:/Android/SDK/cmake/3.6.4111459/share/cmake-3.6/Modules/FindPackageHandleStandardArgs.cmake:148 (message):
Could NOT find JNI (missing: JAVA_AWT_LIBRARY JAVA_JVM_LIBRARY
JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH)
Call Stack (most recent call first):
E:/Android/SDK/cmake/3.6.4111459/share/cmake-3.6/Modules/FindPackageHandleStandardArgs.cmake:388 (_FPHSA_FAILURE_MESSAGE)
E:/Android/SDK/cmake/3.6.4111459/share/cmake-3.6/Modules/FindJNI.cmake:314 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
CMakeLists.txt:4 (find_package)
-- Configuring incomplete, errors occurred!
See also "E:/Users/xxxxx/AndroidStudioProjects/MyApplication/app/.externalNativeBuild/cmake/debug/armeabi-v7a/CMakeFiles/CMakeOutput.log".

Could NOT find JNI (missing: JAVA_AWT_LIBRARY JAVA_JVM_LIBRARY
Solved with
sudo apt-get install -y openjdk-8-jdk
sudo apt-get install -y default-jdk
export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64

As the CMake version bundled with Android tries to tell you, it can't find the JNI package because some parts were missing:
missing: JAVA_AWT_LIBRARY JAVA_JVM_LIBRARY JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH
Checking the documentation for FindJNI (https://cmake.org/cmake/help/latest/module/FindJNI.html) these variables are set to the locations of libraries and headers not shipped with the Android version of JNI (to little surprise, Android does not included the AWT library for instance).
When running find_package(JNI REQUIRED), the FindJNI code checks if these variables are set and if not, issues an error.
A workaround is to set these variables yourself, before calling find_package:
# We are only interested in finding jni.h: we do not care about extended JVM
# functionality or the AWT library.
set(JAVA_AWT_LIBRARY NotNeeded)
set(JAVA_JVM_LIBRARY NotNeeded)
set(JAVA_INCLUDE_PATH2 NotNeeded)
set(JAVA_AWT_INCLUDE_PATH NotNeeded)
find_package(JNI REQUIRED)
Be aware though, that your code will only be able to use jni.h and its functionality: if it tries to access any other part of the JNI package it will fail (probably at compile time) because essentially, you have tricked CMake into thinking that the entire package was found, when in reality only a part of it exists in the Android setup.

I found a solution that works for me:
cmake_minimum_required(VERSION 3.10)
project("ktaglib")
set(JAVA_AWT_LIBRARY "$ENV{JAVA_HOME}/lib/libjawt.so")
set(JAVA_JVM_LIBRARY "$ENV{JAVA_HOME}/lib/server/libjvm.so")
set(JAVA_INCLUDE_PATH "$ENV{JAVA_HOME}/include")
set(JAVA_INCLUDE_PATH2 "$ENV{JAVA_HOME}/include/linux")
set(JAVA_AWT_INCLUDE_PATH "$ENV{JAVA_HOME}/include")
find_package(JNI REQUIRED)
You must set the environment variable JAVA_HOME="/usr/lib/jvm/java-11-openjdk-amd64" beforehand.
More info: https://github.com/dockcross/dockcross/issues/576

Same on alpine:edge docker image, fixed using:
ENV JAVA_HOME=/usr/lib/jvm/java-1.8-openjdk
RUN apk add --no-cache openjdk8
ref: https://pkgs.alpinelinux.org/contents?branch=edge&name=openjdk8&arch=x86_64&repo=community

Unable to decompress snappy file, even after specifying -Djava.library.path=/*/*/

Exception in thread "main"
java.lang.RuntimeException: native snappy library not available: this version of libhadoop was built without snappy support.
at org.apache.hadoop.io.compress.SnappyCodec.checkNativeCodeLoaded(SnappyCodec.java:65)
at org.apache.hadoop.io.compress.SnappyCodec.getDecompressorType(SnappyCodec.java:193)
at org.apache.hadoop.io.compress.CodecPool.getDecompressor(CodecPool.java:178)
at org.apache.hadoop.io.compress.CompressionCodec$Util.createInputStreamWithCodecPool(CompressionCodec.java:157)
at org.apache.hadoop.io.compress.SnappyCodec.createInputStream(SnappyCodec.java:164)
I could see snappy library is installed properly. I have mentioned lib path using -Djava.library.path, still resulting in same error.
Any suggestions please?
hadoop checknative -a
Native library checking:
hadoop: true /opt/cloudera/parcels/CDH-5.7.1-1.cdh5.7.1.p0.11/lib/hadoop/lib/native/libhadoop.so.1.0.0
zlib: true /lib64/libz.so.1
snappy: true /opt/cloudera/parcels/CDH-5.7.1-1.cdh5.7.1.p0.11/lib/hadoop/lib/native/libsnappy.so.1
lz4: true revision:10301
bzip2: true /lib64/libbz2.so.1
openssl: true /usr/lib64/libcrypto.so

Looks like you're running into:
Snappy may complain Hadoop is built without snappy if libhadoop is not found.
https://issues.apache.org/jira/browse/HADOOP-13684
You should debug for the libhadoop.so and look at your LD_LIBRARY_PATH for starters.

Issue resolved.
I was using incorrect version of hadoop-core jar file in my classpath.
After modifying to use the current CDH version of hadoop core jar, was able to perform snappy compression and decompression.

Using JNAerator to access a library under Mac OSX

If I run JNAerator using the header for my library, the process gobbles processor time and never seems to finish - after first issuing warnings:
adrian$ java -Xmx128m -jar ~/JNAerator/jnaerator/target/jnaerator-0.13-SNAPSHOT-shaded.jar /Users/adrian/DRAMSim2/DRAMSim.h -mode StandaloneJar
Warning: no -library option for file 'DRAMSim.h', using "DRAMSim".
Auto-configuring parser...
Parsing native headers...
/usr/include/sys/cdefs.h:74:25: warning: #warning "Unsupported compiler detected"
/usr/include/_types/_wctype_t.h:30:19: warning: No newline before end of file
So, I have also tried the -ScanSymbols option:
java -Xmx128m -jar ~/JNAerator/jnaerator/target/jnaerator-0.13-SNAPSHOT-shaded.jar -scanSymbols -mode StandaloneJar
Auto-configuring parser...
Parsing native headers...
Normalizing parsed code...
Generating libraries...
Compiling JNAerated files...
[....]
Copying runtime classes...
Generating out.jar
#
# SUCCESS: JNAeration completed !
# Output mode is 'StandaloneJar(JAR with bindings and runtime dependencies)
#
# => '/Users/adrian/groovy/simul/src/simul/./out.jar'
And out.jar has a great many .class files but no .java and I have no idea how to use it.
Using -noComp -noJar as suggested in the wiki generates no output at all ...
adrian$ java -Xmx128m -jar ~/JNAerator/jnaerator/target/jnaerator-0.13-SNAPSHOT-shaded.jar -scanSymbols -noComp -noJar
WARNING: option (?i)-noComp is deprecated and might be removed in future versions.
WARNING: option (?i)-noJar is deprecated and might be removed in future versions.
WARNING: legacy options (?i)-noJar and (?i)-noComp used, defaulting -mode to Directory
Auto-configuring parser...
Parsing native headers...
Normalizing parsed code...
Generating libraries...
#
# SUCCESS: JNAeration completed !
# Output mode is 'Directory(Bindings sources in simple file hierarchy)
#
# => '/Users/adrian/groovy/simul/src/simul/.'
What am I doing wrong? Or is this a hopeless case?

CentOS Java application error with SELinux

I have a CentOS box hosting a Drupal 7 site. I've attempted to run a Java application called Tika on it, to index files using Apache Solr search.
I keep running into an issue only when SELinux is enabled:
extract using tika: OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x00007f1ed9000000, 2555904, 1) failed; error='Permission denied' (errno=13)
#
# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (malloc) failed to allocate 2555904 bytes for committing reserved memory.
# An error report file with more information is saved as:
# /tmp/jvm-2356/hs_error.log
This does not happen if I disable selinux. If I run the command from SSH, it works fine -- but not in browser. This is the command it is running:
java '-Dfile.encoding=UTF8' -cp '/var/www/drupal/sites/all/modules/contrib/apachesolr_attachments/tika' -jar '/var/www/drupal/sites/all/modules/contrib/apachesolr_attachments/tika/tika-app-1.11.jar' -t '/var/www/drupal/sites/all/modules/contrib/apachesolr_attachments/tests/test-tika.pdf'
Here is the log from SELinux at /var/log/audit/audit.log:
type=AVC msg=audit(1454636072.494:3351): avc: denied { execmem } for pid=11285 comm="java" scontext=unconfined_u:system_r:httpd_t:s0 tcontext=unconfined_u:system_r:httpd_t:s0 tclass=process
type=SYSCALL msg=audit(1454636072.494:3351): arch=c000003e syscall=9 success=no exit=-13 a0=7fdfe5000000 a1=270000 a2=7 a3=32 items=0 ppid=2377 pid=11285 auid=506 uid=48 gid=48 euid=48 suid=48 fsuid=48 egid=48 sgid=48 fsgid=48 tty=(none) ses=1 comm="java" exe="/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.95.x86_64/jre/bin/java" subj=unconfined_u:system_r:httpd_t:s0 key=(null)
Is there a way I can run this with SELinux enabled? I do not know the policy name of Tika (or should I use Java?) so I'm unsure where to go from here...

This worked for me...
I have tika at /var/apache-tika/tika-app-1.14.jar
setsebool -P httpd_execmem 1
chcon -t httpd_exec_t /var/apache-tika/tika-app-1.14.jar
Using the sealert tools (https://wiki.centos.org/HowTos/SELinux) helped track down the correct selinux type.

All of your context messages reference httpd_t, so I would run
/usr/sbin/getsebool -a | grep httpd
And experiment with enabling properties that show as off. It's been a while since I ran a database-backed website (Drupal, WordPress, etc.) on CentOS, but as I recall, these two were required to be enabled:
httpd_can_network_connect
httpd_can_network_connect_db
to enable a property with persistence, run
setsebool -P httpd_can_network_connect on
etc.

The booleans you're looking for are:
httpd_execmem
httpd_read_user_content
How to find:
audit2why -i /var/log/audit/audit.log will tell you this.
Part of package: policycoreutils-python-utils