Develop Reference

Solr 8.3.1: could not find or load org.apache.solr.util.SolrCLI

So I'm new to Solr and am following tutorials for the most part using Solr 8.3.1 (the most recent release as of posting).
I've got Java version 1.8.0_181 installed on my Windows 10 machine and I've added solr/bin to the PATH variable.
When I run solr start I get:
/d/Program Files and Documents/solr-8.3.1/bin/solr: line 1525: ulimit: -m: invalid option
ulimit: usage: ulimit [-SHabcdefiklmnpqrstuvxPT] [limit]
*** [WARN] *** Your open file limit is currently 256.
It should be set to 65000 to avoid operational disruption.
If you no longer wish to see this warning, set SOLR_ULIMIT_CHECKS to false in your profile or solr.in.sh
*** [WARN] *** Your Max Processes Limit is currently 256.
It should be set to 65000 to avoid operational disruption.
If you no longer wish to see this warning, set SOLR_ULIMIT_CHECKS to false in your profile or solr.in.sh
/d/Program Files and Documents/solr-8.3.1/bin/solr: line 1542: [: !=: unary operator expected
NOTE: Please install lsof as this script needs it to determine if Solr is listening on port 8983.
Started Solr server on port 8983 (pid=). Happy searching!
Which says to me that it started running, but when I run solr status I get:
Found 1 Solr nodes:
Solr process 56136 from /d/Program Files and Documents/solr-8.3.1/bin/solr-8983.pid not found.
Which doesn't seem right. I continued with the tutorial anyway and ran solr start -e cloud and got:
$ solr start -e cloud
/d/Program Files and Documents/solr-8.3.1/bin/solr: line 1525: ulimit: -m: invalid option
ulimit: usage: ulimit [-SHabcdefiklmnpqrstuvxPT] [limit]
*** [WARN] *** Your open file limit is currently 256.
It should be set to 65000 to avoid operational disruption.
If you no longer wish to see this warning, set SOLR_ULIMIT_CHECKS to false in your profile or solr.in.sh
*** [WARN] *** Your Max Processes Limit is currently 256.
It should be set to 65000 to avoid operational disruption.
If you no longer wish to see this warning, set SOLR_ULIMIT_CHECKS to false in your profile or solr.in.sh
/d/Program Files and Documents/solr-8.3.1/bin/solr: line 1542: [: !=: unary operator expected
Error: Could not find or load main class org.apache.solr.util.SolrCLI
I tried solr start -e techproducts with the same result.
I've seen answers for this with earlier versions of Solr and usually the answers involved updating the Solr version... Which I'm already at the most recent? I'm sure I'm missing something dumb, but any pointers in the right direction would be much appreciated! Thanks so much!
EDIT 1: Solved! Was using Git Bash which is Cygwin-based. Works like a charm with Windows Command Prompt and with Windows Powershell.
Output for solr start:
Java HotSpot(TM) 64-Bit Server VM warning: JVM cannot use large page memory because it does not have enough privilege to lock pages in memory.
Waiting up to 30 to see Solr running on port 8983
Started Solr server on port 8983. Happy searching!
Output for solr status:
Found Solr process 50764 running on port 8983
{
"solr_home":"D:\\Program Files and Documents\\solr-8.3.1\\server\\solr",
"version":"8.3.1 a3d456fba2cd1b9892defbcf46a0eb4d4bb4d01f - ishan - 2019-11-29 11:51:37",
"startTime":"2019-12-19T22:20:25.127Z",
"uptime":"0 days, 0 hours, 0 minutes, 14 seconds",
"memory":"176.3 MB (%34.4) of 512 MB"}
Output for solr start -e cloud:
Welcome to the SolrCloud example!
This interactive session will help you launch a SolrCloud cluster on your local workstation.
To begin, how many Solr nodes would you like to run in your local cluster? (specify 1-4 nodes) [2]:

Seems like you're running the *nix-version of bin/solr under cygwin from the /d/... path. Under Windows you should use the bin/solr.cmd command with the standard command line console (´cmd.exe`).
It seems the solr.in script contains options not recognized by the version you have of bash inside cygwin. I'm guessing that could also affect the setup of the classpath which means that the classes aren't found where they'd be expected to.

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

Build OpenJDK 9 in CentOS5

I was trying to build OpenJDK 9 in Centos 5. I used
sh ./configure --disable-warnings-as-errors
make all
I am getting the following error.
Building target 'all' in configuration 'linux-x86_64-normal-server-release'
/root/jdk9/build/linux-x86_64-normal-server-
release/support/native/java.base/libjava/io_util_md.o: In function
`handleSetLength':
/root/jdk9/jdk/src/java.base/unix/native/libjava/io_util_md.c:228:
undefined reference to `fallocate64'
collect2: ld returned 1 exit status
/usr/bin/objcopy: '/root/jdk9/build/linux-x86_64-normal-server-
release/support/modules_libs/java.base/libjava.so': No such file
gmake[3]: *** [/root/jdk9/build/linux-x86_64-normal-server-
release/support/modules_libs/java.base/libjava.so] Error 1
gmake[2]: *** [java.base-libs] Error 2
ERROR: Build failed for target 'all' in configuration 'linux-x86_64-normal-
server-release' (exit code 2)
=== Output from failing command(s) repeated here ===
* For target support_native_java.base_libjava_BUILD_LIBJAVA_link:
/root/jdk9/build/linux-x86_64-normal-server-
release/support/native/java.base/libjava/io_util_md.o: In function
`handleSetLength':
/root/jdk9/jdk/src/java.base/unix/native/libjava/io_util_md.c:228:
undefined reference to `fallocate64'
collect2: ld returned 1 exit status
* All command lines available in /root/jdk9/build/linux-x86_64-normal-
server-release/make-support/failure-logs.
=== End of repeated output ===
No indication of failed target found.
Hint: Try searching the build log for '] Error'.
Hint: See common/doc/building.html#troubleshooting for assistance.
make[1]: *** [main] Error 2
make: *** [all] Error 2
I also tried other make targets such as make images and make install. But still getting the same error. My GCC version is gcc (GCC) 4.4.7 which I manually installed because Centos 5 by default has an older version.

Building JDK requires at least GCC 5.0 (see Building the JDK: CC).
This seems to be a problem in the glibc version (see redhat-issue, util-linux). So, updating your glibc to the latest version might solve it.
If you don't want to update your system's glibc, here is another alternative:
By looking at the man page of fallocate, we find that the description mentions that posix_fallocate(3) is a portable, POSIX.1-specified version of it, in case the mode parameter has the default value (0). The same applies to fallocate64.
Since all the occurrences of the aforementioned error already use the default mode value, you can replace them with posix_fallocate64() (instead of commenting them out as you mentioned in another comment).
The denoted man page says that:
This default behavior [of fallocate with mode=0] closely resembles the
behavior of the posix_fallocate(3) library function, and is intended
as a method of optimally implementing that function.

java.lang.NoClassDefFoundError error running RNetLogo on 64-bit Ubuntu 16.04 - but is the issue rJava or NetLogo?

The issue
I am attempting to start an instance of NetLogo in R using the RNetLogo package, which has rJava as a dependency.
During installation of rJava 0.9-9 (the latest development snapshot from rforge), I get the following errors:
warning: [options] bootstrap class path not set in conjunction with -source 1.6
This appears to refer to Java version 6, even though I have version 8 only on my machine. However, the developer of rJava appears to say here that as long as the package installs and loads correctly, which it does, then users should ignore the warnings. Furthermore, .jinit() appears to run correctly:
> .jinit()
[1] 0
and the correct version of Java is detected:
> .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
[1] "1.8.0_151-8u151-b12-0ubuntu0.16.04.2-b12"
So, having loaded RNetLogo, I attempt to start a NetLogo instance. Here is the minimal code I'm running:
library(RNetLogo)
nl.path <- "~/NetLogo 6.0.2/app"
NLStart(nl.path, gui = FALSE, nl.jarname='netlogo-6.0.2.jar')
Which returns the following errors:
java.lang.NoClassDefFoundError: org/nlogo/workspace/Controllable
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
Caused by: java.lang.ClassNotFoundException
at RJavaClassLoader.findClass(RJavaClassLoader.java:383)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 2 more
I get the same issue using RStudio or running R from the terminal (including running as root).
My full sessionInfo():
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=en_GB.UTF-8
[9] LC_ADDRESS=en_GB.UTF-8 LC_TELEPHONE=en_GB.UTF-8 LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RNetLogo_1.0-4 igraph_1.1.2 rJava_0.9-9
loaded via a namespace (and not attached):
[1] compiler_3.4.3 magrittr_1.5 tools_3.4.3 pkgconfig_2.0.1
Attempted fixes
Based on other users' issues that appear to be related, I also tried to following:
° Setting environment variables in /etc/profile.d/:
export JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64"
export PATH="$PATH:$HOME/bin:$JAVA_HOME/bin"
export LD_LIBRARY_PATH="/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server"
export CLASSPATH="$ClASSPATH:$HOME/R/x86_64-pc-linux-gnu-library/3.4/rJava/java"
° Running
sudo R CMD javareconf -e
° Adding a couple of lines proposed as mac OS fixes to the start of my script:
Sys.setenv(NOAWT=1)
dyn.load('/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjvm.so')
Thanks in advance.

I spent a lot of time staring at this question, assuming I had the same issue because I was getting the same error. So, for future readers: On Ubuntu 17.10, with rJava 0.9-9, NetLogo 6.0.3 and RNetLogo 1.0-4, the same error results when using the Oracle 9 Java SDK. Going back to 8 solves it.
For the OP: The ~/ in nl.path might be the problem. On my system it doesn't work, but specifying the full path (that is, home/user_name/...) does.

I had the same problem with rNetLogo 1.0-4 for NetLogo 5.3.1 in combination with openjdk-8 on Ubuntu 16.04. I tried openjdk-8 and Oracle Java 8 (using ppa:webupd8team/java) with no luck.
In the end it works with rJava as Ubuntu package (r-cran-rjava) and going back to rNetLogo 1.0-0 (with I suppose did the trick), still using Oracle Java 8.
url = 'https://cran.r-project.org/src/contrib/Archive/RNetLogo/RNetLogo_1.0-0.tar.gz'
install.packages(url, repos=NULL, type="source")

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