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Each subdirectory contains a number of JAGS script files named test1.cmd,
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Each subdirectory contains a number of JAGS script files named test1.cmd,
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test2.cmd, ... etc. designed to run the examples as they were presented
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test2.cmd, ... etc. designed to run the examples as they were presented
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in the classic BUGS examples book.
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in the classic BUGS examples book.
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Volume 1 also contains R script files test1.R, test2.R to run the
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There are also R script files test1.R, test2.R ... to run the
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examples using the rjags interface from JAGS to R.
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examples using the rjags interface from JAGS to R.
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Some of the examples have been modified. In such cases, there is a
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Some of the examples have been modified. In such cases, there is a
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ReadMe file explaining the changes. Some examples cannot be run at all,
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ReadMe file explaining the changes. Some examples cannot be run at all,
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and these are obviously not included in the testing process.
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and these are not included in the testing process.
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Make targets
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------------
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The test suite uses GNU make.  To run the tests, change directory into
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either "vol1" or "vol2" and invoke make with one of the following targets.
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make check  Will run all the examples and check the results against
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make check  Will run all the examples and check the results against
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            the benchmark run.  The check ensures that the posterior
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            the benchmark run.  The check ensures that the posterior
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            mean of the monitored nodes is not more than 0.15 standard
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            mean of the monitored nodes is not more than 0.15 standard
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            deviations away from the benchmark mean. This is a heuristic
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            deviations away from the benchmark mean. 
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            test that could probably be improved.
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make Rcheck (Volume 1 only) Runs examples using the rjags interface.
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make Rcheck Runs examples using the rjags interface.
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make checktime Runs all the examples and records the times in the file
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            "times" (replacing any existing file). The "times"
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            file records the directory name, the name of the command
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            file and the number of seconds in user mode and kernel
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            mode in separate columns.
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            This requires the GNU version of time.
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make clean  Cleans up any files that may have been created during
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make clean  Cleans up any files that may have been created during
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            make check, or during debugging
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            make check, or during debugging
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make bench  Creates new benchmark results
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make bench  Creates new benchmark results
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make distclean Deletes the benchmark results
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make distclean Deletes the benchmark results
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In order to run make for a specific example, use the variable "EXAMPLES":
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make check EXAMPLES=line
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Debugging an example
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--------------------
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If "Make check" fails for example foo, then make will report an error in
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make taget "check_foo".  The log file "check.log" in subdirectory "foo"
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can be inspected to see what went wrong. This log file includes the
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output produced by JAGS when running the model and by R when checking
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the output. Similarly, "make Rcheck" exands to targets of the form
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"Rcheck_foo" and the log file is "Rcheck.log".
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Note that the tests in "make check" and "make Rcheck" are not deterministic and 
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will occasionally fail just by chance.  You may run "make check" again 
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when this happens to see if the error is consistently reproduced.
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Re-running the examples
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-----------------------
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Once all the tests have been successfully completed in a sub-directory,
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an empty marker file will be created (check.OK or Rcheck.OK) and the 
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corresponding checks will be skipped.  To re-run the checks, first use
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"make clean" to remove the marker files.
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Parallel make
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-------------
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The examples in separate directories can be run in parallel for increased
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efficiency.  Use the "-j" argument to run examples in parallel, e.g
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make -j4 check
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Will run 4 parallel make jobs.