I have an R package that was passing all Travis CI builds successfully and randomly started to fail. I've pondered where the problem is at but I can't seem to fix it.
Here is the travi.yaml from the package
Here is the failing log of Travis-CI
Here is the last log the passed (about 2-3 logs behind the last fail)
I think the fail might be related to line 1495 from the last log that passed:
The command "for name in $(find "${RCHECK_DIR}" -type f -name "*out");do echo ">>> Filename: ${name} <<<";cat ${name};done" exited with 0.
which does not appear in the failed log from above. After thoroughly checking my tests with devtools:
R CMD check results
0 errors | 0 warnings | 0 notes
I don't know what it might be. I thought it was related to some examples taking too much time (some examples pass the 5 second thresholds, so I comment them out but the failing persists. I tried posting this in the Rstudio community but no luck so far.
Any ideas?
Related
The Jim Hester YouTube video video looks like a potentially really helpful way to put breakpoints in Rcpp code that passes some variables in unexpected ways. However, when I follow the start up directions (Rstudio console copied below) it fails with a message that is not helpful to a new user of lldb.
gcn#GCN-MacBook-Pro-7 ISIMIPData % R -d lldb
(lldb) target create "/Library/Frameworks/R.framework/Resources/bin/exec/R"
Current executable set to '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64).
(lldb) run
error: process exited with status -1 (attach failed (Not allowed to attach to process. Look in the console messages (Console.app), near the debugserver entries when the attached failed. The subsystem that denied the attach permission will likely have logged an informative message about why it was denied.))
(lldb)
The Console.app output that I could find is not very useful.
A later post post describes an updated process but it too fails in a similar way. I'm using Rstudio version 1.4.1717 with R version 4.1.
I'm trying to execute a command remotely through Robot Framework which is failing through Robot framework and giving me the wrong exit status of 13.
But if we run this manually exit status of TTman.sh is 112 which is actually pass(Not the standard return codes).
am I doing something wrong here?
You are not getting the remote code of the remote command, in fact the RC 13 you are getting from the run is most probably from the robotframework - on run completion its RC is the number of failed cases. I.e. 13 cases should have failed, when you observed this.
To get the return code of your command, a few changes in the case are needed; this is how the semi-last line should look like, with explanations below:
${rc}= Execute Command your_command_from_the_question &>/dev/null; echo $?
First, all the output of your command (stdout & stderr) is redirected to /dev/null - to not return it. Then the special var $? is printed - it holds the RC of the last executed command (and is available in most *sh variants, like bash).
Finally, that value is stored in the ${rc} robotframework variable, and you can do whatever checks you need on it, further in the case.
This approach has one drawback - as stderr is hidden, you will not be able to see any errors coming from running the command. But if it was not, then they would be interleaved with the RC, which would have required further processing of the {rc} var, to get the desired value. If you need it (the stderr output in case of failures), change accordingly.
P.S. don't add screenshots of a source in a question, it is much less usable than a text version.
I've tried to run command in R 2.15.2
rsaga.geoprocessor(lib="ta_channels", module=0, param=list(ELEVATION="DEMflt.sgrd", CHNLNTWRK=paste("channels", i, ".sgrd", sep=""), CHNLROUTE="channel_route.sgrd", SHAPES="channels.shp", INIT_GRID="DEMflt.sgrd", DIV_CELLS=3, MINLEN=40), show.output.on.console=FALSE)
and I'm constantly getting this warning:
Warning message:
running command '"C:/Users/Nenad/Documents/R/win-library/2.15/RSAGA/SAGA-GIS/saga_cmd.exe" ta_preprocessor 2 -DEM "DEM1.sgrd" -RESULT "DEMflt.sgrd" -MINSLOPE "0.05"' had status 1
I use windows 8 and also tried to ran R as admin.
Any idea what is the problem? Thanks!
Idk how actual it is, but I've been struggling with "had status 1" warning a lot. Especially it got really annoying when I tried to use seasonal package to conduct the X13-ARIMA-SEATS seasonal decomposition of time series. The seasonal::seas command just didn't work, because in the code of this command there is a stop condition when running a certain stuff with cmd.exe returns non-zero status. While, as it was mentioned before, 'status 1' doesn't prevent command execution, in case of seasonal package it does.
The problem in my case was caused by some mistake in Windows Registry (Win 10), that in turn caused warning System cannot find the path specified when launching CMD.exe or PowerShell, which caused warning inside R as well. So to fix it:
Press Win+R -> regedit
In HKEY_CURRENT_USER\SOFTWARE\Microsoft\Command Processor folder clean the value of Autorun record (it should be empty)
Do the same for Autorun in HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Command Processor
After these actions annoying warning with "has status 1" has gone and seasonal::seas started to work perfectly.
Hope it will be usefull for somebody.
Running system commands from R can be really tricky. In my experience, as long as the exit code is not 127 then the command did run, and you could use the intern=TRUE switch in the system command for a more verbose output. If you run the command again, the warning message could contain a errmsg attribute as well for some more info. hth
I am building a Qt GUI application via Jenkins. I added 3 build steps:
Building the test executable
Running the test executable
compiling a coverage report with gcovr
For some reason, the shell task for running the test executable stops after execution. Even a simple echo does not run after. The tests are written with Google Test and output xUnit XML files, which are analyzed after the build.
Some tests start the applications user interface, so I installed the jenkins xvnc plugin to get them to run.
The build tasks are as follows:
Build
cd $WORKSPACE/projectfiles/QMake
sh createbin.sh
Test
cd $WORKSPACE/bin
./Application --gtest_output=xml
Coverage Report
cd $WORKSPACE/projectfiles/QMake/out
gcovr -x -o coverage.xml
Now, an echo at the end of the first build task is correctly printed, but an echo at the end of the second is not. The third build task is therefore not even run, although the Google Test output is visible. I thought that maybe the problem is that some of the Google Tests fail, but why whould the script stop executing just because the tests fail?
Maybe someone can give me a hint on why the second task stops.
Edit
The console output looks like this:
Updating svn://repo/ to revision '2012-11-15T06:43:15.228 -0800'
At revision 2053
no change for svn://repo/ since the previous build
Starting xvnc
[VG5] $ vncserver :10
New 'ubuntu:10 (jenkins)' desktop is ubuntu:10
Starting applications specified in /var/lib/jenkins/.vnc/xstartup
Log file is /var/lib/jenkins/.vnc/ubuntu:10.log
[VG5] $ /bin/sh -xe /tmp/hudson7777833632767565513.sh
+ cd /var/lib/jenkins/workspace/projectfiles/QMake
+ sh createbin.sh
... Compiler output ...
+ echo Build Done
Build Done
[VG5] $ /bin/sh -xe /tmp/hudson4729703161621217344.sh
+ cd /var/lib/jenkins/workspace/VG5/bin
+ ./Application --gtest_output=xml
Xlib: extension "XInputExtension" missing on display ":10".
[==========] Running 29 tests from 8 test cases.
... Test output ...
3 FAILED TESTS
Build step 'Execute shell' marked build as failure
Terminating xvnc.
$ vncserver -kill :10
Killing Xvnc4 process ID 1953
Recording test results
Skipping Cobertura coverage report as build was not UNSTABLE or better ...
Finished: FAILURE
Generally, if one Build Step fails, the rest will not be executed.
Pay attention to this line from your log:
[VG5] $ /bin/sh -xe
The -x makes the shell print each command in console before execution.
The -e makes the shell exit with error if any of the commands failed.
A "fail" in this case, would be a return code of not 0 from any of the individual commands.
You can verify this by running this directly on the machine:
./Application --gtest_output=xml
echo $?
If the echo $? displays 0, it indicates successful completion of the previous command. If it displays anything else, it indicates an error code from the previous command (from ./Application), and Jenkins treats it as such.
Now, there are several things at play here. First is that your second Build Step (essentially a temporary shell script /tmp/hudson4729703161621217344.sh) is set to fail if one command fails (the default behaviour). When the Build Step fails, Jenkins will stop and fail the whole job.
You can fix this particular behaviour by adding set +e to the top of your second Build Step. This will not cause the script (Build Step) to fail due to individual command failure (it will display an error for the command, and continue).
However, the overall result of the script (Build Step) is the exit code of the last command. Since in your OP, you only have 2 commands in the script, and the last is failing, it will cause the whole script (Build Step) to be considered a failure, despite the +x that you've added. Note that if you add an echo as the 3rd command, this would actually work, since the last script command (echo) was successful, however this "workaround" is not what you need.
What you need is proper error handling added to your script. Consider this:
set +e
cd $WORKSPACE/bin && ./Application --gtest_output=xml
if ! [ $? -eq 0 ]; then
echo "Tests failed, however we are continuing"
else
echo "All tests passed"
fi
Three things are happening in the script:
First, we are telling shell not to exit on failure of individual commands
Then i've added basic error handling in the second line. The && means "execute ./Application if-and-only-if the previous cd was successful. You never know, maybe the bin folder is missing, or whatever else can happen. BTW, the && internally works on the same error code equals 0 principle
Lastly, there is now proper error handling for the result of ./Application. If the result is not 0, then we show that it had failed, else we show that it had passed. Note, this since the last command is not a (potentially) failing ./Application, but an echo from either of if-else possibilities, the overall result of the script (Built Step) will be a success (i.e 0), and the next Build Step will be executed.
BTW, you can as well put all 3 of your build steps into a single build step with proper error handling.
Yes... this answer may be a little longer than what's required, but i wanted you to understand how Jenkins and shell treat exit codes.
I'm supposed to run some jbehave(automated) tests in bamboo. Once the tests run I'll generate some junit compatible xml files so that bamboo could understand the same. All the jbehave tests are ran as part of a script, because I need to run the jbehave tests in a separate display screen(remember these are automated browser tests). Example script is as follows.
Ex:
export DISPLAY=:0 && xvfb-run --server-args="-screen 0, 1024x768x24"
mvn clean integration-test -DskipTests -P integration-test -Dtest=*
I have one more junit parser task which points to the generated junit compatible xml files. So, once the bamboo build runs and even if all the tests pass, I get red build with the message "No failed tests found, a possible compilation error occurred."
Can somone please help me on this regard.
Your build script might be producing successful test reports, but one (or both, possibly) of your tasks is failing. That means that the failure is probably* occurring after your tests complete. Check your build logs for errors. You might also try logging in to your Bamboo server (as the bamboo user) and running the commands by hand.
I've seen this message in the past when our test task was crashing halfway through the test run, resulting in one malformed report that Bamboo ignored and a bunch of successful reports.
*Check the build log to make sure that your tests are indeed running. If mvn clean doesn't clean out the test report directory, Bamboo might just be parsing stale test reports.
EDIT: (in response to Kishore's links)
It looks like your task to kill Xvfb is what is causing the build to fail.
18-Jul-2012 09:50:18 Starting task 'Kill Xvfb' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
18-Jul-2012 09:50:18
Beginning to execute external process for build 'Functional Tests - Application Release Test - Default Job'
... running command line:
/bin/sh
/tmp/FUNC-APPTEST-JOB1-91-ScriptBuildTask-4153769009554485085.sh
... in: /opt/bamboo-home/xml-data/build-dir/FUNC-APPTEST-JOB1
... using extra environment variables:
<..snip (no meaningful output)..>
18-Jul-2012 09:50:18 Failing task since return code was 1 while expected 0
18-Jul-2012 09:50:18 Finished task 'Kill Xvfb'
What does your "Kill Xvfb" script do? Are you trying something like pkill -f "[x]vfb"? pkill -f silently returns non-zero if it can't match the expression to any processes.
My solution was to make a 'script' task:
#!/bin/bash
/usr/local/bin/phpcs --report=checkstyle --report-file=build/logs/checkstyle.xml --standard=PSR2 ./lib | exit 0
Which always exits with status 0.
This is because PHP code sniffer return exit status 1 when only 1 coding violation (warning / error) is found which causes the built to fail.
Turns out to be a simple fix.
General bamboo behavior is to scan the entire log and see for any failure codes(1). For this specific configuration i had some 6 scripts out of which one of them was to kill the xvfb(frame buffer). For some reason server is not able to kill xvfb and that task was returning a failure code. Because of this, though all the tests passed, bamboo got one of this error codes from previous tasks and build was failing.
Current fix is to remove the task which kills xvfb and the build went green! \o/.