Build failed in Jenkins: Stan #2

[mc.sta...@gmail.com]

See <http://gelman.stat.columbia.edu:8080/job/Stan/2/changes>

Changes:

[carp] added stubs for all of the cholesky corr factors, w/o tests

[bg2382] add factor_U and factor_L functions to transform to CPCs

[bg2382] fix factor_L()

[bg2382] add test of factor_L

[carp] intermediate state of Cholesky to allow pull of Ben's code

[carp] cholesky corr type tested and documented

[carp] updated reference manual Jacobians math steps

[bg2382] make lkj_corr_log not depend on lkj_corr_cholesky_log

[bg2382] hopefully accelerate do_lkj_constant

[bg2382] do not use srand anymore in lkj_corr_test

[bg2382] make lkj_corr_cholesky() work the way it is supposed to

[bg2382] correct explanation of Jeffreys prior

[bg2382] elaborate LKJ transformations

[Daniel Lee] fixed typo.

[Daniel Lee] added template parameter for dom_err_vec to handle indexing

[Daniel Lee] adding test for 0 vs 1 indexing within dom_err_vec

[Daniel Lee] updating with failing tests for 1-indexed error messages

[Daniel Lee] updating spec and test for check_positive_ordered

[Daniel Lee] updating spec and test for check_positive

[Daniel Lee] removing duplicate name in error message

[Daniel Lee] adding tests for 1-indexed messages in matrix checks

[Daniel Lee] adding error_index as a trait

[Daniel Lee] updated all code so it is 1-indexed

[Daniel Lee] fixes #743. Instead of PI, multiplied by 2 and called it TWO_PI

[Daniel Lee] fixing call to dom_err_vec

[carp] removed unused commente code from transform.hpp and upgraded to multiply_lower_tri_self_transpose in corr_matrix_constrain

[Daniel Lee] replaced TWO_PI with 2*stan::math::pi()

[Daniel Lee] added a ifdef for ERROR_INDEX

[Daniel Lee] Update von_mises.hpp

[carp] changed order of factor_U and removed unused factor_L

[Daniel Lee] adding unit test for arg_optimize_algo

[Daniel Lee] updating test with a failing test case for the expected behavior

[Daniel Lee] removing nesterov from argument list

[Daniel Lee] removing nesterov option from command.hpp

[Daniel Lee] updating gitignore

[carp] added trnasform test for range

[carp] fixed bug in K==2 boundary condition for factor_U, with test

[carp] reorder factor_cov_matrix args to match convention, add remaining tests, completes fixes for issue

[Daniel Lee] adding test for 1-indexed check_corr_matrix message

[AStukalov] fix typo in multiply_lower_tri_self_transpose()

------------------------------------------
Started by user Daniel Lee
[EnvInject] - Loading node environment variables.
Building in workspace <http://gelman.stat.columbia.edu:8080/job/Stan/ws/>
> C:\Program Files (x86)\Git\cmd\git.exe rev-parse --is-inside-work-tree
Fetching changes from the remote Git repository
> C:\Program Files (x86)\Git\cmd\git.exe config remote.origin.url https://github.com/stan-dev/stan/
Fetching upstream changes from https://github.com/stan-dev/stan/
> C:\Program Files (x86)\Git\cmd\git.exe --version
using .gitcredentials to set credentials
> C:\Program Files (x86)\Git\cmd\git.exe config --local credential.helper store --file=\"C:\Windows\TEMP\git8341679042831540327.credentials\"
> C:\Program Files (x86)\Git\cmd\git.exe fetch --tags --progress https://github.com/stan-dev/stan/ +refs/heads/*:refs/remotes/origin/*
> C:\Program Files (x86)\Git\cmd\git.exe config --local --remove-section credential
> C:\Program Files (x86)\Git\cmd\git.exe rev-parse "origin/develop^{commit}"
Checking out Revision c7921f6e9a5887a7647ec180c7224ffc52b76149 (origin/develop)
> C:\Program Files (x86)\Git\cmd\git.exe config core.sparsecheckout
> C:\Program Files (x86)\Git\cmd\git.exe checkout -f c7921f6e9a5887a7647ec180c7224ffc52b76149
> C:\Program Files (x86)\Git\cmd\git.exe rev-list 5928850b337e9f4776e479166f5b412a60b43cb1
Starting build job Stan - Doxygen.
Starting build job Stan - Manual.
Finished Build : #2 of Job : Stan - Manual with status :SUCCESS
Finished Build : #2 of Job : Stan - Doxygen with status :SUCCESS
Starting build job Stan - Integration Tests.
Starting build job Stan - Unit Tests.
Starting build job Stan - Header Tests.
Finished Build : #2 of Job : Stan - Integration Tests with status :SUCCESS
Finished Build : #2 of Job : Stan - Header Tests with status :SUCCESS
Finished Build : #2 of Job : Stan - Unit Tests with status :SUCCESS
Starting build job Stan - CmdStan Interface Tests.
Finished Build : #2 of Job : Stan - CmdStan Interface Tests with status :FAILURE
Build step 'MultiJob Phase' marked build as failure

[mc.sta...@gmail.com]

See <http://gelman.stat.columbia.edu:8080/job/Stan/3/>

------------------------------------------
Started by user Daniel Lee
[EnvInject] - Loading node environment variables.
Building in workspace <http://gelman.stat.columbia.edu:8080/job/Stan/ws/>
> C:\Program Files (x86)\Git\cmd\git.exe rev-parse --is-inside-work-tree
Fetching changes from the remote Git repository
> C:\Program Files (x86)\Git\cmd\git.exe config remote.origin.url https://github.com/stan-dev/stan/
Fetching upstream changes from https://github.com/stan-dev/stan/
> C:\Program Files (x86)\Git\cmd\git.exe --version
using .gitcredentials to set credentials

> C:\Program Files (x86)\Git\cmd\git.exe config --local credential.helper store --file=\"C:\Windows\TEMP\git1151398070876071019.credentials\"

> C:\Program Files (x86)\Git\cmd\git.exe fetch --tags --progress https://github.com/stan-dev/stan/ +refs/heads/*:refs/remotes/origin/*
> C:\Program Files (x86)\Git\cmd\git.exe config --local --remove-section credential
> C:\Program Files (x86)\Git\cmd\git.exe rev-parse "origin/develop^{commit}"
Checking out Revision c7921f6e9a5887a7647ec180c7224ffc52b76149 (origin/develop)
> C:\Program Files (x86)\Git\cmd\git.exe config core.sparsecheckout
> C:\Program Files (x86)\Git\cmd\git.exe checkout -f c7921f6e9a5887a7647ec180c7224ffc52b76149

FATAL: Could not checkout null with start point c7921f6e9a5887a7647ec180c7224ffc52b76149
hudson.plugins.git.GitException: Could not checkout null with start point c7921f6e9a5887a7647ec180c7224ffc52b76149
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl$8.execute(CliGitAPIImpl.java:1497)
at hudson.plugins.git.GitSCM.checkout(GitSCM.java:895)
at hudson.model.AbstractProject.checkout(AbstractProject.java:1252)
at hudson.model.AbstractBuild$AbstractBuildExecution.defaultCheckout(AbstractBuild.java:624)
at jenkins.scm.SCMCheckoutStrategy.checkout(SCMCheckoutStrategy.java:86)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:530)
at com.tikal.jenkins.plugins.multijob.MultiJobBuild$MultiJobRunnerImpl.run(MultiJobBuild.java:134)
at hudson.model.Run.execute(Run.java:1732)
at com.tikal.jenkins.plugins.multijob.MultiJobBuild.run(MultiJobBuild.java:73)
at hudson.model.ResourceController.execute(ResourceController.java:88)
at hudson.model.Executor.run(Executor.java:234)
Caused by: hudson.plugins.git.GitException: Error performing git command
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1334)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1301)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1297)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommand(CliGitAPIImpl.java:1084)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommand(CliGitAPIImpl.java:1094)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl$8.execute(CliGitAPIImpl.java:1492)
... 10 more
Caused by: java.lang.InterruptedException
at java.lang.ProcessImpl.waitFor(Unknown Source)
at hudson.Proc$LocalProc.join(Proc.java:319)
at hudson.Proc.joinWithTimeout(Proc.java:168)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1321)
... 15 more

[mc.sta...@gmail.com]

See <http://gelman.stat.columbia.edu:8080/job/Stan/4/>

------------------------------------------
Started by user Daniel Lee
[EnvInject] - Loading node environment variables.
Building in workspace <http://gelman.stat.columbia.edu:8080/job/Stan/ws/>
> C:\Program Files (x86)\Git\cmd\git.exe rev-parse --is-inside-work-tree
Fetching changes from the remote Git repository
> C:\Program Files (x86)\Git\cmd\git.exe config remote.origin.url https://github.com/stan-dev/stan/
Fetching upstream changes from https://github.com/stan-dev/stan/
> C:\Program Files (x86)\Git\cmd\git.exe --version
using .gitcredentials to set credentials

> C:\Program Files (x86)\Git\cmd\git.exe config --local credential.helper store --file=\"C:\Windows\TEMP\git3716708205822110677.credentials\"

> C:\Program Files (x86)\Git\cmd\git.exe fetch --tags --progress https://github.com/stan-dev/stan/ +refs/heads/*:refs/remotes/origin/*
> C:\Program Files (x86)\Git\cmd\git.exe config --local --remove-section credential
> C:\Program Files (x86)\Git\cmd\git.exe rev-parse "origin/develop^{commit}"
Checking out Revision c7921f6e9a5887a7647ec180c7224ffc52b76149 (origin/develop)
> C:\Program Files (x86)\Git\cmd\git.exe config core.sparsecheckout
> C:\Program Files (x86)\Git\cmd\git.exe checkout -f c7921f6e9a5887a7647ec180c7224ffc52b76149

java.io.IOException: Could not checkout c7921f6e9a5887a7647ec180c7224ffc52b76149
at hudson.plugins.git.GitSCM.checkout(GitSCM.java:898)

at hudson.model.AbstractProject.checkout(AbstractProject.java:1252)
at hudson.model.AbstractBuild$AbstractBuildExecution.defaultCheckout(AbstractBuild.java:624)
at jenkins.scm.SCMCheckoutStrategy.checkout(SCMCheckoutStrategy.java:86)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:530)
at com.tikal.jenkins.plugins.multijob.MultiJobBuild$MultiJobRunnerImpl.run(MultiJobBuild.java:134)
at hudson.model.Run.execute(Run.java:1732)
at com.tikal.jenkins.plugins.multijob.MultiJobBuild.run(MultiJobBuild.java:73)
at hudson.model.ResourceController.execute(ResourceController.java:88)
at hudson.model.Executor.run(Executor.java:234)

Caused by: hudson.plugins.git.GitLockFailedException: Could not lock repository. Please try again
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl$8.execute(CliGitAPIImpl.java:1495)
at hudson.plugins.git.GitSCM.checkout(GitSCM.java:895)
... 9 more
Caused by: hudson.plugins.git.GitException: Command "C:\Program Files (x86)\Git\cmd\git.exe checkout -f c7921f6e9a5887a7647ec180c7224ffc52b76149" returned status code 128:
stdout:
stderr: fatal: Unable to create 'C:/Program Files (x86)/Jenkins/jobs/Stan/workspace/.git/index.lock': File exists.

If no other git process is currently running, this probably means a
git process crashed in this repository earlier. Make sure no other git
process is running and remove the file manually to continue.

at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1325)

[mc.sta...@gmail.com]

See <http://gelman.stat.columbia.edu:8080/job/Stan/5/>