java.lang.IllegalStateException: Failed to find all committed files

alin_g · July 27, 2022, 12:58pm

Must-share information (formatted with Markdown):

SonnarScanner CLI - sonar-scanner-cli-4.7.0.2747-linux.zip

This is happening on multiple projects since a few hours ago. We are seeing this on our CI systems:

15:39:39   ERROR: Error during SonarScanner execution
15:39:39   INFO: Final Memory: 38M/134M
15:39:39   java.lang.IllegalStateException: Failed to find all committed files
15:39:39   INFO: ------------------------------------------------------------------------
15:39:39     at org.sonar.scm.git.CompositeBlameCommand.collectAllCommittedFiles(CompositeBlameCommand.java:114)
15:39:39     at org.sonar.scm.git.CompositeBlameCommand.blame(CompositeBlameCommand.java:72)
15:39:39     at org.sonar.scanner.scm.ScmPublisher.publish(ScmPublisher.java:84)
15:39:39     at org.sonar.scanner.scan.SpringProjectScanContainer.doAfterStart(SpringProjectScanContainer.java:362)
15:39:39     at org.sonar.core.platform.SpringComponentContainer.startComponents(SpringComponentContainer.java:188)
15:39:39     at org.sonar.core.platform.SpringComponentContainer.execute(SpringComponentContainer.java:167)
15:39:39     at org.sonar.scanner.bootstrap.SpringGlobalContainer.doAfterStart(SpringGlobalContainer.java:135)
15:39:39     at org.sonar.core.platform.SpringComponentContainer.startComponents(SpringComponentContainer.java:188)
15:39:39     at org.sonar.core.platform.SpringComponentContainer.execute(SpringComponentContainer.java:167)
15:39:39     at org.sonar.batch.bootstrapper.Batch.doExecute(Batch.java:72)
15:39:39     at org.sonar.batch.bootstrapper.Batch.execute(Batch.java:66)
15:39:39     at org.sonarsource.scanner.api.internal.batch.BatchIsolatedLauncher.execute(BatchIsolatedLauncher.java:46)
15:39:39     at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
15:39:39     at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
15:39:39     at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
15:39:39     at java.base/java.lang.reflect.Method.invoke(Unknown Source)
15:39:39     at org.sonarsource.scanner.api.internal.IsolatedLauncherProxy.invoke(IsolatedLauncherProxy.java:60)
15:39:39     at com.sun.proxy.$Proxy0.execute(Unknown Source)
15:39:39     at org.sonarsource.scanner.api.EmbeddedScanner.doExecute(EmbeddedScanner.java:189)
15:39:39     at org.sonarsource.scanner.api.EmbeddedScanner.execute(EmbeddedScanner.java:138)
15:39:39     at org.sonarsource.scanner.cli.Main.execute(Main.java:112)
15:39:39     at org.sonarsource.scanner.cli.Main.execute(Main.java:75)
15:39:39     at org.sonarsource.scanner.cli.Main.main(Main.java:61)
15:39:39   Caused by: org.eclipse.jgit.errors.MissingObjectException: Missing unknown 4c78c69da8b74c0d2b955f0e4b2e6c3e5a5353a6
15:39:39     at org.eclipse.jgit.internal.storage.file.WindowCursor.open(WindowCursor.java:135)
15:39:39     at org.eclipse.jgit.lib.ObjectReader.open(ObjectReader.java:214)
15:39:39     at org.eclipse.jgit.revwalk.RevWalk.parseAny(RevWalk.java:1075)
15:39:39     at org.eclipse.jgit.revwalk.RevWalk.parseCommit(RevWalk.java:985)
15:39:39     at org.sonar.scm.git.CompositeBlameCommand.collectAllCommittedFiles(CompositeBlameCommand.java:101)
15:39:39     ... 22 more

alin_g · July 28, 2022, 11:07am

I had a look at

15:39:39 Caused by: org.eclipse.jgit.errors.MissingObjectException: Missing unknown 4c78c69da8b74c0d2b955f0e4b2e6c3e5a5353a6

That is a merge commit and it does exist.

jacek.poreda · July 29, 2022, 11:40am

Hello @alin_g ,

How do you check out your branch before executing Sonar analysis? What is the version of SonarQube you using?

alin_g · July 29, 2022, 2:11pm

Hello Jacek,

Thank you for looking into this. We recently upgraded to 9.5.
The checkout is handled by TeamCity and this is what it seems to be doing:

 [Update git mirror (/root/agent/system/git/git-0E23E9D8.git)] /usr/bin/git init --bare --initial-branch=main
[10:58:28] :			 [Update git mirror (/root/agent/system/git/git-0E23E9D8.git)] /usr/bin/git config http.sslCAInfo
[10:58:28] :			 [Update git mirror (/root/agent/system/git/git-0E23E9D8.git)] Forced fetch (teamcity.git.fetchAllHeads=true) with +refs/heads/*:refs/heads/* refspec
[10:58:28] :			 [Update git mirror (/root/agent/system/git/git-0E23E9D8.git)] /usr/bin/git -c credential.helper= fetch --progress --recurse-submodules=no origin +refs/heads/*:refs/heads/* (1s)
....
[10:58:29] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] The .git directory is missing in '/root/agent/work/a00796389cbd5412'. Running 'git init'...
[10:58:29] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] /usr/bin/git init --initial-branch=main
[10:58:29] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] /usr/bin/git config lfs.storage /root/agent/system/git/git-0E23E9D8.git/lfs
[10:58:29] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] /usr/bin/git config core.sparseCheckout true
[10:58:29] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] /usr/bin/git config http.sslCAInfo
[10:58:29] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] /usr/bin/git show-ref
[10:58:29] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] /usr/bin/git -c credential.helper= ls-remote origin
[10:58:29] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] Forced fetch (teamcity.git.fetchAllHeads=true) with +refs/heads/*:refs/remotes/origin/* refspec
[10:58:29] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] /usr/bin/git -c credential.helper= fetch --progress --recurse-submodules=no origin +refs/heads/*:refs/remotes/origin/*
[10:58:30] :				 [/usr/bin/git -c credential.helper= fetch --progress --recurse-submodules=no origin +refs/heads/*:refs/remotes/origin/*] 
[10:58:30] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] /usr/bin/git log -n1 --pretty=format:%H%x20%s 430efd8738a1ebcce05f1d34bcbe7756f230f68e --
[10:58:30] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] /usr/bin/git branch
[10:58:30] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] /usr/bin/git update-ref refs/heads/FVCL-105 430efd8738a1ebcce05f1d34bcbe7756f230f68e
[10:58:30] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] /usr/bin/git -c credential.helper= checkout -q -f FVCL-105
[10:58:30] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] /usr/bin/git branch --set-upstream-to=refs/remotes/origin/FVCL-105
[10:58:30] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] Cleaning fvcl-frontend (2) in /root/agent/work/a00796389cbd5412 the file set ALL_UNTRACKED
[10:58:30] :			 [Update checkout directory (/root/agent/work/a00796389cbd5412)] /usr/bin/git clean -f -d -x

These are some of the debug messages before the failure, in case it helps:

[10:59:01] :	 [Step 1/1] 07:59:01.561 INFO: Load project repositories (done) | time=21ms
[10:59:01] :	 [Step 1/1] 07:59:01.562 INFO: SCM collecting changed files in the branch
[10:59:01] :	 [Step 1/1] 07:59:01.593 DEBUG: loading config FileBasedConfig[/root/.config/jgit/config]
[10:59:01] :	 [Step 1/1] 07:59:01.594 DEBUG: readpipe [/usr/bin/git, --version],/usr/bin
[10:59:01] :	 [Step 1/1] 07:59:01.603 DEBUG: readpipe may return 'git version 2.30.2'
[10:59:01] :	 [Step 1/1] 07:59:01.603 DEBUG: remaining output:
[10:59:01] :	 [Step 1/1] 
[10:59:01] :	 [Step 1/1] 07:59:01.603 DEBUG: readpipe [/usr/bin/git, config, --system, --show-origin, --list, -z],/usr/bin
[10:59:01] :	 [Step 1/1] 07:59:01.605 DEBUG: readpipe may return 'null'
[10:59:01] :	 [Step 1/1] 07:59:01.606 DEBUG: remaining output:
[10:59:01] :	 [Step 1/1] 
[10:59:01] :	 [Step 1/1] 07:59:01.624 DEBUG: readpipe rc=128
[10:59:01] :	 [Step 1/1] 07:59:01.624 DEBUG: Exception caught during execution of command '[/usr/bin/git, config, --system, --show-origin, --list, -z]' in '/usr/bin', return code '128', error message 'fatal: unable to read config file '/etc/gitconfig': No such file or directory
[10:59:01] :	 [Step 1/1] '
[10:59:01] :	 [Step 1/1] 07:59:01.625 DEBUG: loading config FileBasedConfig[/root/.gitconfig]
[10:59:01] :	 [Step 1/1] 07:59:01.658 DEBUG: Thread[JGit-FileStoreAttributeReader-1,5,main]: start measure timestamp resolution / (overlay) in /app/.git
[10:59:01] :	 [Step 1/1] 07:59:01.660 DEBUG: Thread[JGit-FileStoreAttributeReader-1,5,main]: end measure timestamp resolution / (overlay) in /app/.git; got PT0.000144S
[10:59:01] :	 [Step 1/1] 07:59:01.660 DEBUG: Thread[JGit-FileStoreAttributeReader-1,5,main]: start measure minimal racy interval in /app/.git
[10:59:01] :	 [Step 1/1] 07:59:01.758 DEBUG: Thread[main,5,main]: use fallback timestamp resolution for directory /app/.git
[10:59:01] :	 [Step 1/1] 07:59:01.761 DEBUG: Thread[main,5,main]: cannot measure timestamp resolution of unborn directory /root/agent/system/git/git-0E23E9D8.git
[10:59:01] :	 [Step 1/1] 07:59:01.761 DEBUG: Thread[main,5,main]: cannot measure timestamp resolution of unborn directory /root/agent/system/git/git-0E23E9D8.git/objects
[10:59:01] :	 [Step 1/1] 07:59:01.768 WARN: Missing unknown 1782328a254865b1361ffd499967730484d5d3b4

Please also note that we’re performing the scan inside a docker container (using FROM node:latest).
Edit: Same issue appears with FROM mcr.microsoft.com/dotnet/sdk:6.0 and then apt -qq install default-jre & dotnet tool install --global dotnet-sonarscanner
Any help is much appreciated.

alin_g · July 29, 2022, 7:41pm

For anyone else running into this with TeamCity, this is what has fixed it:

system · August 5, 2022, 7:41pm

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