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I have a Jenkins job that is checking out a repository, compiling a C project, and then is supposed to stage, commit and push the generated binaries. However, the job fails at staging/committing the binaries because it does not detect any changes and therefore has nothing to commit.

In the PowerShell script that does the compilation, after the binary image is created I copy it to another directory where it is tracked in our repository.

Source binary file:
.\device_test\images\Device_ROYAL_Firmware_Development.0.img

Destination binary file (the one that is tracked):
.\device_platforms\nordic15_2\device_device\device_out\ROYAL_FW_40.04.10.0.bin

Despite the destination binary file showing an updated LastWriteTime before and after being overwritten, git status does not show that file as modified and git add -f binaryfile does nothing.

Build #1
    Copying version header...
    Current FW version: #define DEVICE_FW_VERSION "40.04.10.0"
    Compiling .\device_platforms\nordic15_2\device_device\pca10100e\s112\arm5_no_packs\device.uvprojx...
        Keil build successful! image=.\device_platforms\nordic15_2\device_device\device_out\ROYAL_FW_40.04.10.0.bin
    Image pre-copy modified: 10/17/2022 12:35:44
    Copying image file .\device_platforms\nordic15_2\device_device\device_out\ROYAL_FW_40.04.10.0.bin to .\device_test\images\Device_ROYAL_Firmware_Development.0.img...
    Image post-copy modified: 10/17/2022 12:41:45
    Adding image file .\device_test\images\Device_ROYAL_Firmware_Development.0.img to git...

Running git status before overwriting the file, of course, does not show the file as having been modified.

HEAD detached from 5a36217fa
Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

    modified:   Device_lib/projects/keil/Device_lib.lib
    modified:   Device_platforms/nordic15_2/Device_device/Device_fw_version/Device_fw_version_ROYAL.h
    modified:   Device_platforms/nordic15_2/Device_device/Device_hw_config/Device_hw_config.h
    deleted:    Device_platforms/nordic15_2/Device_device/Device_out/.gitignore

Untracked files:
  (use "git add <file>..." to include in what will be committed)

    Device_major_version_ROBIN.txt
    Device_major_version_ROYAL.txt
    cppcheck-result-Devicelib.xml
    cppcheck-result-Deviceshim.xml
    doxygen/
    git_output.txt
    Device_fw_version_ROBIN.0.h
    Device_fw_version_ROBIN.1.h
    Device_fw_version_ROBIN.2.h
    Device_fw_version_ROBIN.3.h
    Device_fw_version_ROYAL.0.h
    Device_fw_version_ROYAL.1.h
    Device_fw_version_ROYAL.2.h
    Device_fw_version_ROYAL.3.h
    Device_lib/projects/keil/keil_log
    Device_platforms/nordic15_2/Device_device/pca10100e/s112/arm5_no_packs/RTE/_nrf52820_xxaa/
    Device_platforms/nordic15_2/Device_device/pca10100e/s112/arm5_no_packs/keil_log
    Device_test/images/.gitignore

no changes added to commit (use "git add" and/or "git commit -a")

But there are still no changes to the destination file needing to be staged after overwriting the file.

HEAD detached from 5a36217fa
Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

    modified:   Device_lib/projects/keil/Device_lib.lib
    modified:   Device_platforms/nordic15_2/Device_device/Device_fw_version/Device_fw_version_ROYAL.h
    modified:   Device_platforms/nordic15_2/Device_device/Device_hw_config/Device_hw_config.h
    deleted:    Device_platforms/nordic15_2/Device_device/Device_out/.gitignore

Untracked files:
  (use "git add <file>..." to include in what will be committed)

    Device_major_version_ROBIN.txt
    Device_major_version_ROYAL.txt
    cppcheck-result-Devicelib.xml
    cppcheck-result-Deviceshim.xml
    doxygen/
    git_output.txt
    Device_fw_version_ROBIN.0.h
    Device_fw_version_ROBIN.1.h
    Device_fw_version_ROBIN.2.h
    Device_fw_version_ROBIN.3.h
    Device_fw_version_ROYAL.0.h
    Device_fw_version_ROYAL.1.h
    Device_fw_version_ROYAL.2.h
    Device_fw_version_ROYAL.3.h
    Device_lib/projects/keil/keil_log
    Device_platforms/nordic15_2/Device_device/pca10100e/s112/arm5_no_packs/RTE/_nrf52820_xxaa/
    Device_platforms/nordic15_2/Device_device/pca10100e/s112/arm5_no_packs/keil_log
    Device_test/images/.gitignore

no changes added to commit (use "git add" and/or "git commit -a")

For comparison, listing the files in .\device_test\images before overwriting shows the file as being modified at 10/17/2022 12:35 PM

    Directory: E:\jenkins\home\DeviceLib2_dev_src\Device_test\images


Mode                 LastWriteTime         Length Name                                                                 
----                 -------------         ------ ----                                                                 
-a----        10/14/2022   6:51 PM             14 .gitattributes                                                       
-a----        10/15/2022  10:32 AM              6 .gitignore                                                           
-a----        10/14/2022   6:51 PM             86 commit_hash                                                          

... (list shortened)

-a----        10/15/2022  10:27 AM          41316 Device_ROBIN_Firmware_Development.0.img                                
-a----        10/15/2022  10:27 AM          41316 Device_ROBIN_Firmware_Development.1.img                                
-a----        10/15/2022  10:23 AM          41316 Device_ROBIN_Firmware_Development.2.img                                
-a----        10/15/2022  10:24 AM          41316 Device_ROBIN_Firmware_Development.3.img                                
-a----        10/17/2022  12:35 PM          41316 Device_ROYAL_Firmware_Development.0.img                                
-a----        10/17/2022  12:36 PM          41316 Device_ROYAL_Firmware_Development.1.img                                
-a----        10/17/2022  12:37 PM          41316 Device_ROYAL_Firmware_Development.2.img                                
-a----        10/17/2022  12:38 PM          41316 Device_ROYAL_Firmware_Development.3.img                                
-a----        10/14/2022   6:51 PM          40228 Device_Whippet_Firmware_Development.0.img                              
-a----        10/14/2022   6:51 PM          40228 Device_Whippet_Firmware_Development.1.img                              
-a----        10/14/2022   6:51 PM          40228 Device_Whippet_Firmware_Development.2.img                              
-a----        10/14/2022   6:51 PM          40228 Device_Whippet_Firmware_Development.3.img

And shows an updated LastWriteTime of 10/17/2022 12:41 PM after overwriting.

    Directory: E:\jenkins\home\DeviceLib2_dev_src\Device_test\images


Mode                 LastWriteTime         Length Name                                                                 
----                 -------------         ------ ----                                                                 
-a----        10/14/2022   6:51 PM             14 .gitattributes                                                       
-a----        10/15/2022  10:32 AM              6 .gitignore                                                           
-a----        10/14/2022   6:51 PM             86 commit_hash                                                          

... (list shortened)

-a----        10/15/2022  10:27 AM          41316 Device_ROBIN_Firmware_Development.0.img                                
-a----        10/15/2022  10:27 AM          41316 Device_ROBIN_Firmware_Development.1.img                                
-a----        10/15/2022  10:23 AM          41316 Device_ROBIN_Firmware_Development.2.img                                
-a----        10/15/2022  10:24 AM          41316 Device_ROBIN_Firmware_Development.3.img                                
-a----        10/17/2022  12:41 PM          41316 Device_ROYAL_Firmware_Development.0.img                                
-a----        10/17/2022  12:36 PM          41316 Device_ROYAL_Firmware_Development.1.img                                
-a----        10/17/2022  12:37 PM          41316 Device_ROYAL_Firmware_Development.2.img                                
-a----        10/17/2022  12:38 PM          41316 Device_ROYAL_Firmware_Development.3.img                                
-a----        10/14/2022   6:51 PM          40228 Device_Whippet_Firmware_Development.0.img                              
-a----        10/14/2022   6:51 PM          40228 Device_Whippet_Firmware_Development.1.img                              
-a----        10/14/2022   6:51 PM          40228 Device_Whippet_Firmware_Development.2.img                              
-a----        10/14/2022   6:51 PM          40228 Device_Whippet_Firmware_Development.3.img

I can go into the local repository with a command-line, manually copy the source to the destination and git status will correctly show the file as modified. It therefore seems to be isolated when these steps are run by Jenkins. As a starting point, I wonder if the steps taken by the Git SCM plugin in Jenkins have any influence.

git.exe rev-parse --resolve-git-dir localrepo\.git
git.exe config remote.origin.url [email protected]:remoterepo.git
git.exe --version
git --version
git.exe fetch --tags --progress -- [email protected]:remoterepo.git +refs/heads/*:refs/remotes/origin/*
git.exe rev-parse "refs/remotes/origin/branch_name^{commit}"
git.exe config core.sparsecheckout
git.exe checkout -f 63cd0f5b1fd084291ab9f97bd3f03a4d2079101c
git.exe rev-list --no-walk b42d583949d13f5ea9de729b61ab7be81c699bb6

Update:
To @LeGEC's recommendation, git update-index --refresh shows the same unstaged changes- the binary file not being shown in either case.

Device_lib/projects/keil/Device_lib.lib: needs update
Device_platforms/nordic15_2/Device_device/Device_fw_version/Device_fw_version_ROYAL.h: needs update
Device_platforms/nordic15_2/Device_device/Device_hw_config/Device_hw_config.h: needs update
Device_platforms/nordic15_2/Device_device/Device_out/.gitignore: needs update
Improve this question
11
  • Can you check if git update-index --refresh and git update-index --really-refresh have any effect ? Commented Oct 17, 2022 at 19:20
  • Both commands output the same list of files that show up as "changes not staged for commit" seen in git status and still does not include the binary file. I tried it both in the script right after overwriting the tracked binary file and also from command-line. Commented Oct 17, 2022 at 19:45
  • Maybe one of the many answers here? stackoverflow.com/a/24316479/7411885 . My experience is either that I need to git rm --cached plus git reset due to a busted cache, OR that I've just checked out the repo multiple times, and am in the wrong one compared to my tools... Commented Oct 17, 2022 at 20:40
  • "the script fails upon committing which I can see in the git output" : can you please add this output to your question ? (note: copy the text, no screen capture please) "I can go into the local repository [...], copy the binary over manually" what do you mean by copying the binary ? shouldn't the binary already be present in that local repository ? what happens when you don't copy anything and run git status in the pipeline local repo ? Commented Oct 17, 2022 at 20:48
  • @LeGEC The binary is output in one location by the compiler and then copied to another folder where it is tracked. If I run git status without copying manually, the binary file does not show as modified even though it was overwritten by the script. Commented Oct 17, 2022 at 21:38
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