24 KiB
Errors
Command failures and integration errors.
[ERR-20260920-024] git-push-repository-not-found
Logged: 2026-09-20T06:55:24+12:00 Priority: high Status: resolved Area: infra
Summary
The configured HTTPS remote accepted a network connection but did not resolve to a repository visible to the current credentials.
Error
remote: Not found. followed by fatal: repository 'https://git.jinome.org/Jinovo/' not found.
Context
- Added the user-provided address as
origin:https://git.jinome.org/Jinovo. - Attempted to push local
mainand set its upstream. - No commits were uploaded and the local branch/history were unchanged.
Suggested Fix
Obtain the complete clone URL for the concrete repository, including any repository slug and .git suffix required by the server, or configure credentials that can access the existing repository. Do not guess or rewrite the remote without user confirmation.
Metadata
- Reproducible: yes
- Related Files:
.git/config,Progression.md - Pattern-Key: vcs.repository-not-found
- First-Seen: 2026-09-20
- Last-Seen: 2026-09-20
Resolution
- Resolved: 2026-09-20
- Notes: Created the concrete Gitea repository and replaced the account-page URL with its full
.gitclone URL.
[ERR-20260920-025] ssh-config-read-denied
Logged: 2026-09-20 Priority: low Status: resolved Area: infra
Summary
A read-only probe for an existing SSH configuration could not access the user SSH directory under the managed filesystem profile.
Error
Access to the path 'C:\Users\Jino\.ssh' is denied.
Context
The probe was intended only to see whether an existing SSH identity could replace HTTPS authentication. No key content was requested or exposed.
Suggested Fix
Do not weaken filesystem permissions; use the verified HTTPS remote and Git Credential Manager.
Metadata
- Reproducible: yes
- Related Files:
.git/config,Progression.md - Pattern-Key: fs.permission-denied
Resolution
- Resolved: 2026-09-20
- Notes: HTTPS authentication succeeded after the user authorized Credential Manager; SSH inspection is no longer needed.
[ERR-20260920-026] git-https-credential-unavailable
Logged: 2026-09-20 Priority: high Status: resolved Area: infra
Summary
The new remote repository initially had no command-line HTTPS credential available to local Git.
Error
fatal: Cannot prompt because user interactivity has been disabled. followed by fatal: unable to get password from user.
Context
Browser login created the repository, but browser cookies did not authenticate command-line Git. The user subsequently authorized Git Credential Manager.
Suggested Fix
Authorize Git Credential Manager without placing credentials in the remote URL, shell history, or tracked files.
Metadata
- Reproducible: yes
- Related Files:
.git/config,Progression.md - Pattern-Key: auth.missing-credential
Resolution
- Resolved: 2026-09-20
- Notes: Credential Manager authorization completed;
mainpushed successfully and now tracksorigin/main.
[ERR-20260920-027] apply-patch-context-mismatch
Logged: 2026-09-20 Priority: low Status: resolved Area: docs
Summary
A combined archival patch failed because its expected context omitted a blank line before the separator in the error log.
Error
apply_patch verification failed: Failed to find expected lines.
Context
The failed patch made no partial changes. The actual file section was reread before retrying with exact context.
Suggested Fix
Inspect the precise surrounding lines before a multi-file patch and include blank-line structure in the patch context.
Metadata
- Reproducible: yes
- Related Files:
.learnings/ERRORS.md,Progression.md - Pattern-Key: docs.patch-context-mismatch
Resolution
- Resolved: 2026-09-20
- Notes: Reapplied with exact file context.
[ERR-20260920-006] powershell-empty-pipe
Logged: 2026-09-20 Priority: low Status: resolved Area: infra
Summary
A final artifact verification command piped directly from a PowerShell foreach statement and produced an empty-pipe parser error.
Error
ParserError: An empty pipe element is not allowed.
Context
Read-only existence and size verification for the four Stage 0 deliverables and Progression.md.
Suggested Fix
Collect foreach output into an array first, then pipe the array to Format-Table.
Metadata
- Reproducible: yes
- Related Files:
Progression.md - Pattern-Key: shell.nonzero-exit
Resolution
- Resolved: 2026-09-20
- Notes: The corrected command verified all required deliverables exist and contain data.
[ERR-20260920-004] progression-patch-context
Logged: 2026-09-20 Priority: low Status: resolved Area: docs
Summary
A combined large patch failed because one Progression.md context line did not match byte-for-byte.
Error
apply_patch verification failed: Failed to find expected lines
Context
Attempted to create the project charter and update multiple distant sections of the progress archive in one patch.
Suggested Fix
Split artifact creation from progress updates and use smaller, exact context anchors confirmed with rg.
Metadata
- Reproducible: unknown
- Related Files:
Progression.md,research/protocol/project_charter.md - Pattern-Key: config.patch-context-mismatch
Resolution
- Resolved: 2026-09-20
- Notes: Re-read the mandatory context and split the operation into smaller patches.
- Recurrence-Count: 2
- Last-Seen: 2026-09-20
[ERR-20260920-005] spreadsheet-marker-path
Logged: 2026-09-20 Priority: low Status: resolved Area: infra
Summary
The spreadsheet skill's operation marker was not located at the dependency-root path shown by the generic example.
Error
Cannot find module ...dependencies\\container_tools\\mark_artifact_operation_started.mjs
Context
Preparing to author the literature matrix with the bundled artifact runtime.
Suggested Fix
Resolve the marker from the installed spreadsheet skill directory rather than the dependency root.
Metadata
- Reproducible: yes
- Related Files:
research/protocol/literature_matrix.xlsx - Pattern-Key: config.missing-script
Resolution
- Resolved: 2026-09-20
- Notes: Located the marker under the versioned spreadsheet skill and ran it successfully before authoring.
[ERR-20260920-002] restricted-system-inventory
Logged: 2026-09-20 Priority: low Status: resolved Area: infra
Summary
WMI, Get-Volume, and systeminfo returned access denied during the environment audit.
Error
Access denied / 拒绝访问
Context
Attempted read-only OS, RAM, and volume inventory inside the managed Windows execution environment.
Suggested Fix
Use unprivileged fallbacks: .NET runtime information, Microsoft.VisualBasic.Devices.ComputerInfo, and Get-PSDrive.
Metadata
- Reproducible: yes
- Related Files:
research/audit/environment_audit.md - Pattern-Key: fs.permission-denied
Resolution
- Resolved: 2026-09-20
- Notes: Fallback interfaces returned OS architecture, physical RAM, and filesystem free space without escalation.
[ERR-20260920-003] python-package-detection
Logged: 2026-09-20 Priority: low Status: resolved Area: infra
Summary
The first package audit used import names derived mechanically from distribution names and produced unreliable missing-package results; a follow-up also attempted to import absent psutil.
Error
ModuleNotFoundError: No module named 'psutil'
Context
Auditing the local Python scientific stack. Distribution names such as scikit-learn do not map mechanically to import names.
Suggested Fix
Query installed distribution versions directly with importlib.metadata.version() and handle PackageNotFoundError without importing packages.
Metadata
- Reproducible: yes
- Related Files:
research/audit/environment_audit.md - Pattern-Key: deps.module-not-found
Resolution
- Resolved: 2026-09-20
- Notes: The final package table was generated directly from distribution metadata; hardware memory used a .NET fallback.
[ERR-20260920-001] pdf-to-markdown-encoding
Logged: 2026-09-20 Priority: medium Status: resolved Area: docs
Summary
PDF text extraction failed because Python wrote a Unicode character that could not be encoded using the Windows default code page.
Error
UnicodeEncodeError: 'gbk' codec can't encode character
Context
Attempted to extract text from Document/项目的正式定位.pdf before passing it through Pandoc.
Suggested Fix
Force UTF-8 output with PYTHONIOENCODING=utf-8.
Metadata
- Reproducible: yes
- Pattern-Key: shell.encoding-error
[ERR-20260920-007] winget-access-denied
Logged: 2026-09-20 Priority: medium Status: pending Area: infra
Summary
The Windows Package Manager launcher exists but cannot be executed from the managed environment.
Error
Program 'winget.exe' failed to run: 系统无法访问此文件。
Context
Attempted to inventory/install R, Python, and CUDA Toolkit through the standard Windows package manager after the user authorized environment remediation.
Suggested Fix
Use vendor-provided official installers, or retry winget outside the restricted environment if explicit escalation makes the launcher accessible.
Metadata
- Reproducible: yes
- Related Files:
Progression.md,research/audit/environment_audit.md - Pattern-Key: tool.access-denied
[ERR-20260920-008] uv-python-patch-path
Logged: 2026-09-20 Priority: low Status: resolved Area: infra
Summary
The virtual-environment command hard-coded a Python 3.12 patch-version path that differed from the version resolved by uv.
Error
No interpreter found at path .python\\cpython-3.12.11-windows-x86_64-none\\python.exe
Context
uv python install 3.12 correctly resolved CPython 3.12.14, while the following command assumed 3.12.11.
Suggested Fix
Resolve the installed interpreter path from uv python find or enumerate the installation directory rather than hard-coding a patch version.
Metadata
- Reproducible: yes
- Related Files:
Progression.md - Pattern-Key: config.version-path-mismatch
Resolution
- Resolved: 2026-09-20
- Notes: Located
E:\\Model\\.python\\cpython-3.12.14-windows-x86_64-none\\python.exe; subsequent environment creation will use this exact path.
[ERR-20260920-009] research-env-smoke-failures
Logged: 2026-09-20 Priority: high Status: pending Area: infra
Summary
The first research-environment runtime test found cache-permission, package-API, and CPU-only PyTorch problems despite a clean dependency-metadata check.
Error
PermissionError for PyTensor/Matplotlib/skrub cache paths; TypeError: check_array() got an unexpected keyword argument 'force_all_finite'; torch.cuda.is_available() is false.
Context
Executed PyMC sampling, semopy CFA, factor analysis, module imports, and a CUDA matrix multiplication in the new Python 3.12 environment.
Suggested Fix
Redirect all caches into the writable project tree, pin a factor-analyzer-compatible scikit-learn release, and reinstall a matched Torch/TorchVision/TorchAudio set from the official CUDA wheel index.
Metadata
- Reproducible: yes
- Related Files:
research/environment/smoke_test.py,research/environment/smoke-test-result.json,Progression.md - Pattern-Key: deps.runtime-compatibility
Resolution
- Resolved: 2026-09-20
- Notes: Redirected caches into
E:\\Model\\.cache, pinned scikit-learn 1.6.1, and installed matched CUDA 13.0 builds of Torch 2.14.0 and TorchVision 0.29.0. Torchaudio was removed because no same-generation official wheel exists and the project has no audio workload. Final closure is supported by the second smoke test recorded inProgression.md.
[ERR-20260920-010] torchaudio-release-mismatch
Logged: 2026-09-20 Priority: low Status: resolved Area: infra
Summary
The requested CUDA 13.0 Torch 2.14 stack could not be resolved because the official index does not publish torchaudio 2.14.0 for Windows/Python 3.12.
Error
No solution found ... there is no version of torchaudio==2.14.0.
Context
Attempted to align torch, torchvision, and torchaudio at the Torch 2.14 generation using the official CUDA 13.0 wheel index.
Suggested Fix
Do not install torchaudio when the project has no audio workload; keep only matched torch and torchvision CUDA builds.
Metadata
- Reproducible: yes
- Related Files:
research/environment/python-requirements.in,Progression.md - Pattern-Key: deps.release-mismatch
Resolution
- Resolved: 2026-09-20
- Notes: Removed torchaudio from the project requirements and smoke-test contract after verifying the official index.
[ERR-20260920-011] r-installer-file-race
Logged: 2026-09-20 Priority: low Status: resolved Area: infra
Summary
The silent R installer returned before the first immediate Rscript invocation observed the completed target files.
Error
Rscript.exe is not recognized immediately after installer return.
Context
Installed R 4.6.1 into the project-local tools directory with the official CRAN Windows installer.
Suggested Fix
After installer return, poll for the expected executable or perform a separate verification step before declaring failure.
Metadata
- Reproducible: unknown
- Related Files:
Progression.md - Pattern-Key: installer.completion-race
Resolution
- Resolved: 2026-09-20
- Notes: A follow-up inventory showed a complete installation;
Rscriptreported R 4.6.1 x64 successfully.
[ERR-20260920-012] r-smoke-false-positive
Logged: 2026-09-20 Priority: high Status: resolved Area: tests
Summary
The first R smoke test marked the mirt test as passed even though the fitted model reported non-convergence.
Error
The JSON result contained status: passed together with converged: false.
Context
The test wrapper treated any expression that returned without raising an R error as success; the mirt block returned its optimizer flag but did not assert it.
Suggested Fix
Use data generated from an identifiable 2PL model and raise an explicit error unless fit@OptimInfo$converged is true.
Metadata
- Reproducible: yes
- Related Files:
research/environment/r-smoke-test.R,research/environment/r-smoke-test-result.json,Progression.md - Pattern-Key: tests.missing-assertion
Resolution
- Resolved: 2026-09-20
- Notes: Added an explicit convergence assertion, identifiable 2PL simulation, and a higher EM-cycle ceiling. A second run is required for environmental acceptance.
[ERR-20260920-013] tool-poll-key-escaping
Logged: 2026-09-20 Priority: low Status: resolved Area: infra
Summary
Two CUDA installer status polls failed because a hyphenated nested-tool argument key was not quoted in JavaScript.
Error
SyntaxError: Unexpected string / SyntaxError: Invalid or unexpected token.
Context
Polling an already-running installer session; the failed polls did not send input or alter the installer process.
Suggested Fix
Quote hyphenated object keys, e.g. {"yield-time_ms": 30000}.
Metadata
- Reproducible: yes
- Related Files:
Progression.md - Pattern-Key: tooling.javascript-object-key
Resolution
- Resolved: 2026-09-20
- Notes: Corrected the key quoting and continued polling the same session until the installer returned exit code 0.
[ERR-20260920-014] vsdevcmd-nested-quoting
Logged: 2026-09-20 Priority: low Status: resolved Area: infra
Summary
The first CUDA compile command failed before invoking the compiler because nested cmd.exe quoting truncated the Visual Studio path at the first space.
Error
'""C:\\Program' is not recognized as an internal or external command.
Context
Attempted to chain VsDevCmd.bat, nvcc, and the smoke executable in a single quoted cmd.exe /c string.
Suggested Fix
Capture the environment emitted by VsDevCmd.bat && set, import it into the PowerShell process, then invoke nvcc directly with argument boundaries managed by PowerShell.
Metadata
- Reproducible: yes
- Related Files:
research/environment/cuda-smoke.cu,Progression.md - Pattern-Key: shell.windows-nested-quoting
Resolution
- Resolved: 2026-09-20
- Notes: Switched to importing the Visual Studio environment before compiler invocation; the corrected compile is recorded separately in
Progression.md.
[ERR-20260920-015] nvcc-host-compiler-path
Logged: 2026-09-20 Priority: medium Status: resolved Area: infra
Summary
nvcc could not find cl.exe after Visual Studio environment variables were copied from a child cmd process into PowerShell.
Error
nvcc fatal: Cannot find compiler 'cl.exe' in PATH.
Context
The MSVC component and compiler file were installed, but cross-shell environment import was insufficient for nvcc host-tool discovery.
Suggested Fix
Run vcvars64.bat, nvcc, and the resulting binary inside one cmd process using a checked-in build script.
Metadata
- Reproducible: yes
- Related Files:
research/environment/cuda-smoke-build.cmd,research/environment/cuda-smoke.cu,Progression.md - Pattern-Key: toolchain.environment-propagation
Resolution
- Resolved: 2026-09-20
- Notes: Created a single-shell build script after verifying the exact MSVC 14.44 compiler path with vswhere.
[ERR-20260920-016] lock-cache-permissions
Logged: 2026-09-20 Priority: medium Status: resolved Area: infra
Summary
Python and R lock export failed because uv and renv attempted to initialize caches under restricted user-profile directories.
Error
Failed to initialize cache ... uv\\cache and failed to create directory ... R/cache/R/renv.
Context
The runtime caches had been redirected, but the package-manager-specific cache variables were not yet included.
Suggested Fix
Set UV_CACHE_DIR and RENV_PATHS_ROOT to writable project-local directories for both activation and export commands.
Metadata
- Reproducible: yes
- Related Files:
research/environment/activate-research.ps1,Progression.md - Pattern-Key: fs.package-manager-cache-permission
Resolution
- Resolved: 2026-09-20
- Notes: Added project-local uv and renv cache roots; lock export is retried as a separate audited action.
[ERR-20260920-017] r-lock-export-schema
Logged: 2026-09-20 Priority: medium Status: resolved Area: infra
Summary
The R lock snapshot was written, but the auxiliary installed-package export failed due to an assumed metadata column and an incomplete library search path.
Error
subscript out of bounds for the Repository column; renv warned that R-recommended packages were missing.
Context
The export indexed a fixed column list from installed.packages(lib.loc=project_library) and passed only the project library to renv.
Suggested Fix
Combine the project library with .Library, and select only metadata columns that actually exist before writing CSV.
Metadata
- Reproducible: yes
- Related Files:
research/environment/renv.lock,Progression.md - Pattern-Key: data.schema-assumption
Resolution
- Resolved: 2026-09-20
- Notes: The corrected export uses both library roots and intersects requested fields with returned column names; final verification is a separate action.
[ERR-20260920-018] apply-patch-same-file-multiple-operations
Logged: 2026-09-20 Priority: low Status: resolved Area: docs
Summary
A patch attempted to delete and add the same audit file in one invocation and was rejected before making changes.
Error
multiple operations target ... environment_audit.md.
Context
Replacing the completed environment audit while also adding usage documentation and updating progression state.
Suggested Fix
Split full-file replacement into separate delete and add operations, then patch other files separately.
Metadata
- Reproducible: yes
- Related Files:
research/audit/environment_audit.md,Progression.md - Pattern-Key: tooling.patch-operation-conflict
Resolution
- Resolved: 2026-09-20
- Notes: No file changed in the rejected patch; the replacement is retried in valid discrete operations.
[ERR-20260920-019] apply-patch-hunk-order
Logged: 2026-09-20 Priority: low Status: resolved Area: docs
Summary
A combined README/progression patch was rejected because two progression hunks were ordered opposite to their line order in the file.
Error
Failed to find expected lines in Progression.md even though the lines existed.
Context
One hunk targeted a later risk-table line before another hunk targeted an earlier confirmed-facts line.
Suggested Fix
Order update hunks from top to bottom within each file, or split unrelated file additions and updates.
Metadata
- Reproducible: yes
- Related Files:
research/environment/README.md,Progression.md - Pattern-Key: tooling.patch-hunk-order
Resolution
- Resolved: 2026-09-20
- Notes: Added the README separately and applied progression hunks in file order.
[ERR-20260920-020] git-dubious-ownership
Logged: 2026-09-20 Priority: medium Status: resolved Area: infra
Summary
Git refused repository status checks after initialization because the workspace owner differs from the managed execution account.
Error
fatal: detected dubious ownership in repository at 'E:/Model'.
Context
The repository directory is owned by the Windows Administrators group while commands run as CodexSandboxOffline.
Suggested Fix
Add only the exact repository path to Git's global safe.directory; do not use a wildcard.
Metadata
- Reproducible: yes
- Related Files:
.git,Progression.md - Pattern-Key: git.safe-directory
Resolution
- Resolved: 2026-09-20
- Notes: The exact-path exception is applied as the next audited action before staging.
[ERR-20260920-021] git-candidate-node-modules
Logged: 2026-09-20 Priority: medium Status: resolved Area: infra
Summary
The first Git candidate set unintentionally included a nested node_modules tree, expanding the proposed commit to 7,832 files and about 321 MiB.
Error
Candidate-size audit showed large native modules and generated JavaScript under research/experiments/node_modules.
Context
The initial .gitignore covered research runtimes and caches but omitted generic nested Node dependencies.
Suggested Fix
Add **/node_modules/ before staging and rerun the size audit.
Metadata
- Reproducible: yes
- Related Files:
.gitignore,Progression.md - Pattern-Key: git.generated-dependency-tree
Resolution
- Resolved: 2026-09-20
- Notes: Added the nested dependency ignore rule before any files were staged.
[ERR-20260920-022] git-index-lock-permission
Logged: 2026-09-20 Priority: medium Status: resolved Area: infra
Summary
The first staging attempt could read the repository but could not create .git/index.lock under the managed filesystem profile.
Error
fatal: Unable to create 'E:/Model/.git/index.lock': Permission denied.
Context
The workspace is writable, while repository metadata is protected and requires the authorized elevated Git operation path.
Suggested Fix
Retry only the required Git index/commit operations with escalation; do not change workspace ownership or weaken filesystem permissions.
Metadata
- Reproducible: yes
- Related Files:
.git,Progression.md - Pattern-Key: git.index-lock-permission
Resolution
- Resolved: 2026-09-20
- Notes: No files were staged in the failed attempt; the audited candidate set is retried with scoped Git authorization.
[ERR-20260920-023] git-null-excludesfile
Logged: 2026-09-20 Priority: low Status: resolved Area: infra
Summary
Git for Windows rejected NUL as an explicit global excludes file override.
Error
fatal: cannot use NUL as an exclude file.
Context
The override was intended only to silence warnings from an unreadable user-level ignore file; project ignore rules were already valid.
Suggested Fix
Remove the override and tolerate the harmless warning, or use an actual readable empty file if silence is necessary.
Metadata
- Reproducible: yes
- Related Files:
.gitignore,Progression.md - Pattern-Key: git.excludesfile-windows-device
Resolution
- Resolved: 2026-09-20
- Notes: The override is removed; no index changes occurred in the failed attempt.