language-conditioned-psychometric-harmonization-model/.learnings/ERRORS.md

Errors

Command failures and integration errors.

---

[ERR-20260920-036] pdf-text-console-encoding

Logged: 2026-09-20 Priority: low Status: resolved Area: docs

Summary

An exploratory YRBS PDF text scan stopped when Windows console encoding could not print a soft-hyphen character.

Error

UnicodeEncodeError: 'gbk' codec can't encode character.

Context

PDF extraction itself succeeded; only diagnostic console output failed. Source files were unchanged.

Suggested Fix

Configure diagnostic stdout as UTF-8 with replacement before printing extracted PDF text.

Metadata

• Reproducible: yes
• Related Files: research/stage1/yrbs_primary_outcome_source_audit.json
• Pattern-Key: docs.console-encoding

Resolution

• Resolved: 2026-09-20
• Notes: The scan was rerun with UTF-8 stdout and all annual source pages were reviewed.

---

[ERR-20260920-035] gshs-questionnaire-directory-assumption

Logged: 2026-09-20 Priority: low Status: resolved Area: docs

Summary

The first questionnaire inventory command assumed a non-existent 03_questionnaires_and_codebooks directory.

Error

rg returned an OS error because that path does not exist.

Context

The dataset uses GSHS/Questionnaire, while 03_examples is a separate directory. No files were changed.

Suggested Fix

Enumerate the GSHS root before applying a documentation-path convention.

Metadata

• Reproducible: yes
• Related Files: Dataset/GSHS-全球学生健康调查数据/GSHS/Questionnaire
• Pattern-Key: docs.path-assumption

Resolution

• Resolved: 2026-09-20
• Notes: Enumerating the root located the actual questionnaire directory and the audit continued there.

---

[ERR-20260920-034] project-python-document-parser-missing

Logged: 2026-09-20 Priority: low Status: resolved Area: dependencies

Summary

The project research environment does not include python-docx, pypdf, or pdfplumber, so an exploratory source-extraction import failed.

Error

ModuleNotFoundError: No module named 'docx'.

Context

These packages are available in the Codex bundled document runtime. The final component audit uses only the project standard library and records verified source paths, pages/sections, and hashes, so it does not introduce an undeclared runtime dependency.

Suggested Fix

Use the bundled read-only document runtime for source inspection unless document parsing becomes a reproducible project pipeline dependency; only then add and lock the packages in the project environment.

Metadata

• Reproducible: yes
• Related Files: research/stage1/gshs_primary_outcome_component_audit.json
• Pattern-Key: dependency.optional-document-parser

Resolution

• Resolved: 2026-09-20
• Notes: Source text was extracted with the bundled runtime and key PDF pages were rendered with Poppler for visual verification.

---

[ERR-20260920-033] repeated-gshs-pandas-memory-exhaustion

Logged: 2026-09-20 Priority: medium Status: resolved Area: runtime

Summary

An exploratory pandas cross-tab scan again exhausted memory while parsing the 637-column GSHS CSV.

Error

pandas.errors.ParserError: Error tokenizing data. C error: out of memory.

Context

This is a recurrence of ERR-20260920-029 during a new component-level relation check. The source file was not changed.

Suggested Fix

Use a streaming csv.reader scan with fixed column indices for all full-file GSHS audits.

Metadata

• Reproducible: yes
• Related Files: research/stage1/audit_gshs_primary_outcome_components.py
• Pattern-Key: runtime.memory-exhaustion
• Related Error: ERR-20260920-029
• Recurrence Count: 2

Resolution

• Resolved: 2026-09-20
• Notes: The streaming audit completed all 673,499 rows, all 191 components, and all three raw/binary relationship checks without a dense pandas load.

---

[ERR-20260920-032] samhsa-pdf-direct-fetch-forbidden

Logged: 2026-09-20 Priority: medium Status: resolved Area: docs

Summary

SAMHSA PDF endpoints returned HTTP 403 to the web reader, direct download, and in-app browser during the NSDUH source audit.

Error

403 Forbidden from the official PDF URLs; the sandboxed first download attempt also had no network route.

Context

The official documents remained indexed with searchable text, and SAMHSA HTML methodology pages plus year-specific search extracts exposed the required question, routing, variable, and disclosure-risk statements. No local or remote data were changed by the failed reads.

Suggested Fix

Use SAMHSA's indexed official-document text and HTML pages for this audit, retain exact source URLs, and keep page-level PDF visual verification pending rather than claiming it occurred.

Metadata

• Reproducible: yes
• Related Files: research/stage1/nsduh_youth_attempt_source_audit.md
• Pattern-Key: net.access-forbidden

Resolution

• Resolved: 2026-09-20
• Notes: Triangulated the claim across official 2021–2023 restricted-use codebooks, the 2024 questionnaire, 2024 methodology definitions, the 2024 public-use guide, and the local public-use schema. Direct PDF page rendering remains explicitly unverified.

---

[ERR-20260920-031] git-https-authentication-rejected

Logged: 2026-09-20 Priority: high Status: resolved Area: infra

Summary

The remote rejected the previously authorized HTTPS credential when pushing the Stage 1 source-registry commit.

Error

remote: Failed to authenticate user / fatal: Authentication failed

Context

Local commit fb30b60 was created successfully. Local main is one commit ahead of origin/main; no remote history changed.

Suggested Fix

Reauthorize the git.jinome.org entry through Git Credential Manager, then retry git push. Do not store a password or token in repository files.

Metadata

• Reproducible: yes
• Related Files: .git/config, Progression.md
• Pattern-Key: auth.token-expired

Resolution

• Resolved: 2026-09-20
• Notes: Removed only the rejected git.jinome.org cached entry, reauthorized through Git Credential Manager, and pushed local main through ca67e1f without storing credentials in the repository.

---

[ERR-20260920-030] gshs-workbook-column-name

Logged: 2026-09-20 Priority: low Status: resolved Area: docs

Summary

An exploratory GSHS workbook filter referenced column instead of the actual column_name field.

Error

KeyError: 'column'

Context

The workbook schema was printed in the same command and showed the correct field name. The failed command was read-only and changed no data.

Suggested Fix

Inspect the sheet columns first and filter on column_name.

Metadata

• Reproducible: yes
• Related Files: Dataset/GSHS-全球学生健康调查数据/GSHS/02_documentation/GSHS_数据字典.xlsx
• Pattern-Key: runtime.python-exception

Resolution

• Resolved: 2026-09-20
• Notes: Re-ran the read-only extraction using column_name and obtained the intended candidate rows.

---

[ERR-20260920-028] python-assignment-expression-comprehension

Logged: 2026-09-20 Priority: low Status: resolved Area: tests

Summary

An inline audit command used an assignment expression in a comprehension iterable, which Python rejects.

Error

SyntaxError: assignment expression cannot be used in a comprehension iterable expression.

Context

The command was a read-only attempt to aggregate GSHS design-field coverage; no data or project file changed.

Suggested Fix

Use an ordinary loop in a maintained audit script instead of compressing stateful aggregation into a one-liner.

Metadata

• Reproducible: yes
• Related Files: research/stage1/audit_input_sources.py
• Pattern-Key: runtime.python-syntax

Resolution

• Resolved: 2026-09-20
• Notes: Replaced the inline expression with a reusable streaming audit script.

---

[ERR-20260920-029] pandas-csv-memory-exhaustion

Logged: 2026-09-20 Priority: medium Status: resolved Area: tests

Summary

Pandas exhausted memory while parsing the 0.77 GB, 637-column GSHS CSV even though only 12 columns were requested.

Error

pandas.errors.ParserError: Error tokenizing data. C error: out of memory.

Context

The failed read was non-mutating. The GSHS file is wide enough that the C parser's tokenization buffers remain material despite usecols.

Suggested Fix

Stream rows with the standard CSV reader, map only required column indexes, and retain aggregate counters rather than a DataFrame.

Metadata

• Reproducible: yes
• Related Files: research/stage1/audit_input_sources.py
• Pattern-Key: runtime.memory-exhaustion

Resolution

• Resolved: 2026-09-20
• Notes: The streaming implementation completed the full 673,499-row audit without loading the dataset into memory.

---

[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 main and 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 .git clone 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; main pushed successfully and now tracks origin/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 in Progression.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; Rscript reported 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.

---

[ERR-20260920-024] parquet-field-name-assumption

Logged: 2026-09-20 Priority: low Status: resolved Area: data

Summary

A diagnostic PyArrow read requested a non-existent survey_year field from the NSDUH full Parquet.

Error

The full NSDUH schema uses YEAR, not survey_year.

Context

The field name was inferred from the YRBS convention instead of checked against the NSDUH schema. No data were modified.

Suggested Fix

Inspect the authoritative schema before column projection and use the source-specific YEAR field; DuckDB then verified the intended annual counts.

Metadata

• Reproducible: yes
• Related Files: Dataset/可直接分析数据包_NSDUH_YRBS/NSDUH/nsduh_2021_2024_full.parquet
• Pattern-Key: schema.field-name-assumption

Resolution

• Resolved: 2026-09-20
• Notes: Re-ran the count query against YEAR and obtained annual distributions for YUSUITHK and YUSUIPLN.

---

[ERR-20260920-025] yrbs-attempt-response-shape

Logged: 2026-09-20 Priority: medium Status: resolved Area: data

Summary

The first Gate-1 package build assumed all YRBS primary outcomes were binary and stopped on attempt response code 3.

Error

ValueError: Unsupported response code: survey='YRBS' construct='suicide_attempt' code='3' label='2 or 3 times'

Context

Annual source audits correctly retained five attempt-frequency categories, but the canonical response function handled the ordinal mapping only for GSHS. The fail-closed check prevented output files from being written.

Suggested Fix

Apply the shared five-level frequency mapping to both GSHS and YRBS attempt items and rerun all package validations.

Metadata

• Reproducible: yes
• Related Files: research/stage1/build_primary_outcome_package.py, research/stage1/yrbs_primary_outcome_source_audit.json
• Pattern-Key: response-dictionary.shape-assumption

Resolution

• Resolved: 2026-09-20
• Notes: Canonical attempt categories are now zero, one, two_or_three, four_or_five, and six_or_more in both surveys.

---