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[CMAKE] Refactored FindXDR.cmake module#640

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[CMAKE] Refactored FindXDR.cmake module#640
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@philthiel philthiel commented Nov 23, 2017

Configuration problems on macOS using -std=c++11 concerning finding XDR should be resolved now. This should fix #639.

pthiel added 2 commits November 23, 2017 09:54
[CMAKE] Refactored FindXDR.cmake module
d6044e2 
Configuration problems on macOS using -std=c++11 concerning finding XDR
should be resolved now.
[CMAKE] Refactored FindXDR.cmake module fixed for Win
bd50baf 
Manual library searching required.
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tkemmer commented Nov 23, 2017

The FindXDR module seems to work now! However, FindBoost stopped working with your PR on my Mac (Sierra, CMake 3.8, Contrib) for some reason.

Master:

-- Performing Test BALL_XDRREC_CREATE_VOID_VOID_INT - Success
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE  
-- Boost version: 1.60.0

PR:

-- Performing Test BALL_XDRREC_CREATE_VOID_VOID_INT - Success
-- Looking for pthread.h
-- Looking for pthread.h - not found
CMake Error at /Applications/CLion.app/Contents/bin/cmake/share/cmake-3.8/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find Threads (missing: Threads_FOUND)
Call Stack (most recent call first):
  /Applications/CLion.app/Contents/bin/cmake/share/cmake-3.8/Modules/FindPackageHandleStandardArgs.cmake:377 (_FPHSA_FAILURE_MESSAGE)
  /Applications/CLion.app/Contents/bin/cmake/share/cmake-3.8/Modules/FindThreads.cmake:212 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
  /Applications/CLion.app/Contents/bin/cmake/share/cmake-3.8/Modules/CMakeFindDependencyMacro.cmake:55 (find_package)
  /Applications/CLion.app/Contents/bin/cmake/share/cmake-3.8/Modules/FindBoost.cmake:1478 (find_dependency)
  cmake/BALLConfigBoost.cmake:38 (FIND_PACKAGE)
  CMakeLists.txt:133 (INCLUDE)

This problem does not seem to occur with our Sierra and El Capitan build workers, though.

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philthiel commented Nov 23, 2017

CI runs are ok: on macOS it is only the Timer_test that failed. Not related to XDR.

The boost thing is weird, I will look into that.

okohlbacher added a commit that referenced this pull request May 15, 2026
@okohlbacher @claude
docs(v1.6.1): integrate the 5 open PRs as Phase 5.2 (Upstream PR Triage)
f848bc1 
Adds Phase 5.2 as a new in-scope item with per-PR disposition matrix:

- #640 FindXDR refactor: investigate-then-close-or-rebase (XDR may be gone post-Phase-4)
- #600 Travis-CI integration: close .travis.yml part (Travis dead), cherry-pick 4 orthogonal files
- #554 Omega torsion: extract C++ slice (residueRotamerSet, residue.C), defer .sip to Phase 6
- #550 HYP residue: rebase + merge in v1.6.1 (no Python parts, pure C+++data gap fix)
- #546 Insertion code printing: extract C++ slice (residue.{h,C}), defer .sip to Phase 6

Plan breakdown (A/B/C/D) sequenced to avoid residue.C merge conflicts
(C bundles #554+#546; D HYP runs after C OR merges into it).

Release criterion 4 added: each open PR must reach a recorded disposition.

Open question 3 added: XDR-still-used grep verifies #640's path.
Open question 4 added: maintainer policy on cherry-picking from departed contributors.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
okohlbacher added a commit that referenced this pull request May 16, 2026
@okohlbacher @claude @codex
docs(roadmap): add ROADMAP-AUDIT-V1.6.2.md — v1.6.2 scope + overall h…
11c8e0f 
…ygiene audit (3-round Codex-reviewed)

Cross-checks ROADMAP.md against MILESTONE-CONTEXT.md, CONCERNS.md, recent commits,
debug sessions, planning artifacts, and open issues/PRs to surface items deferred
to v1.6.2 (or "v1.6.x housekeeping") that never made it into the backlog, plus
hygiene fixes for stale entries.

Three rounds of adversarial Codex review (v1 REJECT-AND-REWORK → v2 APPROVE-WITH-FIXES
→ v3 APPROVE-AS-IS). Key Codex catches:

- v1 claimed 6 forgotten items: 2 were false positives (ContourSurface bug from
  stale CONCERNS.md; B3 baseline already recorded). 2 were tracking-fixes-not-
  backlog (Phase 9 progress-table row; glwidget debug doc reconcile).
- v2 added Phase 999.21 Qt 6 regressions (CR-01/02/03) based on stale
  05-VERIFICATION.md — all three are actually fixed in current code
  (HTMLPage.C:36, molecularControl.C:500, PresentaBALLView.C:41, pyWidget.C:349).
  REMOVED in v3.
- v2 also overstated 999.7 remaining scope — gl_profile landed in 7b28685.
  NARROWED in v3 to Windows driver capture only.

Net findings:
- 2 real source-level additions for v1.6.2 backlog:
    A1: 999.22 Tier-C warning census + (a)-subset (NOT wholesale ~3700 cleanup)
    A3: 999.21 DockResultFile QtXml dead-code cleanup (1 hour)
- 1 stretch addition:
    A4: 999.23 CIF Bison grammar audit (defer to v1.7 if v1.6.2 fills up)
- 1 progress-cleanup not a backlog item:
    A2: Phase 9 close — CI wiring already in tree (b2bb718 + 61bf5a7),
        only 3 baseline failures need triage + flip gatekeeper to blocking
- §B PR triage decision: use 999.14 with named "5-PR legacy bundle"
  (#640, #600, #554, #550, #546); NOT a new Phase 5.2 unless triage
  turns into real merge code work
- 5 hygiene fixes (§C2/C3/C4 + §D1/D2/D4/D5):
    - Mark Phase 999.4 as COMPLETED via Phase 4.1
    - Narrow Phase 999.7 scope to Windows driver capture only
    - Mark Phase 5.1 B3 baseline carry-forward as RESOLVED (run 25953405453)
    - Remove false ContourSurface bug from CONCERNS.md
    - Update ROADMAP Phase 9 row to reflect partial completion
    - Reconcile glwidget-port-misprojection debug session status
    - Add "Updates / Resolution log" pointer on 05-VERIFICATION.md → 05-HUMAN-UAT.md
      (the recurring trap of stale planning docs misleading future audits)
- §E workflow gap: no v1.6.2 MILESTONE-CONTEXT.md yet; create when v1.6.1 tags
- §F recommended v1.6.2 shape: 5 build-accel/CI-hygiene phases + Phase 9 close +
  999.14 PR triage + 999.21 dead-code; ~7-11 days core effort (patch shape)

Audit is approve-as-is; §G action items totaling ~2 hours of edits can apply
in a separate follow-up commit.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-Authored-By: Codex (GPT-5.5) <noreply@openai.com>
okohlbacher added a commit that referenced this pull request May 16, 2026
@okohlbacher @claude @codex
docs(roadmap): apply ROADMAP-AUDIT-V1.6.2.md §G action items (hygiene…
f176b8b 
… + 3 new backlog entries)

Follow-up commit to 11c8e0f. Applies all 8 §G action items from the audit
in a single focused change.

ROADMAP.md hygiene (§C2/C3/C4 + §D2):
- Phase 9 row: 0/0 Not started → (partial) In Progress (v1.6.2); CI wiring
  + coverage + JUnit reporter landed in b2bb718 + 61bf5a7; 3 baseline
  failures remain (Directory_test, AmberFF_test, AssignBondOrderProcessor_test2).
- Phase 5.1 row: B3 carry-forward marked RESOLVED — 3495 → 0 on run
  25953405453 per 05.1-08-SUMMARY.md + 05.1-UAT.md.
- Phase 999.4 header: "PROMOTED to Phase 4.1" → "COMPLETED via Phase 4.1
  (2026-05-15)" with completion citation.
- Phase 999.7 entry: scope-narrowed per audit §C3. Build-system pain
  (SEED-005-1 Linux aqtinstall, SEED-005-2 Windows vcpkg baseline) and
  macOS gl_profile=(compatibility|none) relaxation all CLOSED by other
  phases (commit 54da903, run 25953405453, commit 7b28685). Only SEED-005-3
  Windows VM driver-behaviour capture remains; defer to v2.0 post-PIPE-01
  unless Windows-access contributor surfaces sooner.
- Phase 999.5 (Open-PR triage): closed as superseded by Phase 999.14.

ROADMAP.md backlog (§B):
- Phase 999.14: added named "5-PR legacy bundle" subtask per audit §B +
  MILESTONE-CONTEXT.md:270-279 (#640 FindXDR, #600 Travis-CI, #554 Omega
  torsion, #550 hydroxyproline AA, #546 residue insertion code). Table
  per-PR with likely category. Bundle-escape clause: spin out as Phase 5.2
  if rebase work exceeds ~3 days. Target milestone explicit: v1.6.2.

ROADMAP.md new backlog entries (§A1/A3/A4):
- Phase 999.21 (DockResultFile QtXml dead-code cleanup, v1.6.2, 1 hour) —
  was Phase 5.1 BLOCKER-A2, never picked up.
- Phase 999.22 (warning census + (a)-subset, v1.6.2, ≤2 weeks) — recast
  from "clean ~3700 warnings wholesale" to census + small-subset-only,
  per Codex correction. Includes residual Windows C4910/C4834.
- Phase 999.23 (CIF Bison grammar audit, v1.6.2 or v1.7, 1-2 days) —
  scope narrowed to CIF only (count 3 vs 5 reconcile during phase);
  other 7 Bison grammars out of scope.

Doc hygiene (§D1/D4/D5):
- CONCERNS.md ContourSurface entry: marked NOT-A-BUG with audit citation
  (implementation at contourSurface.h:302-306 is correct; original audit
  inspected only the declaration). Includes lesson-for-future-audits.
- 05-VERIFICATION.md: added "⚠ STALE FINDINGS" banner pointing readers
  at 05-HUMAN-UAT.md as the rolling-resolution source of truth + new
  `resolution_log:` frontmatter field. Two roadmap audits (v1 + v2)
  were misled by reading this snapshot without cross-checking HUMAN-UAT.
- glwidget-port-misprojection.md: added `audit_notes:` frontmatter
  citing audit §D4 — status stays awaiting_human_verify (cannot be
  auto-closed; needs interactive macOS visual recheck), with explicit
  action for whoever runs the recheck.

§E (v1.6.2 MILESTONE-CONTEXT.md creation) deferred — appropriate
trigger is "v1.6.1 has tagged + shipped," not yet true.

Net ROADMAP delta:
- Active phases unchanged.
- Backlog: 5 v1.6.2 phases → 8 (added 999.21/22/23).
- 999.5 closed (superseded), 999.4 closed (promoted+completed),
  999.7 narrowed.
- Progress table reflects current state for Phase 5.1 (B3 done) and
  Phase 9 (CI wiring landed, 3 failures remain).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-Authored-By: Codex (GPT-5.5) <noreply@openai.com>
okohlbacher added a commit that referenced this pull request May 16, 2026
@okohlbacher @claude
docs(plans): triage + close PLAN.md files (999.22 + Phase 9 + 999.14)
0f0fcf6 
Three remaining v1.6.2 PLAN.md execution prompts, written via /gsd-plan-phase
pattern to complete the milestone planning round:

- 999.22 (WARN-CENSUS-01, CENSUS-ONLY per 2026-05-16 Open Q3):
  Pull tri-OS green CI build logs, build CENSUS.md per-warning x file x
  cause classification tagged (a)/(b)/(c), file three deferral backlog
  stubs (999.22a v1.7 mechanical, 999.22b v2.0 blocked-by-999.6,
  999.22c v1.7 per-site). Zero source-code changes.

- Phase 9 close (TEST-CLOSE-01 + TEST-CLOSE-02):
  Six tasks. Triage the 3 baseline failures (Directory_test, AmberFF_test
  with Linux cross-check for FP-precision-vs-regression diagnosis,
  AssignBondOrderProcessor_test2 fine-penalty), pre-flip green-list
  verification, flip macOS+Linux gatekeeper continue-on-error true->false
  in ci.yml + release.yml mirror, file Phase 999.24 Windows-test-gatekeeper
  backlog stub. Disposition heuristic: <2h -> FIX, 2-8h or FP-driven ->
  QUARANTINE, v2.0-architectural -> KNOWN-CASUALTY.

- 999.14 triage (TRIAGE-01 + TRIAGE-02 + TRIAGE-03):
  Five tasks. Snapshot open issues+PRs to JSON baselines, categorize per
  5-category rubric with templated close comments + decisions.md audit
  trail, stale-docs audit applying f176b8b pattern (banner +
  resolution_log frontmatter) to VERIFICATION.md files with stale rows
  resolved in sibling HUMAN-UAT.md, 5-PR legacy bundle (#640 FindXDR /
  #600 Travis-CI / #554 Omega / #550 HYP / #546 InsertionCode) with
  per-PR scope-check + rebase-or-close + 3-day bundle-escape clause
  routing spillover to Phase 5.2, wire 999.5 <-> 999.14 supersedes
  pointer.

All three closes the v1.6.2 milestone planning round; execution can now
proceed via /gsd-execute-phase 999.16 (and others) without re-planning.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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CHECK_CXX_SOURCE_COMPILES ignores compiler flags on macOS

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@philthiel @tkemmer