INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/standardhealth/fsh-pct --branch master repo DEBUG:root:Time to deadline 35879.99781 seconds Cloning into 'repo'... DEBUG:root:running: wget -q https://github.com/HL7/fhir-ig-publisher/releases/latest/download/publisher.jar -O publisher.jar DEBUG:root:Time to deadline 35877.321139 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35875.849399 seconds npm WARN deprecated inflight@1.0.6: This module is not supported, and leaks memory. Do not use it. Check out lru-cache if you want a good and tested way to coalesce async requests by a key value, which is much more comprehensive and powerful. npm WARN deprecated rimraf@2.6.3: Rimraf versions prior to v4 are no longer supported npm WARN deprecated glob@7.2.3: Glob versions prior to v9 are no longer supported added 139 packages in 9s 14 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 11.6.4 npm notice Changelog: npm notice Run `npm install -g npm@11.6.4` to update! npm notice DEBUG:root:running: java -Xms19000m -Xmx19000m -jar ../publisher.jar -ig ig.json -api-key-file /etc/ig.builder.keyfile.ini -fhir-settings /etc/fhir-settings.json -auto-ig-build -tx http://tx.fhir.org -target https://build.fhir.org/ig/standardhealth/fsh-pct/ -out /scratch/repo DEBUG:root:Time to deadline 35866.541323 seconds FHIR IG Publisher Version 2.0.27 (Git# 07050daf807f). Built 2025-11-28T20:03:59.255Z (5 days old) Detected Java version: 21-ea from /usr/local/openjdk-21 on Linux/amd64 (64bit). 19008MB available dir = /scratch/repo, path = /usr/local/openjdk-21/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin Parameters: -ig ig.json -api-key-file /etc/ig.builder.keyfile.ini -fhir-settings /etc/fhir-settings.json -auto-ig-build -tx http://tx.fhir.org -target https://build.fhir.org/ig/standardhealth/fsh-pct/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Thursday, December 4, 2025, 6:04:14 PM Coordinated Universal Time (2025-12-04T18:04:14Z) Build FHIR IG from /scratch/repo (00:00.028 / 00:00.029, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.003 / 00:00.032, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.036, 97Mb) Found dependency on hl7.fhir.us.core#3.1.0 in Sushi config. Pre-installing (00:00.011 / 00:00.047, 97Mb) Installing hl7.fhir.us.core#3.1.0 to the package cache  Fetching:  Installing hl7.fhir.us.core#3.1.0  done. Found dependency on hl7.fhir.us.mcode#1.0.0 in Sushi config. Pre-installing (00:02.899 / 00:02.947, 80Mb) Installing hl7.fhir.us.mcode#1.0.0 to the package cache  Fetching:  Installing hl7.fhir.us.mcode#1.0.0  done. Run Sushi on /scratch/repo (00:00.951 / 00:03.899, 96Mb) Sushi: info Running SUSHI v3.16.5 (implements FHIR Shorthand specification v3.0.0) (00:00.729 / 00:04.628, 104Mb) Sushi: info Arguments: (00:00.000 / 00:04.628, 104Mb) Sushi: info --require-latest (00:00.000 / 00:04.629, 104Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:04.629, 104Mb) Sushi: info /scratch/repo (00:00.000 / 00:04.629, 104Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.755 / 00:05.385, 104Mb) Sushi: warn Configuration contains unexpected properties: current, 1.0.0. Check that these properties are spelled, capitalized, and indented correctly. (00:00.168 / 00:05.553, 104Mb) Sushi: warn Configuration property publisher has a value with an unexpected type. (00:00.000 / 00:05.553, 104Mb) Sushi: warn Configuration property history has a value with an unexpected type. (00:00.000 / 00:05.554, 104Mb) Sushi: info Importing FSH text... (00:00.000 / 00:05.554, 104Mb) Sushi: info Preprocessed 3 documents with 3 aliases. (00:00.148 / 00:05.703, 104Mb) Sushi: info Imported 2 definitions and 1 instances. (00:00.008 / 00:05.711, 104Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.147 / 00:05.859, 104Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.8.0 (00:00.630 / 00:06.489, 104Mb) Sushi: info Attempting to download hl7.fhir.uv.tools.r4#0.8.0 from https://packages.fhir.org/hl7.fhir.uv.tools.r4/0.8.0 (00:00.001 / 00:06.491, 104Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.8.0 (00:00.824 / 00:07.315, 104Mb) Sushi: info Cached hl7.fhir.uv.tools.r4#0.8.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.tools.r4#0.8.0 (00:00.003 / 00:07.318, 104Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.8.0 with 110 resources (00:00.081 / 00:07.400, 104Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 7.0.0 (00:00.442 / 00:07.842, 104Mb) Sushi: info Attempting to download hl7.terminology.r4#7.0.0 from https://packages.fhir.org/hl7.terminology.r4/7.0.0 (00:00.000 / 00:07.843, 104Mb) Sushi: info Downloaded hl7.terminology.r4#7.0.0 (00:03.007 / 00:10.850, 104Mb) Sushi: info Cached hl7.terminology.r4#7.0.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#7.0.0 (00:00.001 / 00:10.851, 104Mb) Sushi: info Loaded hl7.terminology.r4#7.0.0 with 4096 resources (00:01.726 / 00:12.578, 112Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.437 / 00:13.015, 112Mb) Sushi: info Attempting to download hl7.fhir.uv.extensions.r4#5.2.0 from https://packages.fhir.org/hl7.fhir.uv.extensions.r4/5.2.0 (00:00.000 / 00:13.016, 112Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:02.326 / 00:15.342, 112Mb) Sushi: info Cached hl7.fhir.uv.extensions.r4#5.2.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.extensions.r4#5.2.0 (00:00.001 / 00:15.343, 112Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.337 / 00:15.681, 112Mb) Sushi: info Loaded hl7.fhir.us.core#3.1.0 with 145 resources (00:00.087 / 00:15.769, 112Mb) Sushi: info Loaded hl7.fhir.us.mcode#1.0.0 with 58 resources (00:00.059 / 00:15.828, 112Mb) Sushi: info Attempting to download hl7.fhir.r4.core#4.0.1 from https://packages.fhir.org/hl7.fhir.r4.core/4.0.1 (00:00.000 / 00:15.828, 112Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.275 / 00:19.104, 112Mb) Sushi: info Cached hl7.fhir.r4.core#4.0.1 to /home/fhiruser/.fhir/packages/hl7.fhir.r4.core#4.0.1 (00:00.001 / 00:19.105, 112Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.664 / 00:20.770, 112Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.011 / 00:20.781, 112Mb) Sushi: info Converting FSH to FHIR resources... (00:00.024 / 00:20.805, 112Mb) Sushi: info Converted 2 FHIR StructureDefinitions. (00:00.732 / 00:21.538, 112Mb) Sushi: info Converted 1 FHIR instances. (00:00.121 / 00:21.660, 112Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.000 / 00:21.660, 112Mb) Sushi: info Exported 3 FHIR resources as JSON. (00:00.080 / 00:21.741, 112Mb) Sushi: info Assembling Implementation Guide sources... (00:00.001 / 00:21.743, 112Mb) Sushi: info Generated ImplementationGuide-patient.clinical.trial.matching.json (00:00.063 / 00:21.806, 112Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:21.806, 112Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:21.808, 112Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:21.808, 112Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:21.808, 112Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:21.809, 112Mb) Sushi: | | 2 | 0 | 0 | 0 | | (00:00.000 / 00:21.809, 112Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:21.809, 112Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:21.809, 112Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:21.809, 112Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:21.809, 112Mb) Sushi: | | 0 | 0 | 1 | | (00:00.000 / 00:21.810, 112Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:21.810, 112Mb) Sushi: | | (00:00.000 / 00:21.810, 112Mb) Sushi: =================================================================== (00:00.000 / 00:21.810, 112Mb) Sushi: | You might need some Vitamin Sea 0 Errors 3 Warnings | (00:00.000 / 00:21.810, 112Mb) Sushi: =================================================================== (00:00.000 / 00:21.810, 112Mb) Root directory: /scratch/repo (00:00.028 / 00:21.839, 112Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.770 / 00:22.609, 56Mb) Load Template from fhir.base.template#current (00:00.705 / 00:23.315, 57Mb) Installing fhir.base.template#current to the package cache  Fetching:  Installing fhir.base.template#current  done. Scanning directory: /scratch/repo/template ====================================================================== Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:05.837 / 00:29.153, 393Mb) Core Package hl7.fhir.r4.core#4.0.1 (00:00.000 / 00:29.153, 393Mb) Running Terminology Log: /tmp/ohfu-fhir-ig-166145501377455023.html Connect to Terminology Server at http://tx.fhir.org (00:32.247 / 01:01.401, 428Mb) Installing hl7.fhir.pubpack#0.2.3 to the package cache  Fetching:  Installing hl7.fhir.pubpack#0.2.3  done. Load Package hl7.fhir.pubpack#0.2.3 Installing hl7.fhir.xver-extensions#0.1.0 to the package cache  Fetching:  Installing hl7.fhir.xver-extensions#0.1.0  done. Load Package hl7.fhir.xver-extensions#0.1.0 Load Package hl7.terminology.r4#7.0.0 Load Package hl7.fhir.uv.extensions.r4#5.2.0 Load Package hl7.fhir.us.core#3.1.0 Load Package hl7.fhir.us.mcode#1.0.0 Load Package hl7.fhir.uv.tools.r4#0.8.0 Load R5 Specials Installing hl7.fhir.r5.core#5.0.0 to the package cache  Fetching:  Installing hl7.fhir.r5.core#5.0.0  done. Initialization complete (00:12.701 / 01:14.102, 422Mb) Load IG (00:00.000 / 01:14.103, 422Mb) Load Content (00:00.004 / 01:14.107, 422Mb) Using en-US as the default narrative language. (no language information in Implementation Guide) (00:00.081 / 01:14.189, 422Mb) Process Loaded Resources (00:00.210 / 01:14.399, 430Mb) Generating Snapshots (00:00.130 / 01:14.530, 438Mb) Signing Certificate: RSA key for Subject: OU=IG Publisher, L=Ann Arbor, CN=hl7.org, O=HL7, ST=Missouri, C=us from: OU=IG Publisher, L=Ann Arbor, CN=hl7.org, O=HL7, ST=Missouri, C=us Fetch http://mcodeinitiative.org/codex/us/patient.clinical.trial.matching/package-list.json for version check (00:00.930 / 01:15.460, 646Mb) Checking Language (00:00.363 / 01:15.824, 646Mb) Load Dependency Info (00:00.001 / 01:15.825, 646Mb) Load Info (00:00.001 / 01:15.826, 646Mb) Load Paths (00:00.000 / 01:15.827, 650Mb) Check R4 / R4B (00:00.000 / 01:15.827, 650Mb) Assign Comparison Ids (00:00.020 / 01:15.847, 650Mb) Propagating status (00:00.000 / 01:15.848, 650Mb) Generating Narratives (00:00.000 / 01:15.848, 650Mb) Validating Conformance Resources (00:00.582 / 01:16.431, 798Mb) Check profiles & code systems (00:08.247 / 01:24.678, 761Mb) Check realm rules (00:00.001 / 01:24.680, 761Mb) Previous Version Comparison (00:00.000 / 01:24.680, 761Mb) Checking for Bundles to sign (00:00.019 / 01:24.699, 761Mb) Validating Resources (00:00.000 / 01:24.700, 761Mb) Processing Provenance Records (00:00.000 / 01:24.700, 761Mb) Generating Outputs in /scratch/repo/output (00:00.000 / 01:24.700, 761Mb) Generate Native Outputs (00:00.297 / 01:24.998, 777Mb) Run Template (00:01.919 / 01:26.917, 1009Mb) Generate HTML Outputs (00:00.870 / 01:27.788, 1Gb) Generate Spreadsheets (00:05.024 / 01:32.812, 791Mb) Generate Summaries (00:05.567 / 01:38.380, 499Mb) Generating Summary Outputs (00:00.000 / 01:38.381, 499Mb) DB Cumulative Time invested: 00:00:00.182 Sending Usage Stats to Server (00:04.586 / 01:42.967, 692Mb) ## Memory (MB): Use = 692, Free = 18315, Total = 19008, Max = 19008 (00:00.007 / 01:42.975, 696Mb) Reclaiming memory... (00:00.000 / 01:42.975, 696Mb) ## Memory (MB): Use = 385, Free = 18622, Total = 19008, Max = 19008 (00:00.620 / 01:43.596, 393Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.003 / 01:43.600, 398Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 01:43.600, 398Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 01:43.600, 398Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 01:43.600, 398Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.655 / 01:44.256, 401Mb) Jekyll: Generating... (00:00.000 / 01:44.256, 401Mb) Jekyll: done in 0.901 seconds. (00:00.900 / 01:45.157, 405Mb) Checking Output HTML (00:01.442 / 01:46.600, 689Mb) Processed /scratch/repo/output - % reduction = 100 (17575529 ==> 59408) found 624 files (00:00.808 / 01:47.408, 1Gb) ......................................... ......................................... ... 624 html files, 0 pages invalid xhtml (0%) (00:25.092 / 02:12.501, 5Gb) ... 84952 links, 0 broken links (0%) (00:00.000 / 02:12.501, 5Gb) Generate fragment-usage-analysis.csv (00:00.000 / 02:12.502, 5Gb) Build final .zip (00:00.013 / 02:12.515, 5Gb) Final .zip built (00:01.114 / 02:13.629, 5Gb) Built. Times: loading: 00:01.717, generate: 01:02.186, narrative generation: 00:00.582, realm-rules: 00:00.000, previous-version: 00:00.000, jekyll: 00:01.569, validation: 00:08.245 (#4), template: 00:00.880 (#3) (00:04.382 / 02:18.011, 5Gb) Generating QA (00:00.000 / 02:18.012, 5Gb) Internal error in location for message: 'Error @1, 2: Found / expecting a token name', loc = '/scratch/repo/output/index.html', err = 'The html source has duplicate anchor Ids: mCODE' Validation output in /scratch/repo/output/qa.html Errors: 25, Warnings: 10, Info: 1, Broken Links: 0 (00:00.329 / 02:18.341, 5Gb) Finished @ 12/4/25, 6:06 PM. Max Memory Used = 5Gb (00:00.025 / 02:18.366, 5Gb)