INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/fhir-birthdefectsreporting-ig --branch master repo DEBUG:root:Time to deadline 35879.997911 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 35879.329557 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35876.95532 seconds npm WARN deprecated rimraf@2.6.3: Rimraf versions prior to v4 are no longer supported 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 glob@7.2.3: Glob versions prior to v9 are no longer supported added 140 packages in 5s 15 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 11.4.1 npm notice Changelog: npm notice Run `npm install -g npm@11.4.1` 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/HL7/fhir-birthdefectsreporting-ig/ -out /scratch/repo DEBUG:root:Time to deadline 35871.760984 seconds FHIR IG Publisher Version 2.0.6 (Git# 0e36f4bcb58f). Built 2025-06-10T06:56:14.605Z (41 hours 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/HL7/fhir-birthdefectsreporting-ig/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Thursday, June 12, 2025, 12:36:53 AM Coordinated Universal Time (2025-06-12T00:36:53Z) Build FHIR IG from /scratch/repo (00:00.028 / 00:00.029, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.002 / 00:00.031, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.002 / 00:00.034, 97Mb) Found dependency on hl7.fhir.us.core#7.0.0 in Sushi config. Pre-installing (00:00.005 / 00:00.040, 97Mb) Installing hl7.fhir.us.core#7.0.0 to the package cache Fetching: Installing hl7.fhir.us.core#7.0.0 done. Found dependency on us.nlm.vsac#0.17.0 in Sushi config. Pre-installing (00:01.604 / 00:01.644, 73Mb) Installing us.nlm.vsac#0.17.0 to the package cache Fetching: Installing us.nlm.vsac#0.17.0 done. Found dependency on us.cdc.phinvads#0.12.0 in Sushi config. Pre-installing (00:05.967 / 00:07.611, 553Mb) Installing us.cdc.phinvads#0.12.0 to the package cache Fetching: Installing us.cdc.phinvads#0.12.0 done. Found dependency on hl7.fhir.us.vr-common-library#2.0.0-ballot in Sushi config. Pre-installing (00:18.924 / 00:26.536, 873Mb) Installing hl7.fhir.us.vr-common-library#2.0.0-ballot to the package cache Fetching: Installing hl7.fhir.us.vr-common-library#2.0.0-ballot done. Found dependency on hl7.fhir.us.bfdr#current in Sushi config. Pre-installing (00:00.776 / 00:27.312, 881Mb) Installing hl7.fhir.us.bfdr#current to the package cache Fetching: Installing hl7.fhir.us.bfdr#current done. Run Sushi on /scratch/repo (00:01.849 / 00:29.162, 945Mb) Sushi: info Running SUSHI v3.16.0 (implements FHIR Shorthand specification v3.0.0) (00:00.608 / 00:29.771, 953Mb) Sushi: info Arguments: (00:00.000 / 00:29.771, 953Mb) Sushi: info --require-latest (00:00.000 / 00:29.771, 953Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:29.771, 953Mb) Sushi: info /scratch/repo (00:00.000 / 00:29.772, 953Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.584 / 00:30.357, 953Mb) Sushi: info Importing FSH text... (00:00.121 / 00:30.478, 953Mb) Sushi: info Preprocessed 37 documents with 23 aliases. (00:00.274 / 00:30.753, 953Mb) Sushi: info Imported 25 definitions and 60 instances. (00:00.035 / 00:30.789, 953Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.092 / 00:30.881, 953Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.5.0 (00:00.612 / 00:31.494, 953Mb) Sushi: info Attempting to download hl7.fhir.uv.tools.r4#0.5.0 from https://packages.fhir.org/hl7.fhir.uv.tools.r4/0.5.0 (00:00.000 / 00:31.495, 953Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.5.0 (00:00.730 / 00:32.225, 953Mb) Sushi: info Cached hl7.fhir.uv.tools.r4#0.5.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.tools.r4#0.5.0 (00:00.003 / 00:32.228, 953Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.5.0 with 88 resources (00:00.051 / 00:32.280, 953Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 6.4.0 (00:00.445 / 00:32.725, 953Mb) Sushi: info Attempting to download hl7.terminology.r4#6.4.0 from https://packages.fhir.org/hl7.terminology.r4/6.4.0 (00:00.003 / 00:32.728, 953Mb) Sushi: info Downloaded hl7.terminology.r4#6.4.0 (00:02.653 / 00:35.381, 953Mb) Sushi: info Cached hl7.terminology.r4#6.4.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#6.4.0 (00:00.001 / 00:35.383, 953Mb) Sushi: info Loaded hl7.terminology.r4#6.4.0 with 4381 resources (00:01.288 / 00:36.671, 953Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.442 / 00:37.114, 958Mb) 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 / 00:37.114, 958Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.495 / 00:38.610, 958Mb) 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 / 00:38.611, 958Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.229 / 00:38.841, 958Mb) Sushi: info Loaded hl7.fhir.us.core#7.0.0 with 211 resources (00:00.092 / 00:38.934, 958Mb) Sushi: info Loaded us.nlm.vsac#0.17.0 with 14850 resources (00:07.181 / 00:46.115, 958Mb) Sushi: info Loaded us.cdc.phinvads#0.12.0 with 1967 resources (00:01.701 / 00:47.816, 958Mb) Sushi: info Loaded hl7.fhir.us.vr-common-library#2.0.0-ballot with 87 resources (00:00.051 / 00:47.867, 958Mb) Sushi: info Loaded hl7.fhir.us.bfdr#current with 142 resources (00:00.215 / 00:48.082, 958Mb) 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 / 00:48.083, 958Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.335 / 00:51.419, 958Mb) Sushi: info Cached hl7.fhir.r4.core#4.0.1 to /home/fhiruser/.fhir/packages/hl7.fhir.r4.core#4.0.1 (00:00.003 / 00:51.422, 958Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.170 / 00:52.593, 958Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.012 / 00:52.605, 958Mb) Sushi: info Converting FSH to FHIR resources... (00:00.040 / 00:52.646, 958Mb) Sushi: info Converted 18 FHIR StructureDefinitions. (00:00.822 / 00:53.469, 958Mb) Sushi: info Converted 1 FHIR CodeSystems. (00:00.024 / 00:53.493, 958Mb) Sushi: info Converted 6 FHIR ValueSets. (00:00.123 / 00:53.616, 958Mb) Sushi: info Converted 60 FHIR instances. (00:04.051 / 00:57.667, 958Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.000 / 00:57.668, 958Mb) Sushi: info Exported 85 FHIR resources as JSON. (00:00.072 / 00:57.740, 958Mb) Sushi: info Assembling Implementation Guide sources... (00:00.004 / 00:57.744, 958Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.us.birthdefectreporting.json (00:00.040 / 00:57.785, 958Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:57.786, 958Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:57.787, 958Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:57.787, 958Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:57.787, 958Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:57.788, 958Mb) Sushi: | | 18 | 0 | 0 | 0 | | (00:00.000 / 00:57.788, 958Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:57.788, 958Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:57.788, 958Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:57.788, 958Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:57.788, 958Mb) Sushi: | | 6 | 1 | 60 | | (00:00.000 / 00:57.788, 958Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:57.789, 958Mb) Sushi: | | (00:00.000 / 00:57.789, 958Mb) Sushi: =================================================================== (00:00.000 / 00:57.789, 958Mb) Sushi: | You've turned the tide. 0 Errors 0 Warnings | (00:00.000 / 00:57.789, 958Mb) Sushi: =================================================================== (00:00.000 / 00:57.789, 958Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.608 / 00:58.398, 64Mb) Load Template from fhir.base.template#current (00:00.514 / 00:58.912, 65Mb) Installing fhir.base.template#current to the package cache Fetching: Installing fhir.base.template#current done. Root directory: /scratch/repo (00:02.901 / 01:01.814, 361Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.001 / 01:01.815, 361Mb) Core Package hl7.fhir.r4.core#4.0.1 Running Terminology Log: /tmp/ohfu-fhir-ig-9826827789780088022.html Connect to Terminology Server at http://tx.fhir.org (00:33.988 / 01:35.804, 1Gb) 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#6.4.0 Load Package hl7.fhir.uv.extensions.r4#5.2.0 Installing hl7.terminology.r4#5.5.0 to the package cache Fetching: Installing hl7.terminology.r4#5.5.0 done. Load Package hl7.terminology.r4#5.5.0 Installing hl7.fhir.uv.smart-app-launch#2.0.0 to the package cache Fetching: Installing hl7.fhir.uv.smart-app-launch#2.0.0 done. Load Package hl7.fhir.uv.smart-app-launch#2.0.0 Installing us.nlm.vsac#0.18.0 to the package cache Fetching: Installing us.nlm.vsac#0.18.0 done. Load Package us.nlm.vsac#0.18.0 Installing hl7.fhir.uv.sdc#3.0.0 to the package cache Fetching: Installing hl7.fhir.uv.sdc#3.0.0 done. Ignore Dependency on Core FHIR hl7.fhir.r4.examples#4.0.1, from package 'hl7.fhir.uv.sdc#3.0.0' (00:24.084 / 01:59.888, 1Gb) Load Package hl7.fhir.uv.sdc#3.0.0 Load Package us.cdc.phinvads#0.12.0 Installing hl7.fhir.uv.extensions.r4#5.1.0-snapshot1 to the package cache Fetching: 2025-06-12 00:38:53.926 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:92] Failed to resolve package hl7.fhir.uv.extensions.r4#5.1.0-snapshot1 from server: https://packages2.fhir.org/packages (Not found) 2025-06-12 00:38:54.477 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:92] Failed to resolve package hl7.fhir.uv.extensions.r4#5.1.0-snapshot1 from server: https://packages.fhir.org (Not Found) Installing hl7.fhir.uv.extensions.r4#5.1.0 done. Load Package hl7.fhir.uv.extensions.r4#5.1.0 Load Package hl7.fhir.us.core#7.0.0 Load Package us.nlm.vsac#0.17.0 Load Package us.cdc.phinvads#0.12.0 Installing hl7.terminology.r4#5.3.0 to the package cache Fetching: Installing hl7.terminology.r4#5.3.0 done. Load Package hl7.terminology.r4#5.3.0 Installing hl7.fhir.uv.extensions.r4#1.0.0 to the package cache Fetching: Installing hl7.fhir.uv.extensions.r4#1.0.0 done. Load Package hl7.fhir.uv.extensions.r4#1.0.0 Installing hl7.fhir.us.core#5.0.1 to the package cache Fetching: Installing hl7.fhir.us.core#5.0.1 done. Installing hl7.terminology.r4#3.1.0 to the package cache Fetching: Installing hl7.terminology.r4#3.1.0 done. Load Package hl7.terminology.r4#3.1.0 Installing hl7.fhir.uv.bulkdata#2.0.0 to the package cache Fetching: Installing hl7.fhir.uv.bulkdata#2.0.0 done. Load Package hl7.fhir.uv.bulkdata#2.0.0 Installing us.nlm.vsac#0.7.0 to the package cache Fetching: Installing us.nlm.vsac#0.7.0 done. Load Package us.nlm.vsac#0.7.0 Load Package hl7.fhir.us.core#5.0.1 Installing hl7.fhir.us.odh#1.3.0 to the package cache Fetching: Installing hl7.fhir.us.odh#1.3.0 done. Installing hl7.terminology.r4#5.0.0 to the package cache Fetching: Installing hl7.terminology.r4#5.0.0 done. Load Package hl7.terminology.r4#5.0.0 Load Package hl7.fhir.us.odh#1.3.0 Load Package hl7.fhir.us.vr-common-library#2.0.0-ballot Installing hl7.terminology.r4#6.2.0 to the package cache Fetching: Installing hl7.terminology.r4#6.2.0 done. Load Package hl7.terminology.r4#6.2.0 Installing us.nlm.vsac#0.19.0 to the package cache Fetching: Installing us.nlm.vsac#0.19.0 done. Load Package us.nlm.vsac#0.19.0 Installing hl7.fhir.us.vr-common-library#2.0.0 to the package cache Fetching: Installing hl7.fhir.us.vr-common-library#2.0.0 done. Installing hl7.terminology.r4#6.0.2 to the package cache Fetching: Installing hl7.terminology.r4#6.0.2 done. Load Package hl7.terminology.r4#6.0.2 Load Package hl7.fhir.us.vr-common-library#2.0.0 Load Package hl7.fhir.us.bfdr#current Load Package hl7.fhir.uv.tools.r4#0.5.0 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 (04:31.502 / 06:31.390, 1Gb) Load IG (00:00.000 / 06:31.390, 1Gb) Load Content (00:00.000 / 06:31.391, 1Gb) Using en-US as the default narrative language. (no language information in Implementation Guide) (00:00.134 / 06:31.525, 1Gb) Process Loaded Resources (00:02.307 / 06:33.833, 1Gb) Generating Snapshots (00:00.407 / 06:34.240, 1Gb) loadPrePages from FetchedFile[/scratch/repo/fsh-generated/includes] as /scratch/repo/fsh-generated/includes loadPrePages from FetchedFile[/scratch/repo/input/pagecontent] as /scratch/repo/input/pagecontent Fetch http://hl7.org/fhir/us/birthdefectreporting/package-list.json for version check (00:01.604 / 06:35.845, 1Gb) Processing Conformance Resources (00:00.120 / 06:35.966, 1Gb) Checking Language (00:00.000 / 06:35.966, 1Gb) Load Dependency Info (00:00.001 / 06:35.968, 1Gb) Load Info (00:00.001 / 06:35.969, 1Gb) Load Paths (00:00.000 / 06:35.970, 1Gb) Check R4 / R4B (00:00.000 / 06:35.970, 1Gb) Assign Comparison Ids (00:00.031 / 06:36.002, 1Gb) Propagating status (00:00.000 / 06:36.002, 1Gb) Generating Narratives (00:00.000 / 06:36.003, 1Gb) Validating Conformance Resources (00:22.744 / 06:58.747, 2Gb) Check profiles & code systems (00:56.251 / 07:54.999, 2Gb) Check realm rules (00:00.003 / 07:55.002, 2Gb) Installing hl7.fhir.us.core#8.0.0 to the package cache Fetching: Installing hl7.fhir.us.core#8.0.0 done. US Core Comparisons Finished Previous Version Comparison (00:39.592 / 08:34.595, 12Gb) Validating Resources (00:00.059 / 08:34.654, 12Gb) Processing Provenance Records (00:17.129 / 08:51.784, 2Gb) Generating Outputs in /scratch/repo/output (00:00.000 / 08:51.784, 2Gb) Generate Native Outputs (00:00.288 / 08:52.073, 2Gb) Run Template (00:05.944 / 08:58.018, 3Gb) Generate HTML Outputs (00:01.599 / 08:59.617, 3Gb) Generate Spreadsheets (01:59.089 / 10:58.706, 13Gb) Generate Summaries (00:04.710 / 11:03.417, 12Gb) Generating Summary Outputs (00:00.000 / 11:03.417, 12Gb) DB Cumulative Time invested: 00:00:01.117 Sending Usage Stats to Server (00:26.189 / 11:29.606, 14Gb) ## Memory (MB): Use = 15015, Free = 3992, Total = 19008, Max = 19008 (00:00.009 / 11:29.616, 14Gb) Reclaiming memory... (00:00.000 / 11:29.616, 14Gb) ## Memory (MB): Use = 11899, Free = 7108, Total = 19008, Max = 19008 (00:05.608 / 11:35.225, 11Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 11:35.227, 11Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 11:35.228, 11Gb) * A failure to produce a fragment that is already logged in the output above (00:00.001 / 11:35.228, 11Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 11:35.228, 11Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.480 / 11:35.708, 11Gb) Jekyll: Generating... (00:00.000 / 11:35.708, 11Gb) Jekyll: done in 2.687 seconds. (00:02.686 / 11:38.395, 11Gb) Checking Output HTML (00:02.583 / 11:40.978, 12Gb) found 1398 files (00:00.009 / 11:40.988, 12Gb) ......................................... ......................................... ... 1398 html files, 0 pages invalid xhtml (0%) (00:13.925 / 11:54.913, 12Gb) ... 208889 links, 10 broken links (0%) (00:00.000 / 11:54.913, 12Gb) Generate fragment-usage-analysis.csv (00:00.000 / 11:54.913, 12Gb) Build final .zip (00:00.009 / 11:54.923, 12Gb) Final .zip built (00:05.738 / 12:00.662, 12Gb) Installing hl7.fhir.r4.examples#4.0.1 to the package cache Fetching: Installing hl7.fhir.r4.examples#4.0.1 done. Installing hl7.fhir.uv.extensions#5.1.0-snapshot1 to the package cache Fetching: Installing hl7.fhir.uv.extensions#5.1.0-snapshot1 done. Installing hl7.terminology.r5#5.3.0 to the package cache Fetching: Installing hl7.terminology.r5#5.3.0 done. Built. Times: loading: 00:04.574, generate: 06:10.111, narrative generation: 00:22.743, realm-rules: 00:39.592, previous-version: 00:00.000, jekyll: 00:03.193, validation: 01:13.374 (#86), template: 00:01.607 (#3) (00:45.416 / 12:46.078, 16Gb) Generating QA (00:00.000 / 12:46.078, 16Gb) Validation output in /scratch/repo/output/qa.html Errors: 1, Warnings: 141, Info: 126, Broken Links: 10 (00:00.497 / 12:46.576, 16Gb) Finished. Max Memory Used = 16Gb (00:00.018 / 12:46.594, 16Gb)