INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/davinci-atr --branch master repo DEBUG:root:Time to deadline 35879.998219 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 35879.331418 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35878.213054 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 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 -> 11.4.0 npm notice Changelog: npm notice Run `npm install -g npm@11.4.0` 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/davinci-atr/ -out /scratch/repo DEBUG:root:Time to deadline 35873.129202 seconds FHIR IG Publisher Version 1.8.26 (Git# d479a7160a38). Built 2025-05-08T09:23:30.587Z (7 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/HL7/davinci-atr/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Thursday, May 15, 2025, 9:07:22 PM Coordinated Universal Time (2025-05-15T21:07:22Z) Build FHIR IG from /scratch/repo (00:00.025 / 00:00.025, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.002 / 00:00.028, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.002 / 00:00.030, 97Mb) Load Template from hl7.davinci.template#current (00:00.942 / 00:00.973, 78Mb) Installing hl7.davinci.template#current to the package cache Fetching: Installing hl7.davinci.template#current done. Load Template from hl7.fhir.template#current (00:01.098 / 00:02.072, 158Mb) Installing hl7.fhir.template#current to the package cache Fetching: Installing hl7.fhir.template#current done. Load Template from hl7.base.template#current (00:00.148 / 00:02.220, 158Mb) Installing hl7.base.template#current to the package cache Fetching: Installing hl7.base.template#current done. Load Template from fhir.base.template#current (00:00.147 / 00:02.368, 158Mb) Installing fhir.base.template#current to the package cache Fetching: Installing fhir.base.template#current done. Root directory: /scratch/repo (00:03.754 / 00:06.122, 131Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.002 / 00:06.124, 131Mb) Core Package hl7.fhir.r4.core#4.0.1 Installing hl7.fhir.r4.core#4.0.1 to the package cache Fetching: Installing hl7.fhir.r4.core#4.0.1 done. Running Terminology Log: /tmp/ohfu-fhir-ig-16537184214555424837.html Connect to Terminology Server at http://tx.fhir.org (00:32.698 / 00:38.822, 951Mb) Installing hl7.fhir.pubpack#0.2.1 to the package cache Fetching: Installing hl7.fhir.pubpack#0.2.1 done. Load Package hl7.fhir.pubpack#0.2.1 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 Installing hl7.terminology.r4#6.3.0 to the package cache Fetching: Installing hl7.terminology.r4#6.3.0 done. Load Package hl7.terminology.r4#6.3.0 Installing hl7.fhir.uv.extensions.r4#5.2.0 to the package cache Fetching: Installing hl7.fhir.uv.extensions.r4#5.2.0 done. Load Package hl7.fhir.uv.extensions.r4#5.2.0 Installing hl7.fhir.us.core.3.1.1#3.1.1 to the package cache Fetching: Installing hl7.fhir.us.core.3.1.1#3.1.1 done. Installing hl7.fhir.us.core#3.1.1 to the package cache Fetching: Installing hl7.fhir.us.core#3.1.1 done. Load Package hl7.fhir.us.core#3.1.1 Load Package hl7.fhir.us.core.3.1.1#3.1.1 Installing hl7.fhir.us.core.v610#6.1.0 to the package cache Fetching: Installing hl7.fhir.us.core.v610#6.1.0 done. Installing hl7.fhir.us.core#6.1.0 to the package cache Fetching: Installing hl7.fhir.us.core#6.1.0 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 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.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 hl7.fhir.uv.smart-app-launch#2.1.0 to the package cache Fetching: Installing hl7.fhir.uv.smart-app-launch#2.1.0 done. Load Package hl7.fhir.uv.smart-app-launch#2.1.0 Installing us.nlm.vsac#0.11.0 to the package cache Fetching: Installing us.nlm.vsac#0.11.0 done. Load Package us.nlm.vsac#0.11.0 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' (00:44.602 / 01:23.424, 1Gb) Load Package hl7.fhir.uv.sdc#3.0.0 Installing us.cdc.phinvads#0.12.0 to the package cache Fetching: Installing us.cdc.phinvads#0.12.0 done. Load Package us.cdc.phinvads#0.12.0 Installing ihe.formatcode.fhir#1.1.0 to the package cache Fetching: Installing ihe.formatcode.fhir#1.1.0 done. Load Package ihe.formatcode.fhir#1.1.0 Load Package hl7.fhir.us.core#6.1.0 Load Package hl7.fhir.us.core.v610#6.1.0 Installing hl7.fhir.us.core#7.0.0 to the package cache Fetching: Installing hl7.fhir.us.core#7.0.0 done. 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.extensions.r4#5.1.0-snapshot1 to the package cache Fetching: 2025-05-15 21:09:15.844 [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) 2025-05-15 21:09:16.266 [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 hl7.fhir.uv.bulkdata#2.0.0 Load Package hl7.fhir.uv.smart-app-launch#2.1.0 Installing hl7.fhir.us.davinci-pdex-plan-net#1.2.0 to the package cache Fetching: Installing hl7.fhir.us.davinci-pdex-plan-net#1.2.0 done. 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 hl7.fhir.us.core.v311#3.1.1 to the package cache Fetching: Installing hl7.fhir.us.core.v311#3.1.1 done. Load Package hl7.fhir.us.core.v311#3.1.1 Installing hl7.fhir.us.davinci-hrex#1.1.0 to the package cache Fetching: Installing hl7.fhir.us.davinci-hrex#1.1.0 done. Installing hl7.terminology.r4#6.1.0 to the package cache Fetching: Installing hl7.terminology.r4#6.1.0 done. Load Package hl7.terminology.r4#6.1.0 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 Load Package hl7.fhir.us.davinci-hrex#1.1.0 Load Package hl7.fhir.us.davinci-pdex-plan-net#1.2.0 Load Package hl7.fhir.us.davinci-hrex#1.1.0 Installing hl7.fhir.uv.subscriptions-backport.r4#1.1.0 to the package cache Fetching: Installing hl7.fhir.uv.subscriptions-backport.r4#1.1.0 done. Ignore Dependency on Core FHIR hl7.fhir.r4.core#4.0.0, from package 'hl7.fhir.uv.subscriptions-backport.r4#1.1.0' (01:09.283 / 02:32.707, 885Mb) Load Package hl7.fhir.uv.subscriptions-backport.r4#1.1.0 Installing hl7.fhir.us.davinci-cdex#2.1.0 to the package cache Fetching: Installing hl7.fhir.us.davinci-cdex#2.1.0 done. Installing hl7.fhir.us.davinci-pas#2.1.0 to the package cache Fetching: Installing hl7.fhir.us.davinci-pas#2.1.0 done. Installing hl7.fhir.us.davinci-crd#2.0.0 to the package cache Fetching: Installing hl7.fhir.us.davinci-crd#2.0.0 done. 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.us.davinci-hrex#1.0.0 to the package cache Fetching: Installing hl7.fhir.us.davinci-hrex#1.0.0 done. Installing hl7.fhir.us.udap-security#0.1.0 to the package cache Fetching: Installing hl7.fhir.us.udap-security#0.1.0 done. Load Package hl7.fhir.us.udap-security#0.1.0 Load Package hl7.fhir.us.davinci-hrex#1.0.0 Load Package hl7.fhir.us.davinci-crd#2.0.0 Installing hl7.fhir.us.carin-bb#2.0.0 to the package cache Fetching: Installing hl7.fhir.us.carin-bb#2.0.0 done. 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.carin-bb#2.0.0 Load Package hl7.fhir.us.davinci-pas#2.1.0 Installing hl7.fhir.us.davinci-dtr#2.1.0 to the package cache Fetching: Installing hl7.fhir.us.davinci-dtr#2.1.0 done. Installing hl7.fhir.us.davinci-crd#2.1.0 to the package cache Fetching: Installing hl7.fhir.us.davinci-crd#2.1.0 done. Load Package hl7.fhir.us.davinci-crd#2.1.0 Load Package hl7.fhir.us.davinci-dtr#2.1.0 Load Package hl7.fhir.us.davinci-cdex#2.1.0 Installing hl7.fhir.uv.tools.r4#0.5.0 to the package cache Fetching: Installing hl7.fhir.uv.tools.r4#0.5.0 done. 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 (01:39.149 / 04:11.857, 1Gb) Load Content (00:00.000 / 04:11.858, 1Gb) Using en-US as the default narrative language. (no language information in Implementation Guide) (00:00.118 / 04:11.976, 1Gb) Process Loaded Resources (00:02.097 / 04:14.074, 1Gb) Generating Snapshots (00:00.502 / 04:14.577, 1Gb) loadPrePages from FetchedFile[/scratch/repo/input/includes] as /scratch/repo/input/includes loadPrePages from FetchedFile[/scratch/repo/input/pagecontent] as /scratch/repo/input/pagecontent Fetch http://hl7.org/fhir/us/davinci-atr/package-list.json for version check (00:01.617 / 04:16.195, 1Gb) Processing Conformance Resources (00:00.125 / 04:16.320, 1Gb) Checking Language (00:00.000 / 04:16.320, 1Gb) Load Dependency Info (00:00.001 / 04:16.321, 1Gb) Load Info (00:00.001 / 04:16.323, 1Gb) Load Paths (00:00.000 / 04:16.324, 1Gb) Check R4 / R4B (00:00.000 / 04:16.324, 1Gb) Assign Comparison Ids (00:00.013 / 04:16.337, 1Gb) Propagating status (00:00.000 / 04:16.338, 1Gb) Generating Narratives (00:00.065 / 04:16.403, 1Gb) Validating Conformance Resources (00:03.054 / 04:19.458, 1Gb) Check profiles & code systems (00:51.843 / 05:11.301, 2Gb) Check realm rules (00:00.002 / 05:11.304, 2Gb) Installing hl7.fhir.us.core#8.0.0-ballot to the package cache Fetching: Installing hl7.fhir.us.core#8.0.0-ballot done. US Core Comparisons Finished Previous Version Comparison (00:03.910 / 05:15.214, 3Gb) Installing hl7.fhir.us.davinci-atr#2.0.0 to the package cache Fetching: Installing hl7.fhir.us.davinci-atr#2.0.0 done. Installing hl7.fhir.uv.bulkdata#1.0.1 to the package cache Fetching: Installing hl7.fhir.uv.bulkdata#1.0.1 done. Installing hl7.fhir.us.davinci-pdex-plan-net#1.1.0 to the package cache Fetching: Installing hl7.fhir.us.davinci-pdex-plan-net#1.1.0 done. Installing hl7.fhir.us.davinci-cdex#2.0.0 to the package cache Fetching: Installing hl7.fhir.us.davinci-cdex#2.0.0 done. Installing hl7.fhir.us.davinci-pas#1.2.0-ballot to the package cache Fetching: Installing hl7.fhir.us.davinci-pas#1.2.0-ballot done. Installing hl7.fhir.us.davinci-dtr#1.1.0-ballot to the package cache Fetching: Installing hl7.fhir.us.davinci-dtr#1.1.0-ballot done. Installing hl7.fhir.uv.sdc#3.0.0-preview to the package cache Fetching: Installing hl7.fhir.uv.sdc#3.0.0-preview done. Installing hl7.fhir.r4.examples#4.0.1 to the package cache Fetching: Installing hl7.fhir.r4.examples#4.0.1 done. Validating Resources (00:47.303 / 06:02.518, 3Gb) Processing Provenance Records (00:02.187 / 06:04.706, 3Gb) Generating Outputs in /scratch/repo/output (00:00.000 / 06:04.706, 3Gb) Generate Native Outputs (00:00.187 / 06:04.894, 3Gb) Run Template (00:03.354 / 06:08.248, 4Gb) Generate HTML Outputs (00:03.885 / 06:12.134, 1Gb) Generate Spreadsheets (01:20.926 / 07:33.061, 11Gb) Generate Summaries (00:03.947 / 07:37.008, 11Gb) Generating Summary Outputs (00:00.000 / 07:37.008, 11Gb) DB Cumulative Time invested: 00:00:00.581 Sending Usage Stats to Server (00:26.497 / 08:03.506, 13Gb) ## Memory (MB): Use = 14294, Free = 4713, Total = 19008, Max = 19008 (00:00.005 / 08:03.511, 13Gb) Reclaiming memory... (00:00.000 / 08:03.511, 13Gb) ## Memory (MB): Use = 10775, Free = 8232, Total = 19008, Max = 19008 (00:04.985 / 08:08.497, 10Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.006 / 08:08.504, 10Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.005 / 08:08.509, 10Gb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 08:08.509, 10Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 08:08.509, 10Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.605 / 08:09.115, 10Gb) Jekyll: Generating... (00:00.000 / 08:09.116, 10Gb) Jekyll: done in 2.336 seconds. (00:02.335 / 08:11.452, 10Gb) Checking Output HTML (00:02.500 / 08:13.952, 11Gb) found 1135 files (00:00.007 / 08:13.960, 11Gb) ........................................ ........................................ ... 1135 html files, 0 pages invalid xhtml (0%) (00:10.177 / 08:24.138, 16Gb) ... 171466 links, 0 broken links (0%) (00:00.000 / 08:24.138, 16Gb) Generate fragment-usage-analysis.csv (00:00.000 / 08:24.138, 16Gb) Build final .zip (00:00.006 / 08:24.145, 16Gb) Final .zip built (00:01.739 / 08:25.884, 16Gb) 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: 00:04.461, generate: 04:24.583, propagating status: 00:00.065, narrative generation: 00:03.054, realm-rules: 00:03.910, previous-version: 00:47.280, jekyll: 00:02.975, validation: 00:53.964 (#48), template: 00:04.390 (#3) (00:15.019 / 08:40.904, 13Gb) Generating QA (00:00.000 / 08:40.904, 13Gb) Validation output in /scratch/repo/output/qa.html Errors: 0, Warnings: 0, Info: 0, Broken Links: 0 (00:00.206 / 08:41.110, 13Gb) Finished. Max Memory Used = 16Gb (00:00.013 / 08:41.124, 13Gb)