INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/vr-common-library --branch master repo DEBUG:root:Time to deadline 35879.997737 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 35879.027652 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35877.806951 seconds npm WARN deprecated glob@7.2.3: Glob versions prior to v9 are no longer supported 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. added 140 packages in 7s 15 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 11.3.0 npm notice Changelog: npm notice Run `npm install -g npm@11.3.0` 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/vr-common-library/ -out /scratch/repo DEBUG:root:Time to deadline 35870.506153 seconds FHIR IG Publisher Version 1.8.25 (Git# cb0bf1b2d5d9). Built 2025-04-26T01:19:48.173Z (9 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/vr-common-library/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Monday, May 5, 2025, 4:47:09 PM Coordinated Universal Time (2025-05-05T16:47:09Z) Build FHIR IG from /scratch/repo (00:00.034 / 00:00.035, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.004 / 00:00.039, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.004 / 00:00.043, 97Mb) Run Sushi on /scratch/repo (00:02.783 / 00:02.826, 121Mb) Sushi: info Running SUSHI v3.15.1 (implements FHIR Shorthand specification v3.0.0) (00:00.819 / 00:03.645, 129Mb) Sushi: info Arguments: (00:00.000 / 00:03.646, 129Mb) Sushi: info --require-latest (00:00.000 / 00:03.647, 129Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:03.647, 129Mb) Sushi: info /scratch/repo (00:00.000 / 00:03.647, 129Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.851 / 00:04.499, 129Mb) Sushi: info Importing FSH text... (00:00.189 / 00:04.688, 129Mb) Sushi: warn RuleSet UnmatchedMapConcept contains unused parameters: targetcode, targetdisplay (00:00.548 / 00:05.237, 129Mb) Sushi: File: /scratch/repo/input/fsh/conceptmaps/DEF_ConceptMapRuleSets.fsh (00:00.000 / 00:05.237, 129Mb) Sushi: Line: 28 - 34 (00:00.000 / 00:05.238, 129Mb) Sushi: warn RuleSet RequireMetaProfile contains unused parameter: profile (00:00.199 / 00:05.437, 129Mb) Sushi: File: /scratch/repo/input/fsh/rulesets/DEF_Rulesets.fsh (00:00.000 / 00:05.438, 129Mb) Sushi: Line: 83 - 94 (00:00.000 / 00:05.438, 129Mb) Sushi: warn RuleSet AddMetaProfile contains unused parameter: profile (00:00.000 / 00:05.438, 129Mb) Sushi: File: /scratch/repo/input/fsh/rulesets/DEF_Rulesets.fsh (00:00.000 / 00:05.439, 129Mb) Sushi: Line: 96 - 99 (00:00.000 / 00:05.439, 129Mb) Sushi: info Preprocessed 99 documents with 47 aliases. (00:00.101 / 00:05.540, 129Mb) Sushi: info Imported 72 definitions and 40 instances. (00:03.429 / 00:08.970, 129Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.160 / 00:09.130, 129Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.5.0 (00:00.652 / 00:09.782, 129Mb) 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 (00:00.001 / 00:09.784, 129Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.5.0 (00:00.728 / 00:10.512, 129Mb) 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 / 00:10.516, 129Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.5.0 with 88 resources (00:00.076 / 00:10.592, 129Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 6.3.0 (00:00.471 / 00:11.064, 137Mb) Sushi: info Attempting to download hl7.terminology.r4#6.3.0 from https://packages.fhir.org/hl7.terminology.r4/6.3.0 (00:00.000 / 00:11.065, 137Mb) Sushi: info Downloaded hl7.terminology.r4#6.3.0 (00:02.805 / 00:13.870, 137Mb) Sushi: info Cached hl7.terminology.r4#6.3.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#6.3.0 (00:00.001 / 00:13.872, 137Mb) Sushi: info Loaded hl7.terminology.r4#6.3.0 with 4374 resources (00:01.903 / 00:15.776, 137Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.493 / 00:16.269, 137Mb) 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 / 00:16.270, 137Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.572 / 00:17.842, 137Mb) 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 / 00:17.844, 137Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.366 / 00:18.210, 137Mb) Sushi: info Attempting to download hl7.fhir.us.core#5.0.1 from https://packages.fhir.org/hl7.fhir.us.core/5.0.1 (00:00.000 / 00:18.211, 137Mb) Sushi: info Downloaded hl7.fhir.us.core#5.0.1 (00:01.634 / 00:19.845, 137Mb) Sushi: info Cached hl7.fhir.us.core#5.0.1 to /home/fhiruser/.fhir/packages/hl7.fhir.us.core#5.0.1 (00:00.001 / 00:19.847, 137Mb) Sushi: info Loaded hl7.fhir.us.core#5.0.1 with 194 resources (00:00.163 / 00:20.011, 137Mb) Sushi: info Attempting to download us.nlm.vsac#0.19.0 from https://packages.fhir.org/us.nlm.vsac/0.19.0 (00:00.000 / 00:20.012, 137Mb) Sushi: info Attempting to download us.nlm.vsac#0.19.0 from https://packages2.fhir.org/packages/us.nlm.vsac/0.19.0 (00:00.528 / 00:20.540, 137Mb) Sushi: info Downloaded us.nlm.vsac#0.19.0 (00:08.549 / 00:29.089, 137Mb) Sushi: info Cached us.nlm.vsac#0.19.0 to /home/fhiruser/.fhir/packages/us.nlm.vsac#0.19.0 (00:00.002 / 00:29.092, 137Mb) Sushi: info Loaded us.nlm.vsac#0.19.0 with 15332 resources (00:11.084 / 00:40.176, 137Mb) Sushi: info Attempting to download us.cdc.phinvads#0.12.0 from https://packages.fhir.org/us.cdc.phinvads/0.12.0 (00:00.001 / 00:40.177, 137Mb) Sushi: info Downloaded us.cdc.phinvads#0.12.0 (00:03.725 / 00:43.903, 137Mb) Sushi: info Cached us.cdc.phinvads#0.12.0 to /home/fhiruser/.fhir/packages/us.cdc.phinvads#0.12.0 (00:00.002 / 00:43.905, 137Mb) Sushi: info Loaded us.cdc.phinvads#0.12.0 with 1967 resources (00:02.485 / 00:46.391, 137Mb) 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 / 00:46.392, 137Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.284 / 00:49.676, 137Mb) 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 / 00:49.678, 137Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.532 / 00:51.211, 137Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.014 / 00:51.225, 137Mb) Sushi: info Converting FSH to FHIR resources... (00:00.077 / 00:51.302, 137Mb) Sushi: info Converted 32 FHIR StructureDefinitions. (00:09.402 / 01:00.704, 137Mb) Sushi: info Converted 10 FHIR CodeSystems. (00:00.351 / 01:01.055, 137Mb) Sushi: info Converted 30 FHIR ValueSets. (00:01.002 / 01:02.058, 137Mb) Sushi: info Converted 40 FHIR instances. (00:21.588 / 01:23.646, 137Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 01:23.648, 137Mb) Sushi: info Exported 112 FHIR resources as JSON. (00:00.258 / 01:23.906, 137Mb) Sushi: info Assembling Implementation Guide sources... (00:00.005 / 01:23.912, 137Mb) Sushi: warn Files not in the supported file types (.md and .xml) were detected. These files will be included without any processing. (00:00.425 / 01:24.337, 137Mb) Sushi: File: /scratch/repo/input/pagecontent (00:00.000 / 01:24.337, 137Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.us.vr-common-library.json (00:00.006 / 01:24.343, 137Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 01:24.344, 137Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.002 / 01:24.346, 137Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:24.347, 137Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 01:24.347, 137Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:24.347, 137Mb) Sushi: | | 13 | 19 | 0 | 0 | | (00:00.000 / 01:24.347, 137Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:24.348, 137Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:24.348, 137Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 01:24.348, 137Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:24.348, 137Mb) Sushi: | | 30 | 10 | 40 | | (00:00.000 / 01:24.349, 137Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:24.349, 137Mb) Sushi: | | (00:00.000 / 01:24.349, 137Mb) Sushi: =================================================================== (00:00.000 / 01:24.350, 137Mb) Sushi: | Don't get stuck in the doldrums. 0 Errors 4 Warnings | (00:00.000 / 01:24.350, 137Mb) Sushi: =================================================================== (00:00.000 / 01:24.350, 137Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.905 / 01:25.255, 55Mb) Load Template from hl7.fhir.template#current (00:00.767 / 01:26.023, 57Mb) Installing hl7.fhir.template#current to the package cache Fetching: Installing hl7.fhir.template#current done. Load Template from hl7.base.template#current (00:01.162 / 01:27.186, 105Mb) Installing hl7.base.template#current to the package cache Fetching: Installing hl7.base.template#current done. Load Template from fhir.base.template#current (00:00.242 / 01:27.429, 105Mb) Installing fhir.base.template#current to the package cache Fetching: Installing fhir.base.template#current done. Root directory: /scratch/repo (00:05.551 / 01:32.980, 401Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.002 / 01:32.982, 401Mb) Core Package hl7.fhir.r4.core#4.0.1 Running Terminology Log: /tmp/ohfu-fhir-ig-11336073218826382514.html Connect to Terminology Server at http://tx.fhir.org (00:38.605 / 02:11.588, 237Mb) 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 Load Package hl7.terminology.r4#6.3.0 Load Package hl7.fhir.uv.extensions.r4#5.2.0 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 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#0.7.0 to the package cache Fetching: Installing us.nlm.vsac#0.7.0 done. Load Package us.nlm.vsac#0.7.0 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' (02:20.856 / 04:32.444, 611Mb) Load Package hl7.fhir.uv.sdc#3.0.0 Load Package hl7.fhir.us.core#5.0.1 Load Package us.nlm.vsac#0.19.0 Load Package us.cdc.phinvads#0.12.0 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 (00:19.231 / 04:51.676, 1Gb) Load Content (00:00.000 / 04:51.677, 1Gb) Using en-US as the default narrative language. (no language information in Implementation Guide) (00:00.259 / 04:51.936, 1Gb) Process Loaded Resources (00:02.939 / 04:54.875, 532Mb) Generating Snapshots (00:01.285 / 04:56.160, 828Mb) Unsupported feature in slicing at Patient.name: the slicing element at path Patient.name.family.extension has slicing open, by value=url, and this nested slicing is not supported loadPrePages from FetchedFile[/scratch/repo/input/includes] as /scratch/repo/input/includes 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/vr-common-library/package-list.json for version check (00:02.485 / 04:58.646, 1Gb) Processing Conformance Resources (00:00.307 / 04:58.953, 1Gb) Checking Language (00:00.000 / 04:58.953, 1Gb) Load Dependency Info (00:00.003 / 04:58.957, 1Gb) Load Info (00:00.001 / 04:58.959, 1Gb) Load Paths (00:00.000 / 04:58.960, 1Gb) Check R4 / R4B (00:00.000 / 04:58.960, 1Gb) Assign Comparison Ids (00:00.255 / 04:59.215, 522Mb) Propagating status (00:00.000 / 04:59.216, 522Mb) Generating Narratives (00:00.000 / 04:59.216, 522Mb) Validating Conformance Resources (00:05.370 / 05:04.586, 1Gb) Check profiles & code systems (00:44.155 / 05:48.742, 1Gb) Check realm rules (00:00.007 / 05:48.750, 1Gb) 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 (00:14.845 / 06:03.595, 2Gb) Validating Resources (00:00.055 / 06:03.651, 2Gb) Processing Provenance Records (00:02.967 / 06:06.618, 2Gb) Generating Outputs in /scratch/repo/output (00:00.000 / 06:06.618, 2Gb) Generate Native Outputs (00:00.299 / 06:06.918, 2Gb) Run Template (00:34.705 / 06:41.624, 2Gb) Generate HTML Outputs (00:02.786 / 06:44.410, 2Gb) XSLT Error: Error reported by XML parser: Premature end of file. Exception generating xslt page /scratch/repo/temp/pages/_includes/temp for _includes/temp in /scratch/repo/temp/pages: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Premature end of file. (01:49.469 / 08:33.880, 5Gb) Generate Spreadsheets (00:00.005 / 08:33.885, 5Gb) Generate Summaries (00:08.159 / 08:42.044, 5Gb) Generating Summary Outputs (00:00.000 / 08:42.045, 5Gb) DB Cumulative Time invested: 00:00:32.909 Sending Usage Stats to Server (00:17.010 / 08:59.055, 7Gb) ## Memory (MB): Use = 7329, Free = 11678, Total = 19008, Max = 19008 (00:00.015 / 08:59.071, 7Gb) Reclaiming memory... (00:00.000 / 08:59.071, 7Gb) ## Memory (MB): Use = 4616, Free = 14378, Total = 19008, Max = 19008 (00:05.065 / 09:04.137, 4Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 09:04.138, 4Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.003 / 09:04.141, 4Gb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 09:04.142, 4Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 09:04.142, 4Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.583 / 09:04.726, 4Gb) Jekyll: Generating... (00:00.000 / 09:04.726, 4Gb) Jekyll: done in 6.235 seconds. (00:06.234 / 09:10.960, 4Gb) Checking Output HTML (00:07.421 / 09:18.382, 7Gb) found 1916 files (00:00.012 / 09:18.394, 7Gb) ........................................ ........................................ ... 1916 html files, 0 pages invalid xhtml (0%) (00:51.990 / 10:10.385, 7Gb) ... 543950 links, 0 broken links (0%) (00:00.000 / 10:10.385, 7Gb) Generate fragment-usage-analysis.csv (00:00.000 / 10:10.385, 7Gb) Build final .zip (00:00.016 / 10:10.402, 7Gb) Final .zip built (00:08.014 / 10:18.416, 7Gb) Installing hl7.fhir.r4.examples#4.0.1 to the package cache Fetching: Installing hl7.fhir.r4.examples#4.0.1 done. Built. Times: loading: 00:07.275, generate: 06:08.983, narrative generation: 00:05.370, realm-rules: 00:14.845, previous-version: 00:00.000, jekyll: 00:06.851, validation: 00:46.692 (#113), template: 00:02.799 (#3) (00:49.520 / 11:07.937, 9Gb) Generating QA (00:00.000 / 11:07.937, 9Gb) Sending usage stats failed: Connection timed out Validation output in /scratch/repo/output/qa.html Errors: 3, Warnings: 86, Info: 16, Broken Links: 0 (00:34.593 / 11:42.530, 11Gb) Finished. Max Memory Used = 11Gb (00:00.036 / 11:42.566, 11Gb)