INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/personal-health-record-format-ig --branch jami-feedback-2 repo DEBUG:root:Time to deadline 35879.998239 seconds Cloning into 'repo'... 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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 35839.504501 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35838.235459 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 139 packages in 7s 14 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 11.7.0 npm notice Changelog: npm notice Run `npm install -g npm@11.7.0` 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/personal-health-record-format-ig/ -out /scratch/repo DEBUG:root:Time to deadline 35830.578304 seconds FHIR IG Publisher Version 2.0.29 (Git# 826a7eb003d6). Built 2025-12-17T01:19:30.102Z (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/HL7/personal-health-record-format-ig/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Monday, December 22, 2025, 5:40:21 AM Coordinated Universal Time (2025-12-22T05:40:21Z) 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 (00:00.004 / 00:00.036, 97Mb) Found dependency on hl7.fhir.uv.ips#1.1.0 in Sushi config. Pre-installing (00:00.011 / 00:00.048, 97Mb) Installing hl7.fhir.uv.ips#1.1.0 to the package cache  Fetching:  Installing hl7.fhir.uv.ips#1.1.0  done. Run Sushi on /scratch/repo (00:03.056 / 00:03.105, 89Mb) Sushi: info Running SUSHI v3.16.5 (implements FHIR Shorthand specification v3.0.0) (00:00.729 / 00:03.834, 98Mb) Sushi: info Arguments: (00:00.000 / 00:03.835, 98Mb) Sushi: info --require-latest (00:00.000 / 00:03.835, 98Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:03.836, 98Mb) Sushi: info /scratch/repo (00:00.000 / 00:03.836, 98Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.748 / 00:04.585, 98Mb) Sushi: info Importing FSH text... (00:00.163 / 00:04.749, 98Mb) Sushi: info Preprocessed 260 documents with 35 aliases. (00:00.699 / 00:05.448, 98Mb) Sushi: info Imported 117 definitions and 92 instances. (00:00.353 / 00:05.802, 98Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.166 / 00:05.968, 98Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.9.0 (00:00.614 / 00:06.583, 105Mb) Sushi: info Attempting to download hl7.fhir.uv.tools.r4#0.9.0 from https://packages.fhir.org/hl7.fhir.uv.tools.r4/0.9.0 (00:00.001 / 00:06.584, 105Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.9.0 (00:00.876 / 00:07.461, 105Mb) Sushi: info Cached hl7.fhir.uv.tools.r4#0.9.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.tools.r4#0.9.0 (00:00.003 / 00:07.464, 105Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.9.0 with 117 resources (00:00.080 / 00:07.545, 105Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 7.0.1 (00:00.458 / 00:08.003, 105Mb) Sushi: info Attempting to download hl7.terminology.r4#7.0.1 from https://packages.fhir.org/hl7.terminology.r4/7.0.1 (00:00.000 / 00:08.004, 105Mb) Sushi: info Downloaded hl7.terminology.r4#7.0.1 (00:02.711 / 00:10.715, 105Mb) Sushi: info Cached hl7.terminology.r4#7.0.1 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#7.0.1 (00:00.001 / 00:10.717, 105Mb) Sushi: info Loaded hl7.terminology.r4#7.0.1 with 4096 resources (00:01.681 / 00:12.398, 105Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.457 / 00:12.855, 105Mb) 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 / 00:12.856, 105Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.452 / 00:14.308, 105Mb) 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 / 00:14.309, 105Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.428 / 00:14.738, 105Mb) Sushi: info Loaded hl7.fhir.uv.ips#1.1.0 with 104 resources (00:00.121 / 00:14.860, 105Mb) 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 / 00:14.861, 105Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.332 / 00:18.193, 105Mb) Sushi: info Cached hl7.fhir.r4.core#4.0.1 to /home/fhiruser/.fhir/packages/hl7.fhir.r4.core#4.0.1 (00:00.002 / 00:18.196, 105Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.799 / 00:19.996, 105Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.013 / 00:20.009, 105Mb) Sushi: info Converting FSH to FHIR resources... (00:00.023 / 00:20.033, 105Mb) Sushi: info Converted 58 FHIR StructureDefinitions. (00:10.487 / 00:30.520, 105Mb) Sushi: info Converted 22 FHIR CodeSystems. (00:07.600 / 00:38.121, 105Mb) Sushi: info Converted 37 FHIR ValueSets. (00:01.229 / 00:39.350, 105Mb) Sushi: info Converted 92 FHIR instances. (00:21.336 / 01:00.686, 105Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 01:00.688, 105Mb) Sushi: info Exported 204 FHIR resources as JSON. (00:00.515 / 01:01.203, 105Mb) Sushi: info Assembling Implementation Guide sources... (00:00.006 / 01:01.210, 105Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.uv.phr.json (00:00.051 / 01:01.262, 105Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 01:01.262, 105Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 01:01.264, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:01.264, 105Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 01:01.265, 105Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:01.265, 105Mb) Sushi: | | 54 | 0 | 4 | 0 | | (00:00.000 / 01:01.265, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:01.265, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:01.266, 105Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 01:01.266, 105Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:01.266, 105Mb) Sushi: | | 37 | 22 | 92 | | (00:00.000 / 01:01.266, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:01.266, 105Mb) Sushi: | | (00:00.000 / 01:01.267, 105Mb) Sushi: =================================================================== (00:00.000 / 01:01.267, 105Mb) Sushi: | You're in the swim of things now! 0 Errors 0 Warnings | (00:00.000 / 01:01.267, 105Mb) Sushi: =================================================================== (00:00.000 / 01:01.267, 105Mb) Root directory: /scratch/repo (00:00.030 / 01:01.298, 105Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.746 / 01:02.044, 56Mb) Load Template from hl7.fhir.template#current (00:00.706 / 01:02.750, 65Mb) Installing hl7.fhir.template#current to the package cache  Fetching:  Installing hl7.fhir.template#current  done.  Load Template from hl7.base.template#current (00:00.692 / 01:03.442, 121Mb) Installing hl7.base.template#current to the package cache  Fetching:  Installing hl7.base.template#current  done.  Load Template from fhir2.base.template#current (00:00.113 / 01:03.556, 121Mb) Installing fhir2.base.template#current to the package cache  Fetching:  Installing fhir2.base.template#current  done. Scanning directory: /scratch/repo/template ====================================================================== Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:04.750 / 01:08.307, 401Mb) Core Package hl7.fhir.r4.core#4.0.1 (00:00.000 / 01:08.307, 401Mb) Running Terminology Log: /tmp/ohfu-fhir-ig-13630034587946274065.html Connect to Terminology Server at http://tx.fhir.org (00:28.501 / 01:36.809, 463Mb) 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#7.0.1 Load Package hl7.fhir.uv.extensions.r4#5.2.0 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 fhir.dicom#2022.4.20221006 to the package cache  Fetching:  Installing fhir.dicom#2022.4.20221006  done. Load Package fhir.dicom#2022.4.20221006 Load Package hl7.fhir.uv.ips#1.1.0 Load Package hl7.fhir.uv.tools.r4#0.9.0 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. Cannot find or generate snapshot for base definition http://hl7.org/fhir/StructureDefinition/CanonicalResource from http://hl7.org/fhir/StructureDefinition/TestCases Initialization complete (01:19.062 / 02:55.871, 702Mb) Load IG (00:00.000 / 02:55.872, 702Mb) Load Translations (00:00.003 / 02:55.875, 702Mb) Load Content (00:00.000 / 02:55.875, 702Mb) Using en as the default narrative language. (Implementation Guide param i18n-default-lang) (00:00.150 / 02:56.026, 718Mb) Process Loaded Resources (00:02.586 / 02:58.612, 974Mb) Generating Snapshots (00:01.016 / 02:59.629, 1Gb) 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://hl7.org/fhir/uv/phr/package-list.json for version check (00:07.299 / 03:06.928, 1Gb) Checking Language (00:00.166 / 03:07.095, 1Gb) Load Dependency Info (00:00.008 / 03:07.103, 1Gb) Load Info (00:00.002 / 03:07.106, 1Gb) Load Paths (00:00.001 / 03:07.108, 1Gb) Check R4 / R4B (00:00.001 / 03:07.109, 1Gb) Assign Comparison Ids (00:00.090 / 03:07.200, 1Gb) Propagating status (00:00.000 / 03:07.200, 1Gb) Generating Narratives (00:00.242 / 03:07.442, 1Gb) Validating Conformance Resources (00:08.418 / 03:15.861, 1Gb) Check profiles & code systems (00:44.573 / 04:00.435, 1Gb) Check realm rules (00:00.012 / 04:00.447, 1Gb) Previous Version Comparison (00:00.000 / 04:00.447, 1Gb) Checking for Bundles to sign (00:00.114 / 04:00.562, 1Gb) Validating Resources (00:00.000 / 04:00.563, 1Gb) Processing Provenance Records (00:07.031 / 04:07.594, 2Gb) Generating Translation artifacts (00:00.000 / 04:07.595, 2Gb) Generating Outputs in /scratch/repo/output (00:00.003 / 04:07.598, 2Gb) Generate Native Outputs (00:00.522 / 04:08.121, 2Gb) Run Template (00:35.929 / 04:44.050, 2Gb) **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): ECG Lead Codes **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): Observation State of Mind Codes **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): Body Temperature Measurement Location Codes **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): ECG Classification Codes **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): ECG Classification Codes **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): ECG Lead Codes **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): ECG Symptoms Status Codes Generate HTML Outputs (00:02.946 / 04:46.996, 2Gb) Generate Spreadsheets (01:44.369 / 06:31.366, 5Gb) Generate Summaries (00:17.505 / 06:48.871, 3Gb) Generating Summary Outputs (en) (00:00.000 / 06:48.872, 3Gb) DB Cumulative Time invested: 00:00:09.494 Sending Usage Stats to Server (00:13.047 / 07:01.919, 4Gb) ## Memory (MB): Use = 4341, Free = 14666, Total = 19008, Max = 19008 (00:00.011 / 07:01.931, 4Gb) Reclaiming memory... (00:00.000 / 07:01.931, 4Gb) ## Memory (MB): Use = 854, Free = 18149, Total = 19008, Max = 19008 (00:01.328 / 07:03.259, 866Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 07:03.261, 866Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 07:03.261, 866Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 07:03.261, 866Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 07:03.261, 866Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.543 / 07:03.804, 886Mb) Jekyll: Generating... (00:00.000 / 07:03.804, 886Mb) Jekyll has failed. Complete output from running Jekyll:  Liquid Exception: Could not locate the included file 'dependency-table.xhtml' in any of ["/scratch/repo/temp/pages/_includes"]. Ensure it exists in one of those directories and, if it is a symlink, does not point outside your site source. in en/inde (00:13.829 / 07:17.634, 891Mb) Note: Check that Jekyll is installed correctly (00:00.000 / 07:17.634, 891Mb) Publishing Content Failed: Process exited with an error: 1 (Exit value: 1) (00:00.081 / 07:17.716, 902Mb) (00:00.000 / 07:17.716, 902Mb) Use -? to get command line help (00:00.000 / 07:17.716, 902Mb) (00:00.000 / 07:17.716, 902Mb) Stack Dump (for debugging): (00:00.000 / 07:17.716, 902Mb) org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1) at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404) at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166) at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:153) at org.hl7.fhir.igtools.publisher.PublisherGenerator.runJekyll(PublisherGenerator.java:3824) at org.hl7.fhir.igtools.publisher.PublisherGenerator.runTool(PublisherGenerator.java:3711) at org.hl7.fhir.igtools.publisher.PublisherGenerator.generate(PublisherGenerator.java:390) at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:428) at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:232) at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:1594)