INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/personal-health-record-format-ig --branch jami-updates repo DEBUG:root:Time to deadline 35879.998206 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 35837.631781 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35836.413215 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 139 packages in 6s 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 35830.167522 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, 5:41:24 AM Coordinated Universal Time (2025-12-22T05:41:24Z) 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 (00:00.003 / 00:00.031, 97Mb) Found dependency on hl7.fhir.uv.ips#1.1.0 in Sushi config. Pre-installing (00:00.009 / 00:00.040, 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 (00:03.218 / 00:03.258, 89Mb) Sushi: info Running SUSHI v3.16.5 (implements FHIR Shorthand specification v3.0.0) (00:00.707 / 00:03.966, 98Mb) Sushi: info Arguments: (00:00.000 / 00:03.967, 98Mb) Sushi: info --require-latest (00:00.000 / 00:03.967, 98Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:03.967, 98Mb) Sushi: info /scratch/repo (00:00.000 / 00:03.968, 98Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.674 / 00:04.643, 98Mb) Sushi: info Importing FSH text... (00:00.172 / 00:04.816, 98Mb) Sushi: info Preprocessed 260 documents with 35 aliases. (00:00.676 / 00:05.492, 98Mb) Sushi: info Imported 117 definitions and 92 instances. (00:00.373 / 00:05.865, 98Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.190 / 00:06.056, 98Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.9.0 (00:00.632 / 00:06.689, 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 / 00:06.690, 105Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.9.0 (00:00.844 / 00:07.534, 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 (00:00.002 / 00:07.537, 105Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.9.0 with 117 resources (00:00.093 / 00:07.630, 105Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 7.0.1 (00:00.471 / 00:08.102, 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 / 00:08.103, 105Mb) Sushi: info Downloaded hl7.terminology.r4#7.0.1 (00:02.815 / 00:10.918, 105Mb) Sushi: info Cached hl7.terminology.r4#7.0.1 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#7.0.1 (00:00.001 / 00:10.920, 105Mb) Sushi: info Loaded hl7.terminology.r4#7.0.1 with 4096 resources (00:01.705 / 00:12.625, 105Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.465 / 00:13.090, 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 / 00:13.090, 105Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.505 / 00:14.595, 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 / 00:14.596, 105Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.424 / 00:15.021, 105Mb) Sushi: info Loaded hl7.fhir.uv.ips#1.1.0 with 104 resources (00:00.134 / 00:15.156, 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 / 00:15.157, 105Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.563 / 00:18.720, 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 / 00:18.722, 105Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.759 / 00:20.481, 105Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.018 / 00:20.500, 105Mb) Sushi: info Converting FSH to FHIR resources... (00:00.026 / 00:20.526, 105Mb) Sushi: info Converted 58 FHIR StructureDefinitions. (00:10.091 / 00:30.618, 105Mb) Sushi: info Converted 22 FHIR CodeSystems. (00:06.969 / 00:37.588, 105Mb) Sushi: info Converted 37 FHIR ValueSets. (00:01.036 / 00:38.624, 105Mb) Sushi: info Converted 92 FHIR instances. (00:20.794 / 00:59.418, 105Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 00:59.419, 105Mb) Sushi: info Exported 204 FHIR resources as JSON. (00:00.522 / 00:59.942, 105Mb) Sushi: info Assembling Implementation Guide sources... (00:00.007 / 00:59.949, 105Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.uv.phr.json (00:00.054 / 01:00.004, 105Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 01:00.004, 105Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 01:00.006, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:00.006, 105Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 01:00.006, 105Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:00.006, 105Mb) Sushi: | | 54 | 0 | 4 | 0 | | (00:00.000 / 01:00.007, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:00.007, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:00.007, 105Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 01:00.007, 105Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:00.007, 105Mb) Sushi: | | 37 | 22 | 92 | | (00:00.000 / 01:00.008, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:00.008, 105Mb) Sushi: | | (00:00.000 / 01:00.008, 105Mb) Sushi: =================================================================== (00:00.000 / 01:00.008, 105Mb) Sushi: | FSHing for compliments? Super job! 0 Errors 0 Warnings | (00:00.000 / 01:00.008, 105Mb) Sushi: =================================================================== (00:00.000 / 01:00.008, 105Mb) Root directory: /scratch/repo (00:00.034 / 01:00.043, 105Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.756 / 01:00.800, 57Mb) Load Template from hl7.fhir.template#current (00:00.691 / 01:01.491, 65Mb) Installing hl7.fhir.template#current to the package cache  Fetching:  Installing hl7.fhir.template#current  done.  Load Template from hl7.base.template#current (00:00.575 / 01:02.067, 121Mb) Installing hl7.base.template#current to the package cache  Fetching:  Installing hl7.base.template#current  done.  Load Template from fhir2.base.template#current (00:00.115 / 01:02.182, 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 (00:04.827 / 01:07.010, 401Mb) Core Package hl7.fhir.r4.core#4.0.1 (00:00.000 / 01:07.011, 401Mb) Running Terminology Log: /tmp/ohfu-fhir-ig-9903885123074701482.html Connect to Terminology Server at http://tx.fhir.org (00:28.254 / 01:35.266, 490Mb) 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 (01:19.791 / 02:55.056, 705Mb) Load IG (00:00.000 / 02:55.057, 705Mb) Load Translations (00:00.003 / 02:55.060, 705Mb) Load Content (00:00.000 / 02:55.060, 705Mb) Using en as the default narrative language. (Implementation Guide param i18n-default-lang) (00:00.141 / 02:55.202, 721Mb) Process Loaded Resources (00:02.467 / 02:57.669, 977Mb) Generating Snapshots (00:00.956 / 02:58.626, 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 (00:07.979 / 03:06.605, 1Gb) Checking Language (00:00.172 / 03:06.778, 1Gb) Load Dependency Info (00:00.008 / 03:06.786, 1Gb) Load Info (00:00.002 / 03:06.789, 1Gb) Load Paths (00:00.001 / 03:06.791, 1Gb) Check R4 / R4B (00:00.001 / 03:06.792, 1Gb) Assign Comparison Ids (00:00.121 / 03:06.914, 1Gb) Propagating status (00:00.000 / 03:06.915, 1Gb) Generating Narratives (00:00.442 / 03:07.357, 1Gb) Validating Conformance Resources (00:08.761 / 03:16.119, 1Gb) Check profiles & code systems (00:43.388 / 03:59.508, 2Gb) Check realm rules (00:00.013 / 03:59.522, 2Gb) Previous Version Comparison (00:00.000 / 03:59.523, 2Gb) Checking for Bundles to sign (00:00.103 / 03:59.626, 2Gb) Validating Resources (00:00.000 / 03:59.626, 2Gb) Processing Provenance Records (00:06.834 / 04:06.461, 2Gb) Generating Translation artifacts (00:00.000 / 04:06.462, 2Gb) Generating Outputs in /scratch/repo/output (00:00.003 / 04:06.465, 2Gb) Generate Native Outputs (00:00.529 / 04:06.995, 2Gb) Run Template (00:35.638 / 04:42.633, 3Gb) **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 (00:02.806 / 04:45.439, 3Gb) Generate Spreadsheets (01:43.140 / 06:28.579, 7Gb) Generate Summaries (00:18.007 / 06:46.587, 4Gb) Generating Summary Outputs (en) (00:00.000 / 06:46.587, 4Gb) DB Cumulative Time invested: 00:00:09.393 Sending Usage Stats to Server (00:12.994 / 06:59.582, 5Gb) ## Memory (MB): Use = 5510, Free = 13497, Total = 19008, Max = 19008 (00:00.009 / 06:59.592, 5Gb) Reclaiming memory... (00:00.000 / 06:59.592, 5Gb) ## Memory (MB): Use = 853, Free = 18154, Total = 19008, Max = 19008 (00:01.220 / 07:00.813, 869Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.022 / 07:00.836, 869Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 07:00.836, 869Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 07:00.836, 869Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 07:00.836, 869Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.520 / 07:01.357, 885Mb) Jekyll: Generating... (00:00.000 / 07:01.357, 885Mb) 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 (00:13.412 / 07:14.769, 901Mb) Note: Check that Jekyll is installed correctly (00:00.000 / 07:14.769, 901Mb) Publishing Content Failed: Process exited with an error: 1 (Exit value: 1) (00:00.074 / 07:14.844, 917Mb) (00:00.000 / 07:14.844, 917Mb) Use -? to get command line help (00:00.000 / 07:14.845, 917Mb) (00:00.000 / 07:14.845, 917Mb) Stack Dump (for debugging): (00:00.000 / 07:14.845, 917Mb) 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)