INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/personal-health-record-format-ig --branch jami-feedback repo DEBUG:root:Time to deadline 35879.997995 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 35836.237235 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35834.966799 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 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 35828.060811 seconds FHIR IG Publisher Version 2.0.29 (Git# 826a7eb003d6). Built 2025-12-17T01:19:30.102Z (45 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/personal-health-record-format-ig/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Thursday, December 18, 2025, 10:46:11 PM Coordinated Universal Time (2025-12-18T22:46:11Z) Build FHIR IG from /scratch/repo (00:00.026 / 00:00.027, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.002 / 00:00.029, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.032, 97Mb) Found dependency on hl7.fhir.uv.ips#1.1.0 in Sushi config. Pre-installing (00:00.009 / 00:00.042, 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 (00:03.188 / 00:03.231, 89Mb) Sushi: info Running SUSHI v3.16.5 (implements FHIR Shorthand specification v3.0.0) (00:00.718 / 00:03.950, 98Mb) Sushi: info Arguments: (00:00.000 / 00:03.950, 98Mb) Sushi: info --require-latest (00:00.000 / 00:03.951, 98Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:03.951, 98Mb) Sushi: info /scratch/repo (00:00.000 / 00:03.951, 98Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.774 / 00:04.726, 98Mb) Sushi: info Importing FSH text... (00:00.158 / 00:04.884, 98Mb) Sushi: info Preprocessed 260 documents with 35 aliases. (00:00.707 / 00:05.592, 98Mb) Sushi: info Imported 117 definitions and 92 instances. (00:00.368 / 00:05.961, 98Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.167 / 00:06.129, 98Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.9.0 (00:00.669 / 00:06.798, 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 / 00:06.800, 105Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.9.0 (00:00.870 / 00:07.670, 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 / 00:07.673, 105Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.9.0 with 117 resources (00:00.082 / 00:07.756, 105Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 7.0.1 (00:00.467 / 00:08.223, 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 / 00:08.223, 105Mb) Sushi: info Downloaded hl7.terminology.r4#7.0.1 (00:02.809 / 00:11.033, 105Mb) Sushi: info Cached hl7.terminology.r4#7.0.1 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#7.0.1 (00:00.001 / 00:11.034, 105Mb) Sushi: info Loaded hl7.terminology.r4#7.0.1 with 4096 resources (00:01.728 / 00:12.763, 105Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.466 / 00:13.229, 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 / 00:13.229, 105Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.514 / 00:14.744, 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 / 00:14.745, 105Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.427 / 00:15.172, 105Mb) Sushi: info Loaded hl7.fhir.uv.ips#1.1.0 with 104 resources (00:00.108 / 00:15.281, 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 / 00:15.281, 105Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.375 / 00:18.656, 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 / 00:18.659, 105Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.733 / 00:20.393, 105Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.016 / 00:20.409, 105Mb) Sushi: info Converting FSH to FHIR resources... (00:00.023 / 00:20.433, 105Mb) Sushi: info Converted 58 FHIR StructureDefinitions. (00:10.269 / 00:30.702, 105Mb) Sushi: info Converted 22 FHIR CodeSystems. (00:06.872 / 00:37.575, 105Mb) Sushi: info Converted 37 FHIR ValueSets. (00:00.984 / 00:38.559, 105Mb) Sushi: info Converted 92 FHIR instances. (00:20.567 / 00:59.127, 105Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 00:59.128, 105Mb) Sushi: info Exported 204 FHIR resources as JSON. (00:00.524 / 00:59.653, 105Mb) Sushi: info Assembling Implementation Guide sources... (00:00.007 / 00:59.661, 105Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.uv.phr.json (00:00.051 / 00:59.712, 105Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:59.713, 105Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:59.715, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:59.715, 105Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:59.715, 105Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:59.715, 105Mb) Sushi: | | 54 | 0 | 4 | 0 | | (00:00.000 / 00:59.716, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:59.716, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:59.716, 105Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:59.716, 105Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:59.717, 105Mb) Sushi: | | 37 | 22 | 92 | | (00:00.000 / 00:59.717, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:59.717, 105Mb) Sushi: | | (00:00.000 / 00:59.717, 105Mb) Sushi: =================================================================== (00:00.000 / 00:59.717, 105Mb) Sushi: | It doesn't get any betta than this! 0 Errors 0 Warnings | (00:00.000 / 00:59.718, 105Mb) Sushi: =================================================================== (00:00.000 / 00:59.718, 105Mb) Root directory: /scratch/repo (00:00.035 / 00:59.753, 105Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.736 / 01:00.490, 56Mb) Load Template from hl7.fhir.template#current (00:00.675 / 01:01.166, 65Mb) Installing hl7.fhir.template#current to the package cache  Fetching:  Installing hl7.fhir.template#current  done.  Load Template from hl7.base.template#current (00:00.540 / 01:01.706, 120Mb) Installing hl7.base.template#current to the package cache  Fetching:  Installing hl7.base.template#current  done.  Load Template from fhir2.base.template#current (00:00.096 / 01:01.802, 120Mb) 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 (00:04.898 / 01:06.700, 392Mb) Core Package hl7.fhir.r4.core#4.0.1 (00:00.000 / 01:06.701, 392Mb) Running Terminology Log: /tmp/ohfu-fhir-ig-12287378410960239479.html Connect to Terminology Server at http://tx.fhir.org (00:23.527 / 01:30.228, 468Mb) 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 (01:09.861 / 02:40.089, 687Mb) Load IG (00:00.000 / 02:40.090, 687Mb) Load Translations (00:00.003 / 02:40.093, 687Mb) Load Content (00:00.000 / 02:40.093, 687Mb) Using en as the default narrative language. (Implementation Guide param i18n-default-lang) (00:00.140 / 02:40.234, 703Mb) Process Loaded Resources (00:02.186 / 02:42.421, 951Mb) Generating Snapshots (00:00.837 / 02:43.258, 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 (00:07.697 / 02:50.956, 1Gb) Checking Language (00:00.156 / 02:51.112, 1Gb) Load Dependency Info (00:00.007 / 02:51.119, 1Gb) Load Info (00:00.002 / 02:51.122, 1Gb) Load Paths (00:00.001 / 02:51.123, 1Gb) Check R4 / R4B (00:00.001 / 02:51.124, 1Gb) Assign Comparison Ids (00:00.124 / 02:51.249, 1Gb) Propagating status (00:00.000 / 02:51.250, 1Gb) Generating Narratives (00:00.226 / 02:51.477, 1Gb) Validating Conformance Resources (00:10.994 / 03:02.471, 1Gb) Check profiles & code systems (00:49.400 / 03:51.872, 2Gb) Check realm rules (00:00.012 / 03:51.884, 2Gb) Previous Version Comparison (00:00.000 / 03:51.884, 2Gb) Checking for Bundles to sign (00:00.104 / 03:51.989, 2Gb) Validating Resources (00:00.000 / 03:51.989, 2Gb) Processing Provenance Records (00:07.900 / 03:59.889, 2Gb) Generating Translation artifacts (00:00.000 / 03:59.890, 2Gb) Generating Outputs in /scratch/repo/output (00:00.002 / 03:59.892, 2Gb) Generate Native Outputs (00:00.400 / 04:00.293, 2Gb) Run Template (00:34.754 / 04:35.047, 4Gb) **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 (00:03.038 / 04:38.086, 4Gb) Generate Spreadsheets (01:41.533 / 06:19.620, 8Gb) Generate Summaries (00:17.124 / 06:36.744, 2Gb) Generating Summary Outputs (en) (00:00.000 / 06:36.745, 2Gb) DB Cumulative Time invested: 00:00:07.908 Sending Usage Stats to Server (00:11.476 / 06:48.221, 3Gb) ## Memory (MB): Use = 3359, Free = 15648, Total = 19008, Max = 19008 (00:00.010 / 06:48.232, 3Gb) Reclaiming memory... (00:00.000 / 06:48.232, 3Gb) ## Memory (MB): Use = 855, Free = 18152, Total = 19008, Max = 19008 (00:01.232 / 06:49.465, 863Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 06:49.466, 875Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 06:49.467, 875Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 06:49.467, 875Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 06:49.467, 875Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.526 / 06:49.994, 887Mb) Jekyll: Generating... (00:00.000 / 06:49.994, 887Mb) 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 (00:12.905 / 07:02.899, 899Mb) Note: Check that Jekyll is installed correctly (00:00.000 / 07:02.900, 899Mb) Publishing Content Failed: Process exited with an error: 1 (Exit value: 1) (00:00.077 / 07:02.977, 911Mb) (00:00.000 / 07:02.977, 911Mb) Use -? to get command line help (00:00.000 / 07:02.977, 911Mb) (00:00.000 / 07:02.977, 911Mb) Stack Dump (for debugging): (00:00.000 / 07:02.977, 911Mb) 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)