INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/personal-health-record-format-ig --branch jami-feedback-3 repo DEBUG:root:Time to deadline 35879.998018 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 35839.6524 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35838.332391 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 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 35831.823047 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, 6:18:41 AM Coordinated Universal Time (2025-12-22T06:18:41Z) Build FHIR IG from /scratch/repo (00:00.028 / 00:00.028, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.002 / 00:00.031, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.034, 97Mb) Found dependency on hl7.fhir.uv.ips#1.1.0 in Sushi config. Pre-installing (00:00.009 / 00:00.044, 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 (00:03.230 / 00:03.274, 89Mb) Sushi: info Running SUSHI v3.16.5 (implements FHIR Shorthand specification v3.0.0) (00:00.716 / 00:03.991, 98Mb) Sushi: info Arguments: (00:00.000 / 00:03.991, 98Mb) Sushi: info --require-latest (00:00.000 / 00:03.992, 98Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:03.992, 98Mb) Sushi: info /scratch/repo (00:00.000 / 00:03.992, 98Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.823 / 00:04.816, 98Mb) Sushi: info Importing FSH text... (00:00.158 / 00:04.974, 98Mb) Sushi: info Preprocessed 260 documents with 35 aliases. (00:00.718 / 00:05.693, 98Mb) Sushi: info Imported 117 definitions and 92 instances. (00:00.395 / 00:06.088, 98Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.174 / 00:06.263, 105Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.9.0 (00:00.600 / 00:06.863, 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 / 00:06.864, 105Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.9.0 (00:00.850 / 00:07.715, 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 / 00:07.718, 105Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.9.0 with 117 resources (00:00.097 / 00:07.815, 105Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 7.0.1 (00:00.472 / 00:08.287, 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 / 00:08.288, 105Mb) Sushi: info Downloaded hl7.terminology.r4#7.0.1 (00:02.826 / 00:11.114, 105Mb) Sushi: info Cached hl7.terminology.r4#7.0.1 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#7.0.1 (00:00.001 / 00:11.116, 105Mb) Sushi: info Loaded hl7.terminology.r4#7.0.1 with 4096 resources (00:01.740 / 00:12.856, 105Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.467 / 00:13.324, 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 / 00:13.324, 105Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.538 / 00:14.863, 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 / 00:14.864, 105Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.442 / 00:15.307, 105Mb) Sushi: info Loaded hl7.fhir.uv.ips#1.1.0 with 104 resources (00:00.136 / 00:15.443, 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 / 00:15.444, 105Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.255 / 00:18.699, 105Mb) Sushi: info Cached hl7.fhir.r4.core#4.0.1 to /home/fhiruser/.fhir/packages/hl7.fhir.r4.core#4.0.1 (00:00.003 / 00:18.703, 105Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.931 / 00:20.634, 105Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.012 / 00:20.646, 105Mb) Sushi: info Converting FSH to FHIR resources... (00:00.023 / 00:20.670, 105Mb) Sushi: info Converted 58 FHIR StructureDefinitions. (00:10.416 / 00:31.087, 105Mb) Sushi: info Converted 22 FHIR CodeSystems. (00:07.177 / 00:38.264, 105Mb) Sushi: info Converted 37 FHIR ValueSets. (00:01.047 / 00:39.311, 105Mb) Sushi: info Converted 92 FHIR instances. (00:21.130 / 01:00.442, 105Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 01:00.443, 105Mb) Sushi: info Exported 204 FHIR resources as JSON. (00:00.529 / 01:00.973, 105Mb) Sushi: info Assembling Implementation Guide sources... (00:00.007 / 01:00.981, 105Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.uv.phr.json (00:00.057 / 01:01.037, 105Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 01:01.038, 105Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.002 / 01:01.040, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:01.040, 105Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 01:01.040, 105Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:01.040, 105Mb) Sushi: | | 54 | 0 | 4 | 0 | | (00:00.000 / 01:01.040, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:01.041, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:01.041, 105Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 01:01.041, 105Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:01.041, 105Mb) Sushi: | | 37 | 22 | 92 | | (00:00.000 / 01:01.041, 105Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:01.041, 105Mb) Sushi: | | (00:00.000 / 01:01.042, 105Mb) Sushi: =================================================================== (00:00.000 / 01:01.042, 105Mb) Sushi: | You're sailing along smoothly. 0 Errors 0 Warnings | (00:00.000 / 01:01.042, 105Mb) Sushi: =================================================================== (00:00.000 / 01:01.042, 105Mb) Root directory: /scratch/repo (00:00.036 / 01:01.079, 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 / 01:01.835, 56Mb) Load Template from hl7.fhir.template#current (00:00.662 / 01:02.497, 65Mb) Installing hl7.fhir.template#current to the package cache  Fetching:  Installing hl7.fhir.template#current  done.  Load Template from hl7.base.template#current (00:00.579 / 01:03.077, 121Mb) Installing hl7.base.template#current to the package cache  Fetching:  Installing hl7.base.template#current  done.  Load Template from fhir2.base.template#current (00:00.110 / 01:03.186, 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 (00:04.667 / 01:07.854, 409Mb) Core Package hl7.fhir.r4.core#4.0.1 (00:00.000 / 01:07.854, 409Mb) Running Terminology Log: /tmp/ohfu-fhir-ig-4218420257069717057.html Connect to Terminology Server at http://tx.fhir.org (00:30.375 / 01:38.230, 502Mb) 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 (01:23.838 / 03:02.068, 727Mb) Load IG (00:00.000 / 03:02.068, 727Mb) Load Translations (00:00.004 / 03:02.073, 733Mb) Load Content (00:00.000 / 03:02.073, 733Mb) Using en as the default narrative language. (Implementation Guide param i18n-default-lang) (00:00.143 / 03:02.217, 751Mb) Process Loaded Resources (00:03.080 / 03:05.297, 1007Mb) Generating Snapshots (00:01.083 / 03:06.380, 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 (00:07.769 / 03:14.150, 1Gb) Checking Language (00:00.208 / 03:14.358, 1Gb) Load Dependency Info (00:00.007 / 03:14.365, 1Gb) Load Info (00:00.003 / 03:14.369, 1Gb) Load Paths (00:00.001 / 03:14.370, 1Gb) Check R4 / R4B (00:00.001 / 03:14.372, 1Gb) Assign Comparison Ids (00:00.130 / 03:14.502, 1Gb) Propagating status (00:00.000 / 03:14.503, 1Gb) Generating Narratives (00:00.392 / 03:14.896, 1Gb) Validating Conformance Resources (00:08.936 / 03:23.833, 1Gb) Check profiles & code systems (00:48.293 / 04:12.126, 1Gb) Check realm rules (00:00.014 / 04:12.141, 1Gb) Previous Version Comparison (00:00.000 / 04:12.142, 1Gb) Checking for Bundles to sign (00:00.102 / 04:12.244, 2Gb) Validating Resources (00:00.000 / 04:12.245, 2Gb) Processing Provenance Records (00:07.295 / 04:19.540, 2Gb) Generating Translation artifacts (00:00.000 / 04:19.541, 2Gb) Generating Outputs in /scratch/repo/output (00:00.002 / 04:19.544, 2Gb) Generate Native Outputs (00:00.474 / 04:20.018, 2Gb) Run Template (00:36.506 / 04:56.525, 5Gb) **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 (00:03.059 / 04:59.585, 5Gb) Generate Spreadsheets (01:44.697 / 06:44.283, 6Gb) Generate Summaries (00:18.029 / 07:02.312, 3Gb) Generating Summary Outputs (en) (00:00.000 / 07:02.313, 3Gb) DB Cumulative Time invested: 00:00:11.446 Sending Usage Stats to Server (00:13.050 / 07:15.363, 4Gb) ## Memory (MB): Use = 4709, Free = 14298, Total = 19008, Max = 19008 (00:00.010 / 07:15.374, 4Gb) Reclaiming memory... (00:00.000 / 07:15.374, 4Gb) ## Memory (MB): Use = 854, Free = 18153, Total = 19008, Max = 19008 (00:01.313 / 07:16.688, 866Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.044 / 07:16.733, 866Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.016 / 07:16.749, 866Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 07:16.749, 866Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 07:16.749, 866Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.496 / 07:17.246, 886Mb) Jekyll: Generating... (00:00.000 / 07:17.246, 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 (00:12.753 / 07:30.000, 890Mb) Note: Check that Jekyll is installed correctly (00:00.000 / 07:30.001, 890Mb) Publishing Content Failed: Process exited with an error: 1 (Exit value: 1) (00:00.081 / 07:30.082, 902Mb) (00:00.000 / 07:30.082, 902Mb) Use -? to get command line help (00:00.000 / 07:30.082, 902Mb) (00:00.000 / 07:30.082, 902Mb) Stack Dump (for debugging): (00:00.000 / 07:30.082, 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)