INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/phenomics-exchange-ig --branch master-old repo DEBUG:root:Time to deadline 35879.99815 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 35865.727435 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35864.708352 seconds npm WARN deprecated rimraf@2.6.3: Rimraf versions prior to v4 are no longer supported npm WARN deprecated glob@7.2.3: Glob versions prior to v9 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 -> 11.6.2 npm notice Changelog: npm notice Run `npm install -g npm@11.6.2` 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/phenomics-exchange-ig/ -out /scratch/repo DEBUG:root:Time to deadline 35857.812335 seconds FHIR IG Publisher Version 2.0.22 (Git# 6bbdf7dc5537). Built 2025-10-22T10:27:38.176Z (30 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/phenomics-exchange-ig/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Thursday, October 23, 2025, 5:15:43 PM Coordinated Universal Time (2025-10-23T17:15:43Z) Build FHIR IG from /scratch/repo (00:00.024 / 00:00.024, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.002 / 00:00.026, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.002 / 00:00.029, 97Mb) Found dependency on hl7.fhir.uv.genomics-reporting#2.0.0 in Sushi config. Pre-installing (00:00.003 / 00:00.033, 97Mb) Installing hl7.fhir.uv.genomics-reporting#2.0.0 to the package cache  Fetching:  Installing hl7.fhir.uv.genomics-reporting#2.0.0  done. Found dependency on hl7.fhir.uv.extensions#current in Sushi config. Pre-installing (00:02.219 / 00:02.253, 72Mb) Installing hl7.fhir.uv.extensions#current to the package cache  Fetching:  Installing hl7.fhir.uv.extensions#current  done. Run Sushi on /scratch/repo (00:01.012 / 00:03.266, 160Mb) Sushi: info Running SUSHI v3.16.5 (implements FHIR Shorthand specification v3.0.0) (00:01.431 / 00:04.697, 168Mb) Sushi: info Arguments: (00:00.000 / 00:04.698, 168Mb) Sushi: info --require-latest (00:00.000 / 00:04.698, 168Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:04.698, 168Mb) Sushi: info /scratch/repo (00:00.000 / 00:04.699, 168Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.573 / 00:05.272, 168Mb) Sushi: info Importing FSH text... (00:00.114 / 00:05.387, 168Mb) Sushi: info Preprocessed 116 documents with 30 aliases. (00:00.310 / 00:05.697, 168Mb) Sushi: info Imported 57 definitions and 41 instances. (00:00.040 / 00:05.738, 168Mb) Sushi: warn Detected FSH entity definitions with duplicate names. While FSH allows for duplicate names across entity types, they can lead to ambiguous results when referring to these entities by name elsewhere (e.g., in references). Consider using unique names in FSH declarations and assigning duplicated names using caret assignment rules instead. Detected duplicate names: DiagnosticMarker, HistologicalDiagnosis, KaryotypicSex, Onset, Taxonomy, TumorGrade, TumorProgression. (00:00.012 / 00:05.750, 168Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.134 / 00:05.885, 168Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.8.0 (00:00.577 / 00:06.463, 176Mb) Sushi: info Attempting to download hl7.fhir.uv.tools.r4#0.8.0 from https://packages.fhir.org/hl7.fhir.uv.tools.r4/0.8.0 (00:00.000 / 00:06.464, 176Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.8.0 (00:00.845 / 00:07.309, 176Mb) Sushi: info Cached hl7.fhir.uv.tools.r4#0.8.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.tools.r4#0.8.0 (00:00.003 / 00:07.312, 176Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.8.0 with 110 resources (00:00.057 / 00:07.369, 176Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 6.5.0 (00:00.480 / 00:07.849, 176Mb) Sushi: info Attempting to download hl7.terminology.r4#6.5.0 from https://packages.fhir.org/hl7.terminology.r4/6.5.0 (00:00.000 / 00:07.850, 176Mb) Sushi: info Downloaded hl7.terminology.r4#6.5.0 (00:03.056 / 00:10.907, 176Mb) Sushi: info Cached hl7.terminology.r4#6.5.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#6.5.0 (00:00.001 / 00:10.908, 176Mb) Sushi: info Loaded hl7.terminology.r4#6.5.0 with 4392 resources (00:01.292 / 00:12.201, 176Mb) Sushi: info Loaded hl7.fhir.uv.genomics-reporting#2.0.0 with 50 resources (00:00.034 / 00:12.235, 176Mb) Sushi: info Loaded hl7.fhir.uv.extensions#current with 827 resources (00:00.333 / 00:12.569, 176Mb) 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 / 00:12.569, 176Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.252 / 00:15.822, 176Mb) 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 / 00:15.824, 176Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.184 / 00:17.008, 176Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.008 / 00:17.016, 176Mb) Sushi: info Converting FSH to FHIR resources... (00:00.018 / 00:17.035, 176Mb) Sushi: info Converted 32 FHIR StructureDefinitions. (00:02.548 / 00:19.583, 176Mb) Sushi: info Converted 5 FHIR CodeSystems. (00:00.409 / 00:19.992, 176Mb) Sushi: info Converted 20 FHIR ValueSets. (00:02.010 / 00:22.003, 176Mb) Sushi: info Converted 41 FHIR instances. (00:02.604 / 00:24.607, 176Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.000 / 00:24.608, 176Mb) Sushi: info Exported 98 FHIR resources as JSON. (00:00.115 / 00:24.723, 176Mb) Sushi: info Assembling Implementation Guide sources... (00:00.004 / 00:24.728, 176Mb) Sushi: info Generated ImplementationGuide-phenomics-exchange.json (00:00.040 / 00:24.768, 176Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:24.769, 176Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:24.771, 176Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:24.771, 176Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:24.771, 176Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:24.771, 176Mb) Sushi: | | 9 | 23 | 0 | 0 | | (00:00.000 / 00:24.771, 176Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:24.772, 176Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:24.772, 176Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:24.772, 176Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:24.772, 176Mb) Sushi: | | 20 | 5 | 41 | | (00:00.000 / 00:24.772, 176Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:24.772, 176Mb) Sushi: | | (00:00.000 / 00:24.773, 176Mb) Sushi: =================================================================== (00:00.000 / 00:24.773, 176Mb) Sushi: | You might need some Vitamin Sea 0 Errors 1 Warning | (00:00.000 / 00:24.774, 176Mb) Sushi: =================================================================== (00:00.000 / 00:24.774, 176Mb) Root directory: /scratch/repo (00:00.044 / 00:24.818, 176Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.542 / 00:25.360, 65Mb) Load Template from hl7.fhir.template#current (00:00.489 / 00:25.849, 65Mb) Installing hl7.fhir.template#current to the package cache  Fetching:  Installing hl7.fhir.template#current  done.  Load Template from hl7.base.template#current (00:00.181 / 00:26.030, 65Mb) Installing hl7.base.template#current to the package cache  Fetching:  Installing hl7.base.template#current  done.  Load Template from fhir2.base.template#current (00:00.174 / 00:26.205, 65Mb) Installing fhir2.base.template#current to the package cache  Fetching:  Installing fhir2.base.template#current  done. Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:03.200 / 00:29.405, 368Mb) Core Package hl7.fhir.r4.core#4.0.1 (00:00.000 / 00:29.406, 368Mb) Running Terminology Log: /tmp/ohfu-fhir-ig-13371945461561552367.html Connect to Terminology Server at http://tx.fhir.org (00:34.946 / 01:04.353, 594Mb) 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#6.5.0 Load Package hl7.fhir.uv.genomics-reporting#2.0.0 Version mismatch. This IG is version 4.0.1, while the IG 'hl7.fhir.uv.extensions' is from version 5.0.0 (will try to run anyway) (00:03.620 / 01:07.973, 453Mb) Installing hl7.terminology.r5#6.5.0 to the package cache  Fetching:  Installing hl7.terminology.r5#6.5.0  done. Installing hl7.fhir.uv.extensions.r5#5.2.0 to the package cache  Fetching:  Installing hl7.fhir.uv.extensions.r5#5.2.0  done. Version mismatch. This IG is for FHIR version 4.0.1, while the package 'hl7.terminology.r5#6.5.0' is for FHIR version 5.0.0 (will ignore that and try to run anyway) (00:02.460 / 01:10.434, 661Mb) Ignore Dependency on Core FHIR hl7.fhir.r5.core#5.0.0, from package 'hl7.fhir.uv.extensions.r5#5.2.0' (00:00.008 / 01:10.442, 669Mb) Load Package hl7.fhir.uv.extensions.r5#5.2.0 Load Package hl7.terminology.r5#6.5.0 Load Package hl7.fhir.uv.extensions#current Load Package hl7.fhir.uv.tools.r4#0.8.0 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 (00:06.573 / 01:17.016, 961Mb) Load IG (00:00.000 / 01:17.016, 961Mb) Load Translations (00:00.000 / 01:17.017, 961Mb) Load Content (00:00.000 / 01:17.017, 961Mb) Using en as the default narrative language. (Implementation Guide param i18n-default-lang) (00:00.096 / 01:17.114, 976Mb) Process Loaded Resources (00:01.734 / 01:18.849, 1Gb) Generating Snapshots (00:00.569 / 01:19.418, 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/phenomics-exchange/package-list.json for version check (00:01.685 / 01:21.104, 839Mb) Processing Conformance Resources (00:00.103 / 01:21.207, 847Mb) Checking Language (00:00.000 / 01:21.207, 847Mb) Load Dependency Info (00:00.003 / 01:21.210, 847Mb) Load Info (00:00.002 / 01:21.213, 853Mb) Load Paths (00:00.001 / 01:21.214, 853Mb) Check R4 / R4B (00:00.001 / 01:21.215, 853Mb) Assign Comparison Ids (00:00.040 / 01:21.256, 861Mb) Propagating status (00:00.000 / 01:21.256, 861Mb) Generating Narratives (00:00.000 / 01:21.256, 861Mb) Validating Conformance Resources (00:05.411 / 01:26.668, 1Gb) Check profiles & code systems (00:16.594 / 01:43.262, 1Gb) Check realm rules (00:00.003 / 01:43.265, 1Gb) Previous Version Comparison (00:00.000 / 01:43.265, 1Gb) Checking for Bundles to sign (00:00.027 / 01:43.293, 1Gb) Validating Resources (00:00.000 / 01:43.293, 1Gb) Processing Provenance Records (00:07.296 / 01:50.589, 1Gb) Generating Translation artifacts (00:00.000 / 01:50.590, 1Gb) Generating Outputs in /scratch/repo/output (00:00.001 / 01:50.592, 1Gb) Generate Native Outputs (00:00.299 / 01:50.891, 1Gb) Run Template (00:08.051 / 01:58.943, 948Mb) **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): Measurement **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): Phenotypic Feature **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): Diagnostic Marker **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): Taxonomy **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): Tumor Grade **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): Tumor Progression **WARNING** Jira file generation will not be correct because multiple artifacts have the same name (ignoring content in "()"): Categories Generate HTML Outputs (00:02.465 / 02:01.408, 861Mb) Generate Spreadsheets (00:27.346 / 02:28.756, 2Gb) Generate Summaries (00:04.488 / 02:33.244, 3Gb) Generating Summary Outputs (en) (00:00.000 / 02:33.244, 3Gb) DB Cumulative Time invested: 00:00:01.631 Sending Usage Stats to Server (00:11.133 / 02:44.378, 5Gb) ## Memory (MB): Use = 5609, Free = 13398, Total = 19008, Max = 19008 (00:00.011 / 02:44.389, 5Gb) Reclaiming memory... (00:00.000 / 02:44.390, 5Gb) ## Memory (MB): Use = 694, Free = 18313, Total = 19008, Max = 19008 (00:00.739 / 02:45.129, 702Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 02:45.130, 710Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 02:45.130, 710Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 02:45.130, 710Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 02:45.131, 710Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.487 / 02:45.618, 729Mb) Jekyll: Generating... (00:00.000 / 02:45.619, 729Mb) Jekyll has failed. Complete output from running Jekyll:  Liquid Exception: Could not locate the included file 'list-simple-name-bundles.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 (00:04.304 / 02:49.923, 737Mb) Note: Check that Jekyll is installed correctly (00:00.000 / 02:49.923, 737Mb) Publishing Content Failed: Process exited with an error: 1 (Exit value: 1) (00:00.021 / 02:49.945, 737Mb) (00:00.000 / 02:49.945, 737Mb) Use -? to get command line help (00:00.000 / 02:49.945, 737Mb) (00:00.000 / 02:49.945, 737Mb) Stack Dump (for debugging): (00:00.000 / 02:49.945, 737Mb) 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:3707) at org.hl7.fhir.igtools.publisher.PublisherGenerator.runTool(PublisherGenerator.java:3594) at org.hl7.fhir.igtools.publisher.PublisherGenerator.generate(PublisherGenerator.java:361) at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:396) at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:218) at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:1487)