INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/tewhatuora/centralRegion-integrationHub-ig --branch master repo DEBUG:root:Time to deadline 35879.998019 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 35878.97876 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35877.608006 seconds 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 npm WARN deprecated rimraf@2.6.3: Rimraf versions prior to v4 are no longer supported added 140 packages in 6s 15 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 11.6.0 npm notice Changelog: npm notice Run `npm install -g npm@11.6.0` 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/tewhatuora/centralRegion-integrationHub-ig/ -out /scratch/repo DEBUG:root:Time to deadline 35871.765483 seconds FHIR IG Publisher Version 2.0.17 (Git# 98facbadd305). Built 2025-09-09T06:53:45.198Z (8 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/tewhatuora/centralRegion-integrationHub-ig/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Thursday, September 18, 2025, 4:49:03 AM Coordinated Universal Time (2025-09-18T04:49:03Z) Build FHIR IG from /scratch/repo (00:00.022 / 00:00.023, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.002 / 00:00.025, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.002 / 00:00.028, 97Mb) Run Sushi on /scratch/repo (00:00.006 / 00:00.034, 97Mb) Sushi: info Running SUSHI v3.16.4 (implements FHIR Shorthand specification v3.0.0) (00:00.547 / 00:00.582, 113Mb) Sushi: info Arguments: (00:00.000 / 00:00.582, 113Mb) Sushi: info --require-latest (00:00.000 / 00:00.582, 113Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.583, 113Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.583, 113Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.805 / 00:01.389, 113Mb) Sushi: info Importing FSH text... (00:00.121 / 00:01.510, 113Mb) Sushi: info Preprocessed 69 documents with 152 aliases. (00:00.755 / 00:02.265, 113Mb) Sushi: info Imported 95 definitions and 35 instances. (00:00.614 / 00:02.880, 113Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.097 / 00:02.977, 113Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.8.0 (00:00.657 / 00:03.635, 113Mb) 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 (00:00.001 / 00:03.635, 113Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.8.0 (00:00.810 / 00:04.446, 113Mb) Sushi: info Cached hl7.fhir.uv.tools.r4#0.8.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.tools.r4#0.8.0 (00:00.002 / 00:04.448, 113Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.8.0 with 110 resources (00:00.063 / 00:04.512, 113Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.470 / 00:04.982, 113Mb) 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 / 00:04.983, 113Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.546 / 00:06.529, 113Mb) 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 / 00:06.531, 113Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.284 / 00:06.815, 113Mb) Sushi: info Attempting to download hl7.terminology.r4#5.5.0 from https://packages.fhir.org/hl7.terminology.r4/5.5.0 (00:00.000 / 00:06.816, 113Mb) Sushi: info Downloaded hl7.terminology.r4#5.5.0 (00:02.550 / 00:09.367, 113Mb) Sushi: info Cached hl7.terminology.r4#5.5.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#5.5.0 (00:00.001 / 00:09.368, 113Mb) Sushi: info Loaded hl7.terminology.r4#5.5.0 with 4260 resources (00:01.229 / 00:10.597, 113Mb) Sushi: info Attempting to download fhir.org.nz.ig.base#2.0.0 from https://packages.fhir.org/fhir.org.nz.ig.base/2.0.0 (00:00.000 / 00:10.598, 113Mb) Sushi: info Downloaded fhir.org.nz.ig.base#2.0.0 (00:00.903 / 00:11.501, 113Mb) Sushi: info Cached fhir.org.nz.ig.base#2.0.0 to /home/fhiruser/.fhir/packages/fhir.org.nz.ig.base#2.0.0 (00:00.001 / 00:11.503, 113Mb) Sushi: info Loaded fhir.org.nz.ig.base#2.0.0 with 106 resources (00:00.036 / 00:11.540, 113Mb) 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 / 00:11.540, 113Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.124 / 00:14.665, 113Mb) 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 / 00:14.666, 113Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.182 / 00:15.849, 113Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 1 resources (00:00.026 / 00:15.876, 113Mb) Sushi: info Converting FSH to FHIR resources... (00:00.018 / 00:15.895, 113Mb) Sushi: info Converted 27 FHIR StructureDefinitions. (00:04.694 / 00:20.589, 113Mb) Sushi: info Converted 37 FHIR CodeSystems. (00:00.722 / 00:21.311, 113Mb) Sushi: info Converted 31 FHIR ValueSets. (00:00.737 / 00:22.049, 113Mb) Sushi: info Converted 35 FHIR instances. (00:08.793 / 00:30.842, 113Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.161 / 00:31.003, 113Mb) Sushi: info Exported 130 FHIR resources as JSON. (00:00.220 / 00:31.223, 113Mb) Sushi: info Assembling Implementation Guide sources... (00:00.003 / 00:31.227, 113Mb) Sushi: info Generated ImplementationGuide-nz.central.ihub.ig.json (00:00.032 / 00:31.259, 113Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:31.260, 113Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:31.261, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:31.261, 113Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:31.261, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:31.262, 113Mb) Sushi: | | 9 | 18 | 0 | 0 | | (00:00.000 / 00:31.262, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:31.262, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:31.262, 113Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:31.262, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:31.263, 113Mb) Sushi: | | 31 | 37 | 35 | | (00:00.000 / 00:31.263, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:31.263, 113Mb) Sushi: | | (00:00.000 / 00:31.263, 113Mb) Sushi: =================================================================== (00:00.000 / 00:31.263, 113Mb) Sushi: | A whale of a job! 0 Errors 0 Warnings | (00:00.000 / 00:31.264, 113Mb) Sushi: =================================================================== (00:00.000 / 00:31.264, 113Mb) Root directory: /scratch/repo (00:00.035 / 00:31.300, 113Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.562 / 00:31.862, 38Mb) Load Template from tewhatuora-cr-template (00:00.471 / 00:32.333, 94Mb) Load Template from fhir.base.template#current (00:00.228 / 00:32.562, 102Mb) Installing fhir.base.template#current to the package cache  Fetching:  Installing fhir.base.template#current  done. Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:04.111 / 00:36.674, 407Mb) Core Package hl7.fhir.r4.core#4.0.1 (00:00.000 / 00:36.674, 407Mb) Running Terminology Log: /tmp/ohfu-fhir-ig-15403982573971870731.html Connect to Terminology Server at http://tx.fhir.org (00:29.327 / 01:06.002, 641Mb) 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.fhir.uv.extensions.r4#5.2.0 Load Package hl7.terminology.r4#5.5.0 Installing hl7.fhir.uv.tools#current to the package cache  Fetching:  Installing hl7.fhir.uv.tools#current  done. Installing hl7.terminology.r5#6.5.0 to the package cache  Fetching:  Installing hl7.terminology.r5#6.5.0  done. Version mismatch. This IG is for FHIR version 4.0.1, while the package 'hl7.fhir.uv.tools#current' is for FHIR version 5.0.0 (will ignore that and try to run anyway) (00:07.757 / 01:13.759, 917Mb) Load Package hl7.terminology.r5#6.5.0 Load Package hl7.fhir.uv.tools#current Installing hl7.terminology.r4#4.0.0 to the package cache  Fetching:  Installing hl7.terminology.r4#4.0.0  done. Load Package hl7.terminology.r4#4.0.0 Load Package fhir.org.nz.ig.base#2.0.0 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 (00:28.302 / 01:42.061, 740Mb) Load IG (00:00.000 / 01:42.061, 740Mb) Load Content (00:00.000 / 01:42.062, 740Mb) Using en_NZ as the default narrative language. (inferred from ImplementationGuide.jurisdiction=NZ) (00:00.136 / 01:42.199, 763Mb) Process Loaded Resources (00:01.432 / 01:43.631, 1019Mb) Generating Snapshots (00:01.033 / 01:44.665, 656Mb) 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 https://fhir-ig.digital.health.nz/crih/package-list.json for version check (00:01.850 / 01:46.515, 830Mb) Processing Conformance Resources (00:00.714 / 01:47.229, 844Mb) Checking Language (00:00.000 / 01:47.229, 844Mb) Load Dependency Info (00:00.003 / 01:47.232, 844Mb) Load Info (00:00.001 / 01:47.234, 844Mb) Load Paths (00:00.000 / 01:47.235, 846Mb) Check R4 / R4B (00:00.000 / 01:47.235, 846Mb) Assign Comparison Ids (00:00.098 / 01:47.334, 886Mb) Propagating status (00:00.000 / 01:47.334, 886Mb) Generating Narratives (00:00.000 / 01:47.335, 886Mb) Validating Conformance Resources (00:03.927 / 01:51.262, 707Mb) Check profiles & code systems (00:36.164 / 02:27.426, 1Gb) Check realm rules (00:00.011 / 02:27.438, 1Gb) Previous Version Comparison (00:00.000 / 02:27.438, 1Gb) Checking for Bundles to sign (00:00.071 / 02:27.510, 1Gb) Validating Resources (00:00.000 / 02:27.511, 1Gb) Processing Provenance Records (00:06.230 / 02:33.742, 2Gb) Generating Outputs in /scratch/repo/output (00:00.000 / 02:33.742, 2Gb) Generate Native Outputs (00:00.236 / 02:33.978, 2Gb) Run Template (00:24.169 / 02:58.147, 4Gb) Generate HTML Outputs (00:03.493 / 03:01.641, 4Gb) Generate Spreadsheets (00:34.607 / 03:36.248, 1Gb) Generate Summaries (00:06.190 / 03:42.439, 5Gb) Generating Summary Outputs (00:00.000 / 03:42.439, 5Gb) DB Cumulative Time invested: 00:00:30.245 Sending Usage Stats to Server (00:12.139 / 03:54.578, 6Gb) ## Memory (MB): Use = 6724, Free = 12283, Total = 19008, Max = 19008 (00:00.006 / 03:54.586, 6Gb) Reclaiming memory... (00:00.000 / 03:54.586, 6Gb) ## Memory (MB): Use = 828, Free = 18179, Total = 19008, Max = 19008 (00:00.729 / 03:55.315, 832Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 03:55.317, 832Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 03:55.317, 832Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 03:55.317, 832Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 03:55.317, 832Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.457 / 03:55.774, 848Mb) Jekyll: Generating... (00:00.000 / 03:55.775, 848Mb) Jekyll has failed. Complete output from running Jekyll:  Liquid Exception: Could not locate the included file 'StructureDefinition-NZCentralRegionAllergyIntolerance-maps-diff-all.xhtml' in any of ["/scratch/repo/temp/pages/_includes"]. Ensure it exists in one of those directories and, if it is a symlink, (00:01.654 / 03:57.429, 856Mb) Note: Check that Jekyll is installed correctly (00:00.000 / 03:57.429, 856Mb) Publishing Content Failed: Process exited with an error: 1 (Exit value: 1) (00:00.032 / 03:57.462, 864Mb) (00:00.000 / 03:57.462, 864Mb) Use -? to get command line help (00:00.000 / 03:57.462, 864Mb) (00:00.000 / 03:57.462, 864Mb) Stack Dump (for debugging): (00:00.000 / 03:57.462, 864Mb) 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:3678) at org.hl7.fhir.igtools.publisher.PublisherGenerator.runTool(PublisherGenerator.java:3565) at org.hl7.fhir.igtools.publisher.PublisherGenerator.generate(PublisherGenerator.java:360) at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:391) at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:218) at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:1482)