INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/tewhatuora/fhir-screening --branch master repo DEBUG:root:Time to deadline 35879.99808 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 35879.428213 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35877.048288 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 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 -> 11.5.2 npm notice Changelog: npm notice Run `npm install -g npm@11.5.2` 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/tewhatuora/fhir-screening/ -out /scratch/repo DEBUG:root:Time to deadline 35870.8958 seconds FHIR IG Publisher Version 2.0.13 (Git# bdf473444570). Built 2025-08-07T03:35:38.89Z (9 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/fhir-screening/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Saturday, August 16, 2025, 5:25:55 AM Coordinated Universal Time (2025-08-16T05:25:55Z) Build FHIR IG from /scratch/repo (00:00.027 / 00:00.027, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.003 / 00:00.030, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.033, 97Mb) Found dependency on fhir.org.nz.ig.base#3.0.0 in Sushi config. Pre-installing (00:00.005 / 00:00.039, 97Mb) Installing fhir.org.nz.ig.base#3.0.0 to the package cache  Fetching:  Installing fhir.org.nz.ig.base#3.0.0  done. Found dependency on hl7.fhir.uv.sdc#3.0.0 in Sushi config. Pre-installing (00:02.508 / 00:02.547, 64Mb) Installing hl7.fhir.uv.sdc#3.0.0 to the package cache  Fetching:  Installing hl7.fhir.uv.sdc#3.0.0  done. Found dependency on tewhatuora.digitaltooling#0.0.11 in Sushi config. Pre-installing (00:02.209 / 00:04.757, 96Mb) Installing tewhatuora.digitaltooling#0.0.11 to the package cache  Fetching:  Installing tewhatuora.digitaltooling#0.0.11  done. Run Sushi on /scratch/repo (00:01.249 / 00:06.007, 104Mb) Sushi: info Running SUSHI v3.16.3 (implements FHIR Shorthand specification v3.0.0) (00:00.671 / 00:06.678, 113Mb) Sushi: info Arguments: (00:00.000 / 00:06.678, 113Mb) Sushi: info --require-latest (00:00.000 / 00:06.679, 113Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:06.679, 113Mb) Sushi: info /scratch/repo (00:00.000 / 00:06.679, 113Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.654 / 00:07.334, 113Mb) Sushi: info Importing FSH text... (00:00.126 / 00:07.460, 113Mb) Sushi: info Preprocessed 29 documents with 26 aliases. (00:00.300 / 00:07.761, 113Mb) Sushi: info Imported 3 definitions and 27 instances. (00:00.090 / 00:07.851, 113Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.138 / 00:07.990, 113Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.8.0 (00:00.681 / 00:08.671, 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 (00:00.000 / 00:08.672, 113Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.8.0 (00:00.843 / 00:09.516, 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 (00:00.004 / 00:09.520, 113Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.8.0 with 110 resources (00:00.069 / 00:09.589, 113Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 6.5.0 (00:00.460 / 00:10.050, 113Mb) 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 / 00:10.050, 113Mb) Sushi: info Downloaded hl7.terminology.r4#6.5.0 (00:03.090 / 00:13.141, 120Mb) Sushi: info Cached hl7.terminology.r4#6.5.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#6.5.0 (00:00.003 / 00:13.145, 120Mb) Sushi: info Loaded hl7.terminology.r4#6.5.0 with 4392 resources (00:01.343 / 00:14.488, 120Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.464 / 00:14.952, 120Mb) 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 / 00:14.953, 120Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.675 / 00:16.629, 120Mb) 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 / 00:16.630, 120Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.268 / 00:16.898, 120Mb) Sushi: info Loaded fhir.org.nz.ig.base#3.0.0 with 106 resources (00:00.044 / 00:16.943, 120Mb) Sushi: info Loaded hl7.fhir.uv.sdc#3.0.0 with 105 resources (00:00.071 / 00:17.014, 120Mb) Sushi: info Loaded tewhatuora.digitaltooling#0.0.11 with 6 resources (00:00.006 / 00:17.021, 120Mb) 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 / 00:17.021, 120Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.376 / 00:20.397, 120Mb) 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 / 00:20.399, 120Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.352 / 00:21.752, 120Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.008 / 00:21.760, 120Mb) Sushi: info Converting FSH to FHIR resources... (00:00.024 / 00:21.785, 120Mb) Sushi: info Converted 1 FHIR StructureDefinitions. (00:00.215 / 00:22.001, 120Mb) Sushi: info Converted 2 FHIR ValueSets. (00:00.061 / 00:22.062, 120Mb) Sushi: info Converted 27 FHIR instances. (00:03.955 / 00:26.018, 120Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.000 / 00:26.019, 120Mb) Sushi: info Exported 25 FHIR resources as JSON. (00:00.023 / 00:26.042, 120Mb) Sushi: info Assembling Implementation Guide sources... (00:00.001 / 00:26.044, 120Mb) Sushi: info Generated ImplementationGuide-tewhatuora.fhir.screening.json (00:00.045 / 00:26.090, 120Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:26.090, 120Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:26.091, 120Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:26.091, 120Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:26.092, 120Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:26.092, 120Mb) Sushi: | | 1 | 0 | 0 | 0 | | (00:00.000 / 00:26.092, 120Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:26.092, 120Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:26.092, 120Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:26.093, 120Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:26.093, 120Mb) Sushi: | | 2 | 0 | 27 | | (00:00.001 / 00:26.094, 120Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:26.095, 120Mb) Sushi: | | (00:00.000 / 00:26.095, 120Mb) Sushi: =================================================================== (00:00.000 / 00:26.095, 120Mb) Sushi: | Fin-tastic job! 0 Errors 0 Warnings | (00:00.000 / 00:26.095, 120Mb) Sushi: =================================================================== (00:00.000 / 00:26.095, 120Mb) Root directory: /scratch/repo (00:00.028 / 00:26.124, 120Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.530 / 00:26.654, 56Mb) Load Template from ./tewhatuora.fhir.template (00:00.473 / 00:27.127, 57Mb) Load Template from fhir.base.template#current (00:00.069 / 00:27.197, 57Mb) 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 (00:03.778 / 00:30.976, 385Mb) Core Package hl7.fhir.r4.core#4.0.1 (00:00.000 / 00:30.976, 385Mb) Running Terminology Log: /tmp/ohfu-fhir-ig-16947706562150327745.html Connect to Terminology Server at http://tx.fhir.org (00:45.085 / 01:16.062, 942Mb) 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.extensions.r4#5.2.0 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#3.0.0 Ignore Dependency on Core FHIR hl7.fhir.r4.examples#4.0.1, from package 'hl7.fhir.uv.sdc#3.0.0' (00:42.903 / 01:58.966, 994Mb) Load Package hl7.fhir.uv.sdc#3.0.0 Installing hl7.fhir.uv.extensions.r4#5.1.0 to the package cache  Fetching:  Installing hl7.fhir.uv.extensions.r4#5.1.0  done. Load Package hl7.fhir.uv.extensions.r4#5.1.0 Installing hl7.terminology.r4#5.5.0 to the package cache  Fetching:  Installing hl7.terminology.r4#5.5.0  done. Load Package hl7.terminology.r4#5.5.0 Load Package tewhatuora.digitaltooling#0.0.11 Installing hl7.fhir.uv.tools.r4#0.7.1 to the package cache  Fetching:  Installing hl7.fhir.uv.tools.r4#0.7.1  done. Load Package hl7.fhir.uv.tools.r4#0.7.1 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 (00:09.573 / 02:08.539, 603Mb) Load IG (00:00.000 / 02:08.539, 603Mb) Load Content (00:00.000 / 02:08.540, 603Mb) Using en_NZ as the default narrative language. (inferred from ImplementationGuide.jurisdiction=NZ) (00:00.091 / 02:08.632, 611Mb) Process Loaded Resources (00:00.773 / 02:09.405, 660Mb) Generating Snapshots (00:00.254 / 02:09.659, 795Mb) loadPrePages from FetchedFile[/scratch/repo/fsh-generated/includes] as /scratch/repo/fsh-generated/includes loadPrePages from FetchedFile[/scratch/repo/input/pagecontent] as /scratch/repo/input/pagecontent 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/screening/package-list.json for version check (00:00.142 / 02:09.801, 819Mb) Processing Conformance Resources (00:00.655 / 02:10.457, 827Mb) Checking Language (00:00.000 / 02:10.457, 827Mb) Load Dependency Info (00:00.000 / 02:10.457, 827Mb) Load Info (00:00.000 / 02:10.458, 827Mb) Load Paths (00:00.000 / 02:10.459, 832Mb) Check R4 / R4B (00:00.000 / 02:10.459, 832Mb) Assign Comparison Ids (00:00.030 / 02:10.490, 840Mb) Propagating status (00:00.000 / 02:10.490, 840Mb) Generating Narratives (00:00.000 / 02:10.491, 840Mb) Validating Conformance Resources (00:00.673 / 02:11.164, 939Mb) Check profiles & code systems (00:10.938 / 02:22.103, 649Mb) Check realm rules (00:00.001 / 02:22.104, 649Mb) Previous Version Comparison (00:00.000 / 02:22.105, 649Mb) Checking for Bundles to sign (00:00.023 / 02:22.128, 649Mb) Validating Resources (00:00.000 / 02:22.129, 649Mb) Processing Provenance Records (00:01.815 / 02:23.944, 658Mb) Generating Outputs in /scratch/repo/output (00:00.000 / 02:23.944, 658Mb) Generate Native Outputs (00:00.324 / 02:24.268, 666Mb) Run Template (00:02.510 / 02:26.779, 1Gb) Generate HTML Outputs (00:02.971 / 02:29.751, 1Gb) Generate Spreadsheets (00:03.236 / 02:32.988, 2Gb) Generate Summaries (00:01.114 / 02:34.102, 2Gb) Generating Summary Outputs (00:00.000 / 02:34.102, 2Gb) DB Cumulative Time invested: 00:00:00.570 Sending Usage Stats to Server (00:12.795 / 02:46.898, 5Gb) ## Memory (MB): Use = 5530, Free = 13477, Total = 19008, Max = 19008 (00:00.007 / 02:46.905, 5Gb) Reclaiming memory... (00:00.000 / 02:46.905, 5Gb) ## Memory (MB): Use = 661, Free = 18346, Total = 19008, Max = 19008 (00:00.885 / 02:47.791, 669Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.003 / 02:47.794, 677Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 02:47.794, 677Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 02:47.795, 677Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 02:47.795, 677Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.432 / 02:48.227, 693Mb) Jekyll: Generating... (00:00.000 / 02:48.228, 693Mb) Jekyll: done in 1.587 seconds. (00:01.586 / 02:49.814, 693Mb) Checking Output HTML (00:01.409 / 02:51.223, 957Mb) found 810 files (00:00.004 / 02:51.228, 957Mb) ........................................ ........................................ ... 810 html files, 2 pages invalid xhtml (0%) (00:03.723 / 02:54.951, 4Gb) ... 24106 links, 4 broken links (0%) (00:00.000 / 02:54.952, 4Gb) Publishing Content Failed: The auto-build infrastructure does not publish IGs unless the publish-box is present (No Publish Box: sample-history-report.html, sample-participant-report.html, summary-fullreport.html and unable to Parse: summary-with-results.html). For further information, see note at http://wiki.hl7.org/index.php?title=FHIR_Implementation_Guide_Publishing_Requirements#HL7_HTML_Standards_considerations (00:00.013 / 02:54.965, 4Gb) (00:00.000 / 02:54.965, 4Gb) Use -? to get command line help (00:00.000 / 02:54.965, 4Gb) (00:00.000 / 02:54.965, 4Gb) Stack Dump (for debugging): (00:00.000 / 02:54.965, 4Gb) org.hl7.fhir.exceptions.FHIRException: The auto-build infrastructure does not publish IGs unless the publish-box is present (No Publish Box: sample-history-report.html, sample-participant-report.html, summary-fullreport.html and unable to Parse: summary-with-results.html). For further information, see note at http://wiki.hl7.org/index.php?title=FHIR_Implementation_Guide_Publishing_Requirements#HL7_HTML_Standards_considerations at org.hl7.fhir.igtools.publisher.Publisher.generate(Publisher.java:9073) at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:1196) at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:1026) at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:15790)