INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/tewhatuora/fhir-screening --branch uat repo DEBUG:root:Time to deadline 35879.997341 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 35879.426361 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35878.35336 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 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 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 35872.348011 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, 5:29:18 AM Coordinated Universal Time (2025-08-16T05:29:18Z) Build FHIR IG from /scratch/repo (00:00.029 / 00:00.029, 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 / 00:00.035, 97Mb) Found dependency on fhir.org.nz.ig.base#3.0.0 in Sushi config. Pre-installing (00:00.004 / 00:00.040, 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 (00:02.884 / 00:02.924, 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 (00:02.421 / 00:05.345, 96Mb) Installing tewhatuora.digitaltooling#0.0.11 to the package cache  Fetching:  Installing tewhatuora.digitaltooling#0.0.11  done. Run Sushi on /scratch/repo (00:00.434 / 00:05.779, 104Mb) Sushi: info Running SUSHI v3.16.3 (implements FHIR Shorthand specification v3.0.0) (00:00.667 / 00:06.447, 120Mb) Sushi: info Arguments: (00:00.000 / 00:06.447, 120Mb) Sushi: info --require-latest (00:00.000 / 00:06.447, 120Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:06.448, 120Mb) Sushi: info /scratch/repo (00:00.000 / 00:06.448, 120Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.836 / 00:07.285, 120Mb) Sushi: info Importing FSH text... (00:00.126 / 00:07.411, 120Mb) Sushi: info Preprocessed 29 documents with 26 aliases. (00:00.312 / 00:07.724, 120Mb) Sushi: info Imported 3 definitions and 27 instances. (00:00.097 / 00:07.822, 120Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.139 / 00:07.961, 120Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.8.0 (00:00.655 / 00:08.617, 120Mb) 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 / 00:08.619, 120Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.8.0 (00:00.834 / 00:09.453, 120Mb) Sushi: info Cached hl7.fhir.uv.tools.r4#0.8.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.tools.r4#0.8.0 (00:00.005 / 00:09.459, 120Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.8.0 with 110 resources (00:00.065 / 00:09.525, 120Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 6.5.0 (00:00.475 / 00:10.001, 120Mb) 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 / 00:10.002, 120Mb) Sushi: info Downloaded hl7.terminology.r4#6.5.0 (00:02.952 / 00:12.954, 120Mb) Sushi: info Cached hl7.terminology.r4#6.5.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#6.5.0 (00:00.001 / 00:12.956, 120Mb) Sushi: info Loaded hl7.terminology.r4#6.5.0 with 4392 resources (00:01.322 / 00:14.279, 120Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.455 / 00:14.734, 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 / 00:14.735, 120Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.597 / 00:16.332, 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 / 00:16.333, 120Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.338 / 00:16.672, 120Mb) Sushi: info Loaded fhir.org.nz.ig.base#3.0.0 with 106 resources (00:00.040 / 00:16.712, 120Mb) Sushi: info Loaded hl7.fhir.uv.sdc#3.0.0 with 105 resources (00:00.054 / 00:16.766, 120Mb) Sushi: info Loaded tewhatuora.digitaltooling#0.0.11 with 6 resources (00:00.004 / 00:16.771, 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 / 00:16.771, 120Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.245 / 00:20.017, 120Mb) Sushi: info Cached hl7.fhir.r4.core#4.0.1 to /home/fhiruser/.fhir/packages/hl7.fhir.r4.core#4.0.1 (00:00.003 / 00:20.020, 120Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.213 / 00:21.234, 120Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.015 / 00:21.249, 120Mb) Sushi: info Converting FSH to FHIR resources... (00:00.021 / 00:21.270, 120Mb) Sushi: info Converted 1 FHIR StructureDefinitions. (00:00.228 / 00:21.499, 120Mb) Sushi: info Converted 2 FHIR ValueSets. (00:00.068 / 00:21.567, 120Mb) Sushi: info Converted 27 FHIR instances. (00:04.096 / 00:25.663, 120Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.000 / 00:25.663, 120Mb) Sushi: info Exported 25 FHIR resources as JSON. (00:00.021 / 00:25.685, 120Mb) Sushi: info Assembling Implementation Guide sources... (00:00.001 / 00:25.687, 120Mb) Sushi: info Generated ImplementationGuide-tewhatuora.fhir.screening.json (00:00.046 / 00:25.733, 120Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:25.733, 120Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:25.735, 120Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:25.735, 120Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:25.735, 120Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:25.735, 120Mb) Sushi: | | 1 | 0 | 0 | 0 | | (00:00.000 / 00:25.735, 120Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:25.735, 120Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:25.736, 120Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:25.736, 120Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:25.736, 120Mb) Sushi: | | 2 | 0 | 27 | | (00:00.000 / 00:25.736, 120Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:25.736, 120Mb) Sushi: | | (00:00.000 / 00:25.737, 120Mb) Sushi: =================================================================== (00:00.000 / 00:25.737, 120Mb) Sushi: | A whale of a job! 0 Errors 0 Warnings | (00:00.000 / 00:25.737, 120Mb) Sushi: =================================================================== (00:00.000 / 00:25.737, 120Mb) Root directory: /scratch/repo (00:00.028 / 00:25.765, 120Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.601 / 00:26.366, 56Mb) Load Template from ./tewhatuora.fhir.template (00:00.548 / 00:26.915, 57Mb) Load Template from fhir.base.template#current (00:00.089 / 00:27.005, 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 (00:04.578 / 00:31.583, 385Mb) Core Package hl7.fhir.r4.core#4.0.1 (00:00.000 / 00:31.583, 385Mb) Running Terminology Log: /tmp/ohfu-fhir-ig-18145241942357630556.html Connect to Terminology Server at http://tx.fhir.org (00:47.646 / 01:19.230, 792Mb) 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' (00:43.948 / 02:03.178, 856Mb) 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 (00:09.921 / 02:13.100, 483Mb) Load IG (00:00.000 / 02:13.100, 483Mb) Load Content (00:00.000 / 02:13.101, 483Mb) Using en_NZ as the default narrative language. (inferred from ImplementationGuide.jurisdiction=NZ) (00:00.094 / 02:13.196, 491Mb) Process Loaded Resources (00:00.759 / 02:13.955, 547Mb) Generating Snapshots (00:00.293 / 02:14.249, 675Mb) 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 (00:00.162 / 02:14.411, 699Mb) Processing Conformance Resources (00:01.168 / 02:15.580, 707Mb) Checking Language (00:00.000 / 02:15.580, 707Mb) Load Dependency Info (00:00.000 / 02:15.581, 707Mb) Load Info (00:00.001 / 02:15.583, 707Mb) Load Paths (00:00.000 / 02:15.583, 713Mb) Check R4 / R4B (00:00.000 / 02:15.583, 713Mb) Assign Comparison Ids (00:00.034 / 02:15.618, 713Mb) Propagating status (00:00.000 / 02:15.618, 713Mb) Generating Narratives (00:00.000 / 02:15.618, 713Mb) Validating Conformance Resources (00:00.849 / 02:16.468, 819Mb) Check profiles & code systems (00:10.697 / 02:27.166, 636Mb) Check realm rules (00:00.001 / 02:27.167, 636Mb) Previous Version Comparison (00:00.000 / 02:27.167, 636Mb) Checking for Bundles to sign (00:00.019 / 02:27.186, 636Mb) Validating Resources (00:00.000 / 02:27.187, 636Mb) Processing Provenance Records (00:01.955 / 02:29.143, 539Mb) Generating Outputs in /scratch/repo/output (00:00.000 / 02:29.143, 539Mb) Generate Native Outputs (00:00.290 / 02:29.433, 548Mb) Run Template (00:02.573 / 02:32.007, 1003Mb) Generate HTML Outputs (00:02.986 / 02:34.993, 1Gb) Generate Spreadsheets (00:03.351 / 02:38.345, 1Gb) Generate Summaries (00:01.105 / 02:39.450, 2Gb) Generating Summary Outputs (00:00.000 / 02:39.450, 2Gb) DB Cumulative Time invested: 00:00:00.652 Sending Usage Stats to Server (00:13.185 / 02:52.635, 5Gb) ## Memory (MB): Use = 5427, Free = 13580, Total = 19008, Max = 19008 (00:00.007 / 02:52.642, 5Gb) Reclaiming memory... (00:00.000 / 02:52.643, 5Gb) ## Memory (MB): Use = 660, Free = 18347, Total = 19008, Max = 19008 (00:00.915 / 02:53.559, 676Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.002 / 02:53.561, 676Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 02:53.561, 676Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 02:53.561, 676Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 02:53.561, 676Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.434 / 02:53.995, 692Mb) Jekyll: Generating... (00:00.000 / 02:53.996, 692Mb) Jekyll: done in 1.485 seconds. (00:01.484 / 02:55.480, 700Mb) Checking Output HTML (00:01.272 / 02:56.753, 964Mb) found 810 files (00:00.005 / 02:56.758, 964Mb) ........................................ ........................................ ... 810 html files, 2 pages invalid xhtml (0%) (00:03.379 / 03:00.138, 4Gb) ... 24106 links, 4 broken links (0%) (00:00.000 / 03:00.138, 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 (00:00.021 / 03:00.159, 4Gb) (00:00.000 / 03:00.159, 4Gb) Use -? to get command line help (00:00.000 / 03:00.160, 4Gb) (00:00.000 / 03:00.160, 4Gb) Stack Dump (for debugging): (00:00.000 / 03:00.160, 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)