INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/genomics-reporting --branch master repo DEBUG:root:Time to deadline 35879.997886 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 35844.154071 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35843.134665 seconds 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. npm WARN deprecated rimraf@2.6.3: Rimraf versions prior to v4 are no longer supported 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 -> 11.6.2 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/genomics-reporting/ -out /scratch/repo DEBUG:root:Time to deadline 35836.624066 seconds FHIR IG Publisher Version 2.0.22 (Git# 6bbdf7dc5537). Built 2025-10-22T10:27:38.176Z (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/genomics-reporting/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Monday, October 27, 2025, 10:54:14 AM Coordinated Universal Time (2025-10-27T10:54:14Z) Build FHIR IG from /scratch/repo (00:00.027 / 00:00.028, 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 / 00:00.034, 97Mb) Run Sushi on /scratch/repo (00:00.008 / 00:00.043, 97Mb) Sushi: info Running SUSHI v3.16.5 (implements FHIR Shorthand specification v3.0.0) (00:00.757 / 00:00.800, 113Mb) Sushi: info Arguments: (00:00.000 / 00:00.801, 113Mb) Sushi: info --require-latest (00:00.000 / 00:00.801, 113Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.801, 113Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.802, 113Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.700 / 00:01.502, 113Mb) Sushi: info Importing FSH text... (00:00.171 / 00:01.674, 113Mb) Sushi: info Preprocessed 45 documents with 38 aliases. (00:01.988 / 00:03.662, 113Mb) Sushi: info Imported 77 definitions and 429 instances. (00:00.233 / 00:03.896, 113Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.153 / 00:04.049, 113Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.8.0 (00:00.613 / 00:04.662, 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 / 00:04.663, 113Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.8.0 (00:00.866 / 00:05.531, 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 (00:00.003 / 00:05.534, 113Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.8.0 with 110 resources (00:00.088 / 00:05.622, 113Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 6.5.0 (00:00.468 / 00:06.090, 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 / 00:06.091, 113Mb) Sushi: info Downloaded hl7.terminology.r4#6.5.0 (00:03.098 / 00:09.190, 113Mb) Sushi: info Cached hl7.terminology.r4#6.5.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#6.5.0 (00:00.001 / 00:09.192, 113Mb) Sushi: info Loaded hl7.terminology.r4#6.5.0 with 4392 resources (00:01.863 / 00:11.056, 113Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.437 / 00:11.493, 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 / 00:11.494, 113Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.521 / 00:13.016, 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 / 00:13.017, 113Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.349 / 00:13.367, 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 / 00:13.368, 113Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.565 / 00:16.934, 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 / 00:16.935, 113Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.770 / 00:18.706, 113Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.017 / 00:18.723, 113Mb) Sushi: info Converting FSH to FHIR resources... (00:00.027 / 00:18.750, 113Mb) Sushi: info Converted 44 FHIR StructureDefinitions. (00:10.119 / 00:28.870, 113Mb) Sushi: info Converted 13 FHIR CodeSystems. (00:00.283 / 00:29.153, 113Mb) Sushi: info Converted 20 FHIR ValueSets. (00:00.422 / 00:29.576, 113Mb) Sushi: info Converted 429 FHIR instances. (02:30.070 / 02:59.647, 113Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 02:59.648, 113Mb) Sushi: info Exported 301 FHIR resources as JSON. (00:00.323 / 02:59.971, 113Mb) Sushi: info Assembling Implementation Guide sources... (00:00.010 / 02:59.981, 113Mb) Sushi: info Generated ImplementationGuide-genomics-reporting.json (00:00.017 / 02:59.999, 113Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 02:59.999, 113Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.002 / 03:00.001, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 03:00.001, 113Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 03:00.002, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 03:00.002, 113Mb) Sushi: | | 19 | 25 | 0 | 0 | | (00:00.000 / 03:00.002, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 03:00.002, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 03:00.003, 113Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 03:00.003, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 03:00.003, 113Mb) Sushi: | | 20 | 13 | 429 | | (00:00.000 / 03:00.003, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 03:00.004, 113Mb) Sushi: | | (00:00.000 / 03:00.004, 113Mb) Sushi: =================================================================== (00:00.000 / 03:00.004, 113Mb) Sushi: | Why pun? Just for for the halibut. 0 Errors 0 Warnings | (00:00.000 / 03:00.004, 113Mb) Sushi: =================================================================== (00:00.000 / 03:00.005, 113Mb) Root directory: /scratch/repo (00:00.039 / 03:00.044, 113Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.828 / 03:00.873, 37Mb) Load Template from hl7.fhir.template (00:00.705 / 03:01.578, 94Mb) Installing hl7.fhir.template#1.0.0 to the package cache  Fetching:  Installing hl7.fhir.template#1.0.0  done.  Load Template from hl7.base.template#1.0.0 (00:01.394 / 03:02.972, 63Mb) Installing hl7.base.template#1.0.0 to the package cache  Fetching:  Installing hl7.base.template#1.0.0  done.  Load Template from fhir.base.template#1.0.0 (00:00.384 / 03:03.357, 71Mb) Installing fhir.base.template#1.0.0 to the package cache  Fetching:  Installing fhir.base.template#1.0.0  done. Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:05.804 / 03:09.161, 383Mb) Core Package hl7.fhir.r4.core#4.0.1 (00:00.000 / 03:09.162, 383Mb) Running Terminology Log: /tmp/ohfu-fhir-ig-3252239117406491883.html Connect to Terminology Server at http://tx.fhir.org (00:32.963 / 03:42.126, 599Mb) 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 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 (00:10.660 / 03:52.786, 330Mb) Load IG (00:00.000 / 03:52.786, 330Mb) Load Content (00:00.000 / 03:52.787, 330Mb) Using en-US as the default narrative language. (no language information in Implementation Guide) (00:00.146 / 03:52.933, 352Mb) Process Loaded Resources (00:03.292 / 03:56.226, 776Mb) Generating Snapshots (00:02.471 / 03:58.698, 762Mb) 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/genomics-reporting/package-list.json for version check (00:02.431 / 04:01.129, 834Mb) Processing Conformance Resources (00:00.186 / 04:01.316, 850Mb) Checking Language (00:00.000 / 04:01.316, 850Mb) Load Dependency Info (00:00.005 / 04:01.322, 858Mb) Load Info (00:00.002 / 04:01.324, 858Mb) Load Paths (00:00.001 / 04:01.326, 861Mb) Check R4 / R4B (00:00.001 / 04:01.327, 861Mb) Assign Comparison Ids (00:00.266 / 04:01.593, 922Mb) Propagating status (00:00.000 / 04:01.594, 922Mb) Generating Narratives (00:00.173 / 04:01.768, 1002Mb) Validating Conformance Resources (00:43.550 / 04:45.318, 1Gb) Check profiles & code systems (00:29.057 / 05:14.375, 1Gb) Check realm rules (00:00.010 / 05:14.386, 1Gb) Previous Version Comparison (00:00.000 / 05:14.386, 1Gb) Installing hl7.fhir.uv.genomics-reporting#3.0.0 to the package cache  Fetching:  Installing hl7.fhir.uv.genomics-reporting#3.0.0  done. Installing hl7.terminology.r4#6.1.0 to the package cache  Fetching:  Installing hl7.terminology.r4#6.1.0  done. Installing hl7.fhir.uv.extensions.r4#5.1.0 to the package cache  Fetching:  Installing hl7.fhir.uv.extensions.r4#5.1.0  done. Checking for Bundles to sign (00:17.497 / 05:31.884, 1Gb) Validating Resources (00:00.000 / 05:31.884, 1Gb) Processing Provenance Records (02:41.950 / 08:13.835, 5Gb) Generating Outputs in /scratch/repo/output (00:00.000 / 08:13.836, 5Gb) Generate Native Outputs (00:00.375 / 08:14.212, 5Gb) Run Template (00:22.632 / 08:36.844, 1Gb) Generate HTML Outputs (00:03.569 / 08:40.414, 1Gb) Generate Spreadsheets (01:01.307 / 09:41.721, 1Gb) Generate Summaries (00:09.958 / 09:51.679, 4Gb) Generating Summary Outputs (00:00.000 / 09:51.680, 4Gb) Table of contents has a section with more than 222 entries. Collapsing will not work reliably DB Cumulative Time invested: 00:00:05.247 Sending Usage Stats to Server (00:16.369 / 10:08.049, 7Gb) ## Memory (MB): Use = 7180, Free = 11827, Total = 19008, Max = 19008 (00:00.014 / 10:08.063, 7Gb) Reclaiming memory... (00:00.000 / 10:08.063, 7Gb) ## Memory (MB): Use = 1067, Free = 17940, Total = 19008, Max = 19008 (00:01.472 / 10:09.536, 1Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.002 / 10:09.538, 1Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 10:09.538, 1Gb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 10:09.538, 1Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 10:09.538, 1Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.589 / 10:10.128, 1Gb) Jekyll: Generating... (00:00.000 / 10:10.128, 1Gb) Jekyll: done in 9.709 seconds. (00:09.708 / 10:19.836, 1Gb) Checking Output HTML (00:06.773 / 10:26.610, 4Gb) Processed /scratch/repo/output - % reduction = 98 (171879799 ==> 3623273) found 3768 files (00:06.275 / 10:32.885, 9Gb) ........................................ ........................................ ... 3768 html files, 0 pages invalid xhtml (0%) (01:35.234 / 12:08.120, 7Gb) ... 791921 links, 0 broken links (0%) (00:00.000 / 12:08.120, 7Gb) Generate fragment-usage-analysis.csv (00:00.000 / 12:08.120, 7Gb) Build final .zip (00:00.011 / 12:08.132, 7Gb) Final .zip built (00:06.813 / 12:14.945, 7Gb) Built. Times: loading: 00:08.529, generate: 08:17.130, propagating status: 00:00.173, narrative generation: 00:43.549, realm-rules: 00:00.000, previous-version: 00:17.429, jekyll: 00:10.366, validation: 03:10.082 (#302), template: 00:03.578 (#3) (00:03.501 / 12:18.447, 8Gb) Generating QA (00:00.000 / 12:18.447, 8Gb) Validation output in /scratch/repo/output/qa.html Errors: 1, Warnings: 36, Info: 17, Broken Links: 0 (00:00.739 / 12:19.187, 8Gb) Finished @ 10/27/25, 11:06 AM. Max Memory Used = 9Gb (00:00.060 / 12:19.247, 8Gb)