INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/bser --branch master repo DEBUG:root:Time to deadline 35879.997977 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 35878.628186 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35877.508881 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 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 -> 11.3.0 npm notice Changelog: npm notice Run `npm install -g npm@11.3.0` 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/HL7/bser/ -out /scratch/repo DEBUG:root:Time to deadline 35870.858147 seconds FHIR IG Publisher Version 1.8.23 (Git# ffc7678c1988). Built 2025-04-04T22:01:54.432Z (3 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/bser/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Tuesday, April 8, 2025, 9:07:31 PM Coordinated Universal Time (2025-04-08T21:07:31Z) Build FHIR IG from /scratch/repo (00:00.031 / 00:00.032, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.002 / 00:00.035, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.038, 97Mb) Run Sushi on /scratch/repo (00:00.005 / 00:00.043, 97Mb) Sushi: info Running SUSHI v3.15.0 (implements FHIR Shorthand specification v3.0.0) (00:00.731 / 00:00.775, 113Mb) Sushi: info Arguments: (00:00.000 / 00:00.775, 113Mb) Sushi: info --require-latest (00:00.000 / 00:00.776, 113Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.776, 113Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.776, 113Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.733 / 00:01.510, 113Mb) Sushi: info Importing FSH text... (00:00.166 / 00:01.676, 113Mb) Sushi: info Preprocessed 101 documents with 41 aliases. (00:00.537 / 00:02.214, 113Mb) Sushi: info Imported 20 definitions and 80 instances. (00:00.069 / 00:02.283, 113Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.204 / 00:02.487, 113Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.4.1 (00:00.590 / 00:03.078, 113Mb) Sushi: info Attempting to download hl7.fhir.uv.tools.r4#0.4.1 from https://packages.fhir.org/hl7.fhir.uv.tools.r4/0.4.1 (00:00.001 / 00:03.079, 113Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.4.1 (00:00.766 / 00:03.845, 113Mb) Sushi: info Cached hl7.fhir.uv.tools.r4#0.4.1 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.tools.r4#0.4.1 (00:00.003 / 00:03.848, 113Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.4.1 with 86 resources (00:00.067 / 00:03.916, 113Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 6.2.0 (00:00.480 / 00:04.397, 113Mb) Sushi: info Attempting to download hl7.terminology.r4#6.2.0 from https://packages.fhir.org/hl7.terminology.r4/6.2.0 (00:00.000 / 00:04.397, 113Mb) Sushi: info Downloaded hl7.terminology.r4#6.2.0 (00:02.589 / 00:06.987, 113Mb) Sushi: info Cached hl7.terminology.r4#6.2.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#6.2.0 (00:00.001 / 00:06.988, 113Mb) Sushi: info Loaded hl7.terminology.r4#6.2.0 with 4323 resources (00:01.793 / 00:08.782, 113Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.474 / 00:09.256, 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 / 00:09.257, 113Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.391 / 00:10.649, 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 / 00:10.650, 113Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.350 / 00:11.001, 113Mb) Sushi: info Attempting to download us.cdc.phinvads#0.12.0 from https://packages.fhir.org/us.cdc.phinvads/0.12.0 (00:00.000 / 00:11.001, 113Mb) Sushi: info Downloaded us.cdc.phinvads#0.12.0 (00:03.627 / 00:14.629, 113Mb) Sushi: info Cached us.cdc.phinvads#0.12.0 to /home/fhiruser/.fhir/packages/us.cdc.phinvads#0.12.0 (00:00.001 / 00:14.630, 113Mb) Sushi: info Loaded us.cdc.phinvads#0.12.0 with 1967 resources (00:02.643 / 00:17.274, 113Mb) Sushi: info Attempting to download us.nlm.vsac#0.11.0 from https://packages.fhir.org/us.nlm.vsac/0.11.0 (00:00.000 / 00:17.275, 113Mb) Sushi: info Downloaded us.nlm.vsac#0.11.0 (00:06.632 / 00:23.907, 113Mb) Sushi: info Cached us.nlm.vsac#0.11.0 to /home/fhiruser/.fhir/packages/us.nlm.vsac#0.11.0 (00:00.001 / 00:23.909, 113Mb) Sushi: info Loaded us.nlm.vsac#0.11.0 with 14323 resources (00:06.687 / 00:30.596, 113Mb) Sushi: info Attempting to download hl7.fhir.us.core#5.0.1 from https://packages.fhir.org/hl7.fhir.us.core/5.0.1 (00:00.001 / 00:30.597, 113Mb) Sushi: info Downloaded hl7.fhir.us.core#5.0.1 (00:01.592 / 00:32.189, 113Mb) Sushi: info Cached hl7.fhir.us.core#5.0.1 to /home/fhiruser/.fhir/packages/hl7.fhir.us.core#5.0.1 (00:00.002 / 00:32.192, 113Mb) Sushi: info Loaded hl7.fhir.us.core#5.0.1 with 194 resources (00:00.135 / 00:32.327, 113Mb) Sushi: info Attempting to download hl7.fhir.us.odh#1.3.0 from https://packages.fhir.org/hl7.fhir.us.odh/1.3.0 (00:00.000 / 00:32.328, 113Mb) Sushi: info Downloaded hl7.fhir.us.odh#1.3.0 (00:00.898 / 00:33.227, 113Mb) Sushi: info Cached hl7.fhir.us.odh#1.3.0 to /home/fhiruser/.fhir/packages/hl7.fhir.us.odh#1.3.0 (00:00.001 / 00:33.228, 113Mb) Sushi: info Loaded hl7.fhir.us.odh#1.3.0 with 10 resources (00:00.025 / 00:33.253, 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 / 00:33.254, 113Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:02.870 / 00:36.124, 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 / 00:36.126, 113Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.645 / 00:37.772, 113Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.017 / 00:37.789, 113Mb) Sushi: info Converting FSH to FHIR resources... (00:00.052 / 00:37.841, 113Mb) Sushi: info Converted 17 FHIR StructureDefinitions. (00:05.107 / 00:42.949, 113Mb) Sushi: info Converted 2 FHIR CodeSystems. (00:00.165 / 00:43.115, 113Mb) Sushi: info Converted 1 FHIR ValueSets. (00:00.058 / 00:43.173, 113Mb) Sushi: info Converted 80 FHIR instances. (00:11.542 / 00:54.716, 113Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 00:54.717, 113Mb) Sushi: info Exported 100 FHIR resources as JSON. (00:00.155 / 00:54.873, 113Mb) Sushi: info Assembling Implementation Guide sources... (00:00.005 / 00:54.878, 113Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.us.bser.json (00:00.051 / 00:54.930, 113Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:54.930, 113Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:54.932, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:54.932, 113Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:54.933, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:54.933, 113Mb) Sushi: | | 16 | 1 | 0 | 0 | | (00:00.000 / 00:54.933, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:54.933, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:54.933, 113Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:54.934, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:54.934, 113Mb) Sushi: | | 1 | 2 | 80 | | (00:00.000 / 00:54.934, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:54.934, 113Mb) Sushi: | | (00:00.000 / 00:54.935, 113Mb) Sushi: =================================================================== (00:00.000 / 00:54.935, 113Mb) Sushi: | Fin-tastic job! 0 Errors 0 Warnings | (00:00.000 / 00:54.935, 113Mb) Sushi: =================================================================== (00:00.000 / 00:54.935, 113Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.876 / 00:55.811, 37Mb) Load Template from hl7.fhir.template#current (00:00.717 / 00:56.529, 93Mb) Installing hl7.fhir.template#current to the package cache Fetching: Installing hl7.fhir.template#current done. Load Template from hl7.base.template#current (00:01.432 / 00:57.961, 103Mb) Installing hl7.base.template#current to the package cache Fetching: Installing hl7.base.template#current done. Load Template from fhir.base.template#current (00:00.212 / 00:58.173, 111Mb) Installing fhir.base.template#current to the package cache Fetching: Installing fhir.base.template#current done. Root directory: /scratch/repo (00:05.114 / 01:03.288, 399Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.002 / 01:03.291, 399Mb) Core Package hl7.fhir.r4.core#4.0.1 Running Terminology Log: /tmp/ohfu-fhir-ig-2522826191511887184.log Connect to Terminology Server at http://tx.fhir.org (00:32.489 / 01:35.781, 256Mb) Installing hl7.fhir.pubpack#0.2.1 to the package cache Fetching: Installing hl7.fhir.pubpack#0.2.1 done. Load Package hl7.fhir.pubpack#0.2.1 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#6.2.0 Load Package hl7.fhir.uv.extensions.r4#5.2.0 Load Package us.cdc.phinvads#0.12.0 Load Package us.nlm.vsac#0.11.0 Installing hl7.terminology.r4#3.1.0 to the package cache Fetching: Installing hl7.terminology.r4#3.1.0 done. Load Package hl7.terminology.r4#3.1.0 Installing hl7.fhir.uv.bulkdata#2.0.0 to the package cache Fetching: Installing hl7.fhir.uv.bulkdata#2.0.0 done. Load Package hl7.fhir.uv.bulkdata#2.0.0 Installing hl7.fhir.uv.smart-app-launch#2.0.0 to the package cache Fetching: Installing hl7.fhir.uv.smart-app-launch#2.0.0 done. Load Package hl7.fhir.uv.smart-app-launch#2.0.0 Installing us.nlm.vsac#0.7.0 to the package cache Fetching: Installing us.nlm.vsac#0.7.0 done. Load Package us.nlm.vsac#0.7.0 Installing hl7.fhir.uv.sdc#3.0.0 to the package cache Fetching: Installing hl7.fhir.uv.sdc#3.0.0 done. Ignore Dependency on Core FHIR hl7.fhir.r4.examples#4.0.1, from package 'hl7.fhir.uv.sdc#3.0.0' (02:10.346 / 03:46.127, 998Mb) Load Package hl7.fhir.uv.sdc#3.0.0 Load Package hl7.fhir.us.core#5.0.1 Installing hl7.terminology.r4#5.0.0 to the package cache Fetching: Installing hl7.terminology.r4#5.0.0 done. Load Package hl7.terminology.r4#5.0.0 Load Package hl7.fhir.us.odh#1.3.0 Load Package hl7.fhir.uv.tools.r4#0.4.1 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 (00:34.841 / 04:20.969, 718Mb) Load Content (00:00.000 / 04:20.969, 718Mb) Using en-US as the default narrative language. (no language information in Implementation Guide) (00:00.128 / 04:21.098, 726Mb) Process Loaded Resources (00:01.538 / 04:22.636, 846Mb) Generating Snapshots (00:00.434 / 04:23.071, 918Mb) 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 Fetch http://hl7.org/fhir/us/bser/package-list.json for version check (00:02.328 / 04:25.400, 715Mb) Processing Conformance Resources (00:00.170 / 04:25.572, 723Mb) Checking Language (00:00.001 / 04:25.572, 723Mb) Load Dependency Info (00:00.013 / 04:25.586, 723Mb) Load Info (00:00.002 / 04:25.588, 723Mb) Load Paths (00:00.000 / 04:25.589, 723Mb) Check R4 / R4B (00:00.000 / 04:25.590, 723Mb) Assign Comparison Ids (00:00.064 / 04:25.654, 731Mb) Propagating status (00:00.000 / 04:25.655, 731Mb) Generating Narratives (00:00.000 / 04:25.655, 731Mb) Validating Conformance Resources (00:03.732 / 04:29.388, 1Gb) Check profiles & code systems (00:28.325 / 04:57.714, 1Gb) Check realm rules (00:00.003 / 04:57.718, 1Gb) Installing hl7.fhir.us.core#8.0.0-ballot to the package cache Fetching: Installing hl7.fhir.us.core#8.0.0-ballot done. US Core Comparisons Finished Previous Version Comparison (00:06.852 / 05:04.571, 1Gb) Validating Resources (00:00.039 / 05:04.610, 1Gb) Processing Provenance Records (00:25.820 / 05:30.430, 992Mb) Generating Outputs in /scratch/repo/output (00:00.000 / 05:30.430, 992Mb) Generate Native Outputs (00:00.261 / 05:30.692, 1009Mb) Run Template (00:08.453 / 05:39.146, 1Gb) Generate HTML Outputs (00:03.021 / 05:42.168, 2Gb) Generate Spreadsheets (00:57.376 / 06:39.544, 3Gb) Generate Summaries (00:06.554 / 06:46.099, 4Gb) Generating Summary Outputs (00:00.000 / 06:46.099, 4Gb) DB Cumulative Time invested: 00:00:01.125 Sending Usage Stats to Server (00:15.218 / 07:01.317, 4Gb) ## Memory (MB): Use = 4328, Free = 14679, Total = 19008, Max = 19008 (00:00.008 / 07:01.326, 4Gb) Reclaiming memory... (00:00.000 / 07:01.326, 4Gb) ## Memory (MB): Use = 3247, Free = 15760, Total = 19008, Max = 19008 (00:03.125 / 07:04.451, 3Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.002 / 07:04.453, 3Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 07:04.453, 3Gb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 07:04.453, 3Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 07:04.453, 3Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.565 / 07:05.019, 3Gb) Jekyll: Generating... (00:00.000 / 07:05.019, 3Gb) Jekyll: done in 3.652 seconds. (00:03.651 / 07:08.670, 3Gb) Checking Output HTML (00:04.265 / 07:12.936, 4Gb) found 1600 files (00:00.013 / 07:12.949, 4Gb) ....................................... ....................................... ... 1600 html files, 0 pages invalid xhtml (0%) (00:30.418 / 07:43.367, 11Gb) ... 316326 links, 102 broken links (0%) (00:00.000 / 07:43.368, 11Gb) Generate fragment-usage-analysis.csv (00:00.000 / 07:43.368, 11Gb) Build final .zip (00:00.009 / 07:43.377, 11Gb) Final .zip built (00:03.910 / 07:47.288, 11Gb) Installing hl7.fhir.r4.examples#4.0.1 to the package cache Fetching: Installing hl7.fhir.r4.examples#4.0.1 done. Built. Times: loading: 00:04.600, generate: 04:14.793, narrative generation: 00:03.732, realm-rules: 00:06.852, previous-version: 00:00.000, jekyll: 00:04.245, validation: 00:53.915 (#101), template: 00:03.031 (#3) (00:53.166 / 08:40.454, 13Gb) Generating QA (00:00.000 / 08:40.454, 13Gb) Sending usage stats failed: Connection timed out Validation output in /scratch/repo/output/qa.html Errors: 211, Warnings: 164, Info: 150, Broken Links: 102 (00:42.159 / 09:22.614, 13Gb) Finished. Max Memory Used = 13Gb (00:00.018 / 09:22.633, 13Gb)