INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/codex-radiation-therapy --branch master repo DEBUG:root:Time to deadline 35879.997856 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 35878.827277 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35877.256555 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 177 packages in 8s 28 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 11.1.0 npm notice Changelog: npm notice Run `npm install -g npm@11.1.0` 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/codex-radiation-therapy/ -out /scratch/repo DEBUG:root:Time to deadline 35869.156839 seconds FHIR IG Publisher Version 1.8.13 (Git# e89cdedc7f58). Built 2025-02-17T04:21:57.376Z (13 hours 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/codex-radiation-therapy/ -out /scratch/repo Start Clock @ Monday, February 17, 2025, 5:31:36 PM Coordinated Universal Time (2025-02-17T17:31:36Z) Build FHIR IG from /scratch/repo (00:00.028 / 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 / 00:00.034, 97Mb) Run Sushi on /scratch/repo (00:00.004 / 00:00.039, 97Mb) Sushi: info Running SUSHI v3.14.0 (implements FHIR Shorthand specification v3.0.0) (00:00.715 / 00:00.754, 113Mb) Sushi: info Arguments: (00:00.000 / 00:00.754, 113Mb) Sushi: info --require-latest (00:00.000 / 00:00.755, 113Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.755, 113Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.755, 113Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.760 / 00:01.516, 113Mb) Sushi: info Importing FSH text... (00:00.158 / 00:01.675, 113Mb) Sushi: info Preprocessed 62 documents with 58 aliases. (00:00.892 / 00:02.567, 113Mb) Sushi: info Imported 53 definitions and 113 instances. (00:00.280 / 00:02.848, 113Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.138 / 00:02.986, 113Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.3.0 (00:00.618 / 00:03.604, 113Mb) Sushi: info Attempting to download hl7.fhir.uv.tools.r4#0.3.0 from https://packages.fhir.org/hl7.fhir.uv.tools.r4/0.3.0 (00:00.001 / 00:03.605, 113Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.3.0 (00:01.056 / 00:04.662, 113Mb) Sushi: info Cached hl7.fhir.uv.tools.r4#0.3.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.tools.r4#0.3.0 (00:00.002 / 00:04.665, 113Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.3.0 with 75 resources (00:00.068 / 00:04.733, 113Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 6.2.0 (00:00.448 / 00:05.181, 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 / 00:05.182, 113Mb) Sushi: info Downloaded hl7.terminology.r4#6.2.0 (00:02.864 / 00:08.046, 113Mb) Sushi: info Cached hl7.terminology.r4#6.2.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#6.2.0 (00:00.001 / 00:08.048, 113Mb) Sushi: info Loaded hl7.terminology.r4#6.2.0 with 4323 resources (00:01.840 / 00:09.888, 113Mb) Sushi: info Attempting to download hl7.fhir.uv.extensions.r4#5.1.0 from https://packages.fhir.org/hl7.fhir.uv.extensions.r4/5.1.0 (00:00.001 / 00:09.890, 113Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.1.0 (00:02.227 / 00:12.117, 113Mb) Sushi: info Cached hl7.fhir.uv.extensions.r4#5.1.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.extensions.r4#5.1.0 (00:00.002 / 00:12.119, 113Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.1.0 with 1397 resources (00:00.684 / 00:12.804, 113Mb) Sushi: info Attempting to download hl7.fhir.us.core#6.1.0 from https://packages.fhir.org/hl7.fhir.us.core/6.1.0 (00:00.001 / 00:12.806, 113Mb) Sushi: info Downloaded hl7.fhir.us.core#6.1.0 (00:01.633 / 00:14.439, 113Mb) Sushi: info Cached hl7.fhir.us.core#6.1.0 to /home/fhiruser/.fhir/packages/hl7.fhir.us.core#6.1.0 (00:00.001 / 00:14.440, 113Mb) Sushi: info Loaded hl7.fhir.us.core#6.1.0 with 210 resources (00:00.134 / 00:14.574, 113Mb) Sushi: info Attempting to download hl7.fhir.us.mcode#4.0.0 from https://packages.fhir.org/hl7.fhir.us.mcode/4.0.0 (00:00.000 / 00:14.574, 113Mb) Sushi: info Downloaded hl7.fhir.us.mcode#4.0.0 (00:01.357 / 00:15.932, 113Mb) Sushi: info Cached hl7.fhir.us.mcode#4.0.0 to /home/fhiruser/.fhir/packages/hl7.fhir.us.mcode#4.0.0 (00:00.001 / 00:15.933, 113Mb) Sushi: info Loaded hl7.fhir.us.mcode#4.0.0 with 171 resources (00:00.114 / 00:16.048, 113Mb) Sushi: info Attempting to download hl7.fhir.uv.ae-research-ig#1.0.1 from https://packages.fhir.org/hl7.fhir.uv.ae-research-ig/1.0.1 (00:00.000 / 00:16.049, 113Mb) Sushi: info Downloaded hl7.fhir.uv.ae-research-ig#1.0.1 (00:00.771 / 00:16.821, 113Mb) Sushi: info Cached hl7.fhir.uv.ae-research-ig#1.0.1 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.ae-research-ig#1.0.1 (00:00.001 / 00:16.821, 113Mb) Sushi: info Loaded hl7.fhir.uv.ae-research-ig#1.0.1 with 76 resources (00:00.031 / 00:16.853, 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 / 00:16.853, 113Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:02.958 / 00:19.812, 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 / 00:19.814, 113Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.548 / 00:21.362, 113Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.012 / 00:21.374, 113Mb) Sushi: info Converting FSH to FHIR resources... (00:00.026 / 00:21.401, 113Mb) Sushi: info Converted 39 FHIR StructureDefinitions. (00:09.567 / 00:30.968, 113Mb) Sushi: info Converted 14 FHIR ValueSets. (00:00.450 / 00:31.419, 113Mb) Sushi: info Converted 113 FHIR instances. (00:30.287 / 01:01.706, 113Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 01:01.708, 113Mb) Sushi: info Exported 166 FHIR resources as JSON. (00:00.249 / 01:01.957, 113Mb) Sushi: info Assembling Implementation Guide sources... (00:00.006 / 01:01.963, 113Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.us.codex-radiation-therapy.json (00:00.107 / 01:02.071, 113Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 01:02.071, 113Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 01:02.073, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:02.073, 113Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 01:02.074, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:02.074, 113Mb) Sushi: | | 16 | 23 | 0 | 0 | | (00:00.000 / 01:02.074, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:02.074, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:02.075, 113Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 01:02.075, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:02.075, 113Mb) Sushi: | | 14 | 0 | 113 | | (00:00.000 / 01:02.075, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:02.076, 113Mb) Sushi: | | (00:00.000 / 01:02.076, 113Mb) Sushi: =================================================================== (00:00.000 / 01:02.076, 113Mb) Sushi: | Ac-clam-ations! 0 Errors 0 Warnings | (00:00.000 / 01:02.076, 113Mb) Sushi: =================================================================== (00:00.000 / 01:02.077, 113Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.865 / 01:02.942, 37Mb) Load Template from hl7.fhir.template#current (00:00.688 / 01:03.631, 94Mb) Installing hl7.fhir.template#current to the package cache Fetching: Installing hl7.fhir.template#current done. Load Template from hl7.base.template#current (00:01.264 / 01:04.895, 95Mb) Installing hl7.base.template#current to the package cache Fetching: Installing hl7.base.template#current done. Load Template from fhir.base.template#current (00:00.166 / 01:05.061, 95Mb) Installing fhir.base.template#current to the package cache Fetching: Installing fhir.base.template#current done. Root directory: /scratch/repo (00:04.620 / 01:09.682, 391Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.002 / 01:09.684, 391Mb) Core Package hl7.fhir.r4.core#4.0.1 Running Terminology Log: /tmp/ohfu-fhir-ig-12704564212111550417.log Connect to Terminology Server at http://tx.fhir.org (00:27.300 / 01:36.985, 248Mb) 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#5.1.0 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 Installing hl7.fhir.uv.extensions.r4#1.0.0 to the package cache Fetching: Installing hl7.fhir.uv.extensions.r4#1.0.0 done. Load Package hl7.fhir.uv.extensions.r4#1.0.0 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#2.1.0 to the package cache Fetching: Installing hl7.fhir.uv.smart-app-launch#2.1.0 done. Load Package hl7.fhir.uv.smart-app-launch#2.1.0 Installing us.nlm.vsac#0.11.0 to the package cache Fetching: Installing us.nlm.vsac#0.11.0 done. Load Package us.nlm.vsac#0.11.0 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' (00:41.879 / 02:18.864, 756Mb) Load Package hl7.fhir.uv.sdc#3.0.0 Installing us.cdc.phinvads#0.12.0 to the package cache Fetching: Installing us.cdc.phinvads#0.12.0 done. Load Package us.cdc.phinvads#0.12.0 Installing ihe.formatcode.fhir#1.1.0 to the package cache Fetching: Installing ihe.formatcode.fhir#1.1.0 done. Load Package ihe.formatcode.fhir#1.1.0 Load Package hl7.fhir.us.core#6.1.0 Installing hl7.fhir.uv.extensions.r4#5.2.0 to the package cache Fetching: Installing hl7.fhir.uv.extensions.r4#5.2.0 done. Load Package hl7.fhir.uv.extensions.r4#5.2.0 Installing hl7.fhir.uv.genomics-reporting#2.0.0 to the package cache Fetching: Installing hl7.fhir.uv.genomics-reporting#2.0.0 done. Load Package hl7.fhir.uv.genomics-reporting#2.0.0 Load Package hl7.fhir.us.mcode#4.0.0 Version mismatch. This IG is version 4.0.1, while the IG 'hl7.fhir.uv.ae-research-ig' is from version 5.0.0 (will try to run anyway) (00:18.628 / 02:37.493, 917Mb) Installing hl7.terminology#5.5.0 to the package cache Fetching: Installing hl7.terminology#5.5.0 done. Load Package hl7.terminology#5.5.0 Load Package hl7.fhir.uv.ae-research-ig#1.0.1 Load Package hl7.fhir.uv.tools.r4#0.3.0 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 (00:07.311 / 02:44.804, 832Mb) Load Content (00:00.000 / 02:44.805, 832Mb) Using en-US as the default narrative language. (no language information in Implementation Guide) (00:00.176 / 02:44.982, 848Mb) Process Loaded Resources (00:05.594 / 02:50.576, 1Gb) Generating Snapshots (00:01.489 / 02:52.065, 660Mb) loadPrePages from FetchedFile[/scratch/repo/input/includes] as /scratch/repo/input/includes 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/codex-radiation-therapy/package-list.json for version check (00:03.623 / 02:55.689, 755Mb) Processing Conformance Resources (00:00.185 / 02:55.874, 763Mb) Checking Language (00:00.000 / 02:55.875, 763Mb) Load Dependency Info (00:00.005 / 02:55.880, 763Mb) Load Info (00:00.002 / 02:55.882, 763Mb) Load Paths (00:00.001 / 02:55.883, 767Mb) Check R4 / R4B (00:00.000 / 02:55.884, 767Mb) Assign Comparison Ids (00:00.061 / 02:55.946, 787Mb) Propagating status (00:00.000 / 02:55.947, 787Mb) Generating Narratives (00:00.000 / 02:55.947, 787Mb) Validating Conformance Resources (00:12.432 / 03:08.379, 1Gb) Check profiles & code systems (00:55.791 / 04:04.171, 10Gb) Check realm rules (00:00.010 / 04:04.181, 10Gb) 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 (00:08.061 / 04:12.243, 2Gb) Installing hl7.fhir.us.codex-radiation-therapy#last to the package cache Fetching: 2025-02-17 17:35:49.520 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:92] Failed to resolve package hl7.fhir.us.codex-radiation-therapy#last from server: https://packages2.fhir.org/packages (Not found) 2025-02-17 17:35:49.944 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:92] Failed to resolve package hl7.fhir.us.codex-radiation-therapy#last from server: https://packages.fhir.org (Not Found) org.hl7.fhir.exceptions.FHIRException: Unable to find package hl7.fhir.us.codex-radiation-therapy#last at org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.loadPackage(FilesystemPackageCacheManager.java:692) at org.hl7.fhir.igtools.publisher.comparators.PreviousVersionComparator.startChecks(PreviousVersionComparator.java:197) at org.hl7.fhir.igtools.publisher.Publisher.checkConformanceResources(Publisher.java:6254) at org.hl7.fhir.igtools.publisher.Publisher.loadConformance2(Publisher.java:6086) at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:1184) at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:1020) at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:14543) Validating Resources (00:01.434 / 04:13.678, 2Gb) Processing Provenance Records (03:24.024 / 07:37.702, 3Gb) Generating Outputs in /scratch/repo/output (00:00.000 / 07:37.703, 3Gb) Generate Native Outputs (00:00.218 / 07:37.922, 3Gb) Run Template (00:18.398 / 07:56.320, 4Gb) Generate HTML Outputs (00:02.939 / 07:59.259, 5Gb) Generate Spreadsheets (00:59.087 / 08:58.347, 3Gb) Generate Summaries (00:08.245 / 09:06.592, 4Gb) Generating Summary Outputs (00:00.000 / 09:06.593, 4Gb) DB Cumulative Time invested: 00:00:01.540 Sending Usage Stats to Server (00:17.637 / 09:24.230, 4Gb) ## Memory (MB): Use = 4696, Free = 14311, Total = 19008, Max = 19008 (00:00.009 / 09:24.240, 4Gb) Reclaiming memory... (00:00.000 / 09:24.240, 4Gb) ## Memory (MB): Use = 3378, Free = 15629, Total = 19008, Max = 19008 (00:03.303 / 09:27.543, 3Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 09:27.545, 3Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 09:27.545, 3Gb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 09:27.545, 3Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 09:27.545, 3Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.506 / 09:28.051, 3Gb) Jekyll: Generating... (00:00.000 / 09:28.051, 3Gb) Jekyll: done in 6.4 seconds. (00:06.399 / 09:34.451, 3Gb) Checking Output HTML (00:06.349 / 09:40.800, 6Gb) found 2220 files (00:00.012 / 09:40.813, 6Gb) ........................................ ........................................ ... 2220 html files, 0 pages invalid xhtml (0%) (00:41.989 / 10:22.803, 3Gb) ... 508548 links, 0 broken links (0%) (00:00.000 / 10:22.804, 3Gb) Generate fragment-usage-analysis.csv (00:00.000 / 10:22.804, 3Gb) Build final .zip (00:00.013 / 10:22.818, 3Gb) Final .zip built (00:05.956 / 10:28.774, 3Gb) Installing hl7.fhir.r4.examples#4.0.1 to the package cache Fetching: Installing hl7.fhir.r4.examples#4.0.1 done. Installing hl7.fhir.uv.extensions.r5#5.1.0 to the package cache Fetching: Installing hl7.fhir.uv.extensions.r5#5.1.0 done. Built. Times: loading: 00:11.068, generate: 08:12.049, narrative generation: 00:12.432, realm-rules: 00:08.061, previous-version: 00:01.365, jekyll: 00:06.939, validation: 04:19.234 (#167), template: 00:02.951 (#3) (00:39.299 / 11:08.074, 5Gb) Generating QA (00:00.000 / 11:08.074, 5Gb) Sending usage stats failed: Connection timed out Validation output in /scratch/repo/output/qa.html Errors: 1, Warnings: 0, Info: 0, Broken Links: 0 (00:31.987 / 11:40.062, 6Gb) Finished. Max Memory Used = 10Gb (00:00.044 / 11:40.106, 6Gb)