INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/fhir-mCODE-ig --branch master repo DEBUG:root:Time to deadline 35879.998242 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 35872.689468 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35871.569836 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 177 packages in 7s 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/fhir-mCODE-ig/ -out /scratch/repo DEBUG:root:Time to deadline 35863.973504 seconds FHIR IG Publisher Version 1.8.12 (Git# 2ea3c5f77906). Built 2025-02-10T17:59:30.819Z (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/fhir-mCODE-ig/ -out /scratch/repo Start Clock @ Sunday, February 16, 2025, 5:58:10 PM Coordinated Universal Time (2025-02-16T17:58:10Z) Build FHIR IG from /scratch/repo (00:00.026 / 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) Run Sushi on /scratch/repo (00:00.004 / 00:00.038, 97Mb) Sushi: info Running SUSHI v3.14.0 (implements FHIR Shorthand specification v3.0.0) (00:00.701 / 00:00.739, 113Mb) Sushi: info Arguments: (00:00.000 / 00:00.739, 113Mb) Sushi: info --require-latest (00:00.000 / 00:00.740, 113Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.740, 113Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.740, 113Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:01.009 / 00:01.750, 113Mb) Sushi: info Importing FSH text... (00:00.168 / 00:01.919, 113Mb) Sushi: info Preprocessed 57 documents with 58 aliases. (00:01.092 / 00:03.011, 113Mb) Sushi: info Imported 157 definitions and 192 instances. (00:02.334 / 00:05.346, 113Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.191 / 00:05.537, 113Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.3.0 (00:00.737 / 00:06.275, 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 / 00:06.276, 113Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.3.0 (00:01.115 / 00:07.391, 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 / 00:07.394, 113Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.3.0 with 75 resources (00:00.065 / 00:07.459, 113Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 6.2.0 (00:00.471 / 00:07.931, 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 / 00:07.931, 113Mb) Sushi: info Downloaded hl7.terminology.r4#6.2.0 (00:02.743 / 00:10.675, 113Mb) Sushi: info Cached hl7.terminology.r4#6.2.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#6.2.0 (00:00.001 / 00:10.677, 113Mb) Sushi: info Loaded hl7.terminology.r4#6.2.0 with 4323 resources (00:01.824 / 00:12.501, 113Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.467 / 00:12.969, 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 / 00:12.970, 113Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.646 / 00:14.617, 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 / 00:14.618, 113Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.347 / 00:14.965, 113Mb) Sushi: info Attempting to download hl7.fhir.uv.genomics-reporting#2.0.0 from https://packages.fhir.org/hl7.fhir.uv.genomics-reporting/2.0.0 (00:00.000 / 00:14.966, 113Mb) Sushi: info Downloaded hl7.fhir.uv.genomics-reporting#2.0.0 (00:01.225 / 00:16.192, 113Mb) Sushi: info Cached hl7.fhir.uv.genomics-reporting#2.0.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.genomics-reporting#2.0.0 (00:00.001 / 00:16.193, 113Mb) Sushi: info Loaded hl7.fhir.uv.genomics-reporting#2.0.0 with 50 resources (00:00.052 / 00:16.246, 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 (00:00.000 / 00:16.246, 113Mb) Sushi: info Downloaded hl7.fhir.us.core#6.1.0 (00:01.747 / 00:17.994, 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 / 00:17.995, 113Mb) Sushi: info Loaded hl7.fhir.us.core#6.1.0 with 210 resources (00:00.135 / 00:18.131, 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 / 00:18.131, 113Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.419 / 00:21.551, 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 / 00:21.552, 113Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.645 / 00:23.198, 113Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.011 / 00:23.209, 113Mb) Sushi: info Converting FSH to FHIR resources... (00:00.025 / 00:23.235, 113Mb) Sushi: info Converted 53 FHIR StructureDefinitions. (00:06.770 / 00:30.006, 113Mb) Sushi: info Converted 1 FHIR CodeSystems. (00:00.074 / 00:30.080, 113Mb) Sushi: info Converted 103 FHIR ValueSets. (00:03.835 / 00:33.916, 113Mb) Sushi: info Converted 192 FHIR instances. (00:25.807 / 00:59.723, 113Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 00:59.725, 113Mb) Sushi: info Exported 349 FHIR resources as JSON. (00:00.357 / 01:00.082, 113Mb) Sushi: info Assembling Implementation Guide sources... (00:00.017 / 01:00.100, 113Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.us.mcode.json (00:00.220 / 01:00.321, 113Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 01:00.321, 113Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 01:00.323, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:00.323, 113Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 01:00.323, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:00.324, 113Mb) Sushi: | | 39 | 14 | 0 | 0 | | (00:00.000 / 01:00.324, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:00.324, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:00.324, 113Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 01:00.325, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:00.325, 113Mb) Sushi: | | 103 | 1 | 192 | | (00:00.000 / 01:00.325, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:00.325, 113Mb) Sushi: | | (00:00.000 / 01:00.326, 113Mb) Sushi: =================================================================== (00:00.000 / 01:00.326, 113Mb) Sushi: | You're sailing along smoothly. 0 Errors 0 Warnings | (00:00.000 / 01:00.327, 113Mb) Sushi: =================================================================== (00:00.000 / 01:00.327, 113Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.810 / 01:01.138, 38Mb) Load Template from #custom-template (00:00.683 / 01:01.821, 102Mb) Load Template from hl7.fhir.template#current (00:00.010 / 01:01.832, 102Mb) Installing hl7.fhir.template#current to the package cache Fetching: Installing hl7.fhir.template#current done. Load Template from hl7.base.template#current (00:01.312 / 01:03.145, 88Mb) Installing hl7.base.template#current to the package cache Fetching: Installing hl7.base.template#current done. Load Template from fhir.base.template#current (00:00.169 / 01:03.314, 96Mb) Installing fhir.base.template#current to the package cache Fetching: Installing fhir.base.template#current done. Root directory: /scratch/repo (00:04.825 / 01:08.140, 400Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.002 / 01:08.143, 400Mb) Core Package hl7.fhir.r4.core#4.0.1 Running Terminology Log: /tmp/ohfu-fhir-ig-2493725846323685901.log Connect to Terminology Server at http://tx.fhir.org (00:24.570 / 01:32.713, 259Mb) 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 hl7.fhir.uv.genomics-reporting#2.0.0 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' (00:40.573 / 02:13.286, 951Mb) 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 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 (00:15.055 / 02:28.342, 646Mb) Load Content (00:00.000 / 02:28.342, 646Mb) Using en-US as the default narrative language. (no language information in Implementation Guide or command line) (00:00.179 / 02:28.521, 670Mb) Translating CQL source (00:00.035 / 02:28.557, 672Mb) Translating CQL source in folder /scratch/repo/input/attachments (00:00.000 / 02:28.557, 672Mb) Process Loaded Resources (00:04.597 / 02:33.154, 1Gb) Generating Snapshots (00:01.907 / 02:35.062, 651Mb) 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/mcode/package-list.json for version check (00:03.618 / 02:38.680, 1Gb) Processing Conformance Resources (00:00.244 / 02:38.925, 1Gb) Checking Language (00:00.000 / 02:38.925, 1Gb) Load Dependency Info (00:00.006 / 02:38.932, 1Gb) Load Info (00:00.002 / 02:38.935, 1Gb) Load Paths (00:00.000 / 02:38.935, 1Gb) Check R4 / R4B (00:00.001 / 02:38.937, 1Gb) Assign Comparison Ids (00:00.091 / 02:39.028, 1Gb) Propagating status (00:00.000 / 02:39.028, 1Gb) Generating Narratives (00:00.000 / 02:39.029, 1Gb) Validating Conformance Resources (00:20.531 / 02:59.560, 1Gb) Check profiles & code systems (01:11.806 / 04:11.366, 6Gb) Check realm rules (00:00.007 / 04:11.374, 6Gb) 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 (00:11.377 / 04:22.751, 12Gb) Installing hl7.fhir.us.mcode#true to the package cache Fetching: 2025-02-16 18:02:34.123 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:92] Failed to resolve package hl7.fhir.us.mcode#true from server: https://packages2.fhir.org/packages (Not found) 2025-02-16 18:02:34.574 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:92] Failed to resolve package hl7.fhir.us.mcode#true from server: https://packages.fhir.org (Not Found) org.hl7.fhir.exceptions.FHIRException: Unable to find package hl7.fhir.us.mcode#true at org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.loadPackage(FilesystemPackageCacheManager.java:718) at org.hl7.fhir.igtools.publisher.comparators.PreviousVersionComparator.startChecks(PreviousVersionComparator.java:197) at org.hl7.fhir.igtools.publisher.Publisher.checkConformanceResources(Publisher.java:6251) at org.hl7.fhir.igtools.publisher.Publisher.loadConformance2(Publisher.java:6087) at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:1185) at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:1021) at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:14434) Validating Resources (00:01.848 / 04:24.600, 1Gb) Processing Provenance Records (00:53.973 / 05:18.574, 5Gb) Generating Outputs in /scratch/repo/output (00:00.000 / 05:18.574, 5Gb) Generate Native Outputs (00:00.301 / 05:18.875, 5Gb) Run Template (00:33.795 / 05:52.671, 8Gb) Generate HTML Outputs (00:05.265 / 05:57.937, 8Gb) Generate Summaries (02:54.591 / 08:52.528, 7Gb) Generating Summary Outputs (00:00.000 / 08:52.529, 7Gb) extension code doesn't follow canonical pattern: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-radiotherapy-modality extension code doesn't follow canonical pattern: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-radiotherapy-technique Table of contents has a section with more than 222 entries. Collapsing will not work reliably DB Cumulative Time invested: 00:00:56.882 Sending Usage Stats to Server (00:22.209 / 09:14.739, 7Gb) ## Memory (MB): Use = 7631, Free = 11376, Total = 19008, Max = 19008 (00:00.008 / 09:14.747, 7Gb) Reclaiming memory... (00:00.000 / 09:14.747, 7Gb) ## Memory (MB): Use = 3072, Free = 15931, Total = 19008, Max = 19008 (00:02.919 / 09:17.666, 3Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 09:17.668, 3Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 09:17.668, 3Gb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 09:17.668, 3Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 09:17.668, 3Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.483 / 09:18.152, 3Gb) Jekyll: Generating... (00:00.000 / 09:18.152, 3Gb) Jekyll: done in 11.892 seconds. (00:11.891 / 09:30.044, 3Gb) Checking Output HTML (00:09.639 / 09:39.683, 7Gb) found 4029 files (00:00.021 / 09:39.705, 7Gb) ........................................ ........................................ ... 4029 html files, 0 pages invalid xhtml (0%) (01:10.203 / 10:49.908, 13Gb) ... 848984 links, 0 broken links (0%) (00:00.000 / 10:49.909, 13Gb) Generate fragment-usage-analysis.csv (00:00.000 / 10:49.909, 13Gb) Build final .zip (00:00.009 / 10:49.919, 13Gb) Final .zip built (00:10.479 / 11:00.398, 13Gb) Installing hl7.fhir.r4.examples#4.0.1 to the package cache Fetching: Installing hl7.fhir.r4.examples#4.0.1 done. Sending usage stats failed: Connection timed out Built. Times: loading: 00:10.582, generate: 09:00.206, narrative generation: 00:20.531, realm-rules: 00:11.377, previous-version: 00:01.403, jekyll: 00:12.442, validation: 02:05.220 (#350), template: 00:05.273 (#3) (00:39.432 / 11:39.830, 4Gb) Generating QA (00:00.000 / 11:39.830, 4Gb) Validation output in /scratch/repo/output/qa.html Errors: 2, Warnings: 0, Info: 1, Broken Links: 0 (00:14.179 / 11:54.010, 7Gb) Finished. Max Memory Used = 13Gb (00:00.080 / 11:54.090, 7Gb)