INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7EE/ig-ee-base --branch master repo DEBUG:root:Time to deadline 35879.997709 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 35879.57909 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35878.407084 seconds added 121 packages in 5s 8 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 10.6.0 npm notice Changelog: npm notice Run `npm install -g npm@10.6.0` 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/HL7EE/ig-ee-base/ -out /scratch/repo DEBUG:root:Time to deadline 35873.212078 seconds FHIR IG Publisher Version 1.6.6 (Git# d1dac76a7c14). Built 2024-04-23T09:27:48.515Z (70 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/HL7EE/ig-ee-base/ -out /scratch/repo Start Clock @ Friday, April 26, 2024, 7:48:11 AM Coordinated Universal Time (2024-04-26T07:48:11Z) Build FHIR IG from /scratch/repo (00:00.030 / 00:00.030, 89Mb) API keys loaded from /etc/fhir-settings.json (00:00.005 / 00:00.035, 89Mb) Package Cache: /var/lib/.fhir/packages (00:00.002 / 00:00.038, 89Mb) Run Sushi on /scratch/repo (00:00.007 / 00:00.046, 89Mb) Sushi: info Running SUSHI v3.9.0 (implements FHIR Shorthand specification v3.0.0-ballot) (00:00.567 / 00:00.613, 97Mb) Sushi: info Arguments: (00:00.000 / 00:00.614, 97Mb) Sushi: info --require-latest (00:00.000 / 00:00.614, 97Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.615, 97Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.615, 97Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.901 / 00:01.517, 97Mb) Sushi: info Importing FSH text... (00:00.176 / 00:01.693, 97Mb) Sushi: info Preprocessed 15 documents with 21 aliases. (00:01.240 / 00:02.934, 97Mb) Sushi: info Imported 46 definitions and 28 instances. (00:00.126 / 00:03.060, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.tools#current... (00:00.003 / 00:03.064, 97Mb) Sushi: info Did not find hl7.fhir.uv.tools#current in /home/fhiruser/.fhir/packages. (00:00.033 / 00:03.097, 97Mb) Sushi: info Downloading hl7.fhir.uv.tools#current... https://build.fhir.org/ig/FHIR/fhir-tools-ig/branches/master/package.tgz (00:00.132 / 00:03.230, 97Mb) Sushi: info Downloaded hl7.fhir.uv.tools#current (00:00.024 / 00:03.255, 97Mb) Sushi: info Loaded package hl7.fhir.uv.tools#current (00:00.152 / 00:03.407, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.terminology.r5#5.5.0... (00:00.543 / 00:03.950, 97Mb) Sushi: info Did not find hl7.terminology.r5#5.5.0 in /home/fhiruser/.fhir/packages. (00:00.035 / 00:03.985, 97Mb) Sushi: info Downloading hl7.terminology.r5#5.5.0... https://packages.fhir.org/hl7.terminology.r5/5.5.0 (00:00.000 / 00:03.986, 97Mb) Sushi: info Downloaded hl7.terminology.r5#5.5.0 (00:02.316 / 00:06.303, 97Mb) Sushi: info Loaded package hl7.terminology.r5#5.5.0 (00:01.874 / 00:08.177, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.extensions#current... (00:00.000 / 00:08.178, 97Mb) Sushi: info Did not find hl7.fhir.uv.extensions#current in /home/fhiruser/.fhir/packages. (00:00.447 / 00:08.626, 97Mb) Sushi: info Downloading hl7.fhir.uv.extensions#current... https://build.fhir.org/ig/HL7/fhir-extensions/branches/master/package.tgz (00:00.064 / 00:08.690, 97Mb) Sushi: info Downloaded hl7.fhir.uv.extensions#current (00:00.022 / 00:08.712, 97Mb) Sushi: info Loaded package hl7.fhir.uv.extensions#current (00:01.132 / 00:09.845, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.r5.core#5.0.0... (00:00.000 / 00:09.846, 97Mb) Sushi: info Did not find hl7.fhir.r5.core#5.0.0 in /home/fhiruser/.fhir/packages. (00:00.630 / 00:10.477, 97Mb) Sushi: info Downloading hl7.fhir.r5.core#5.0.0... https://packages.fhir.org/hl7.fhir.r5.core/5.0.0 (00:00.000 / 00:10.477, 97Mb) Sushi: info Downloaded hl7.fhir.r5.core#5.0.0 (00:03.285 / 00:13.763, 97Mb) Sushi: info Loaded package hl7.fhir.r5.core#5.0.0 (00:02.502 / 00:16.266, 97Mb) Sushi: info Converting FSH to FHIR resources... (00:00.043 / 00:16.309, 97Mb) Sushi: info Converted 19 FHIR StructureDefinitions. (00:02.724 / 00:19.034, 97Mb) Sushi: info Converted 7 FHIR CodeSystems. (01:32.655 / 01:51.689, 121Mb) Sushi: info Converted 20 FHIR ValueSets. (00:01.359 / 01:53.049, 121Mb) Sushi: info Converted 28 FHIR instances. (00:01.355 / 01:54.405, 121Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 01:54.407, 121Mb) Sushi: info Exported 74 FHIR resources as JSON. (00:00.106 / 01:54.513, 121Mb) Sushi: info Assembling Implementation Guide sources... (00:00.003 / 01:54.516, 121Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.ee.base.json (00:00.073 / 01:54.590, 121Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 01:54.591, 121Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.000 / 01:54.592, 121Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:54.592, 121Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 01:54.592, 121Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:54.592, 121Mb) Sushi: | | 11 | 8 | 0 | 0 | | (00:00.000 / 01:54.593, 121Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:54.593, 121Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:54.593, 121Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 01:54.593, 121Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:54.593, 121Mb) Sushi: | | 20 | 7 | 28 | | (00:00.000 / 01:54.594, 121Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:54.594, 121Mb) Sushi: | | (00:00.000 / 01:54.594, 121Mb) Sushi: =================================================================== (00:00.000 / 01:54.594, 121Mb) Sushi: | You're swimming in success! 0 Errors 0 Warnings | (00:00.000 / 01:54.594, 121Mb) Sushi: =================================================================== (00:00.000 / 01:54.595, 121Mb) Load Template from #local-template (00:00.783 / 01:55.378, 37Mb) Load Template from fhir.base.template#current (00:00.016 / 01:55.395, 37Mb) Installing fhir.base.template#current to the package cache Fetching: Installing fhir.base.template#current done. onLoad.findSpreadsheets: onLoad.updateIg: [xslt] Processing /scratch/repo/template/onLoad-ig-working.xml to /scratch/repo/template/onLoad-ig-updated.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onLoad.xslt onLoad.extend: onLoad: Root directory: /scratch/repo (00:04.748 / 02:00.143, 136Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.002 / 02:00.146, 136Mb) Core Package hl7.fhir.r5.core#5.0.0 Running Terminology Log: /tmp/ohfu-fhir-ig-8871115414016044475.log Connect to Terminology Server at http://tx.fhir.org (00:04.332 / 02:04.478, 573Mb) Installing hl7.fhir.pubpack#0.1.7 to the package cache Fetching: Installing hl7.fhir.pubpack#0.1.7 done. Load Package hl7.fhir.pubpack#0.1.7 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.r5#5.5.0 Load Package hl7.fhir.uv.extensions#5.1.0-cibuild Installing hl7.fhir.uv.tools#0.1.0 to the package cache Fetching: Installing hl7.fhir.uv.tools#0.1.0 done. Load Package hl7.fhir.uv.tools#0.1.0 Initialization complete (00:05.090 / 02:09.568, 1Gb) Fetch https://fhir.ee/package-list.json for version check (00:00.003 / 02:09.572, 1Gb) Load Content (00:00.534 / 02:10.106, 1Gb) 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 Processing Conformance Resources (00:02.001 / 02:12.108, 486Mb) Load Dependency Info (00:00.003 / 02:12.111, 486Mb) Load Info (00:00.002 / 02:12.113, 486Mb) Load Resources (00:00.000 / 02:12.114, 486Mb) Load Paths (00:00.342 / 02:12.457, 574Mb) Generating Snapshots (00:00.000 / 02:12.457, 574Mb) Check R4 / R4B (00:00.790 / 02:13.248, 838Mb) Assign Comparison Ids (00:00.047 / 02:13.296, 846Mb) Propagating status (00:00.000 / 02:13.296, 846Mb) Generating Narratives (00:00.000 / 02:13.296, 846Mb) Validating Conformance Resources (00:03.782 / 02:17.079, 1Gb) Check profiles & code systems (00:07.823 / 02:24.902, 1Gb) Check realm rules (00:00.016 / 02:24.918, 1Gb) Previous Version Comparison (00:00.000 / 02:24.919, 1Gb) Validating Resources (00:00.042 / 02:24.962, 1Gb) Processing Provenance Records (00:02.380 / 02:27.343, 759Mb) Generating Outputs in /scratch/repo/output (00:00.001 / 02:27.344, 759Mb) Generate Native Outputs (00:00.351 / 02:27.696, 775Mb) Run Template (00:27.409 / 02:55.104, 1Gb) onGenerate.checkVersions: [xslt] Processing /scratch/repo/template/onGenerate-ig-working.xml to /scratch/repo/template/versions.txt [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.getVersions.xslt [mkdir] Created dir: /scratch/repo/input-cache/schemas onGenerate.r5-schemas: [mkdir] Created dir: /scratch/repo/input-cache/schemas/R5 [get] Getting: http://build.fhir.org/fhir-single.xsd [get] To: /scratch/repo/input-cache/schemas/R5/fhir-single.xsd [get] Getting: http://build.fhir.org/fhir-xhtml.xsd [get] To: /scratch/repo/input-cache/schemas/R5/fhir-xhtml.xsd [get] Getting: http://build.fhir.org/xml.xsd [get] To: /scratch/repo/input-cache/schemas/R5/xml.xsd [get] Getting: http://build.fhir.org/xmldsig-core-schema.xsd [get] To: /scratch/repo/input-cache/schemas/R5/xmldsig-core-schema.xsd onGenerate.r4-schemas: onGenerate.r3-schemas: onGenerate.r2b-schemas: onGenerate.r2-schemas: onGenerate.schemas: onGenerate.data: [xslt] Processing /scratch/repo/template/onGenerate-ig-working.xml to /scratch/repo/temp/pages/_data/artifacts.json [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.data.xslt onGenerate.setup: onGenerate.infoFile: [xslt] Processing /scratch/repo/template/onGenerate-ig-working.xml to /scratch/repo/temp/pages/_data/info.json [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.genJson.xslt onGenerate.processIncludes: [copy] Copying 17 files to /scratch/repo/temp/pages/_includes onGenerate.processIg: [xslt] Processing /scratch/repo/template/onGenerate-ig-working.xml to /scratch/repo/template/onGenerate-ig-working.1.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.group.xslt [xslt] Processing /scratch/repo/template/onGenerate-ig-working.1.xml to /scratch/repo/template/onGenerate-ig-working.2.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.groupSort.xslt [xslt] Processing /scratch/repo/template/onGenerate-ig-working.2.xml to /scratch/repo/template/onGenerate-ig-updated.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.final.xslt onGenerate.igQa: [xslt] Processing /scratch/repo/template/onGenerate-ig-updated.xml to /scratch/repo/template/ongenerate-validation-igqa.json [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.qa.xslt onGenerate.artifactList: [xslt] Processing /scratch/repo/template/onGenerate-ig-updated.xml to /scratch/repo/temp/pages/_includes/artifacts.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/createArtifactSummary.xslt check-plantumlfiles: onGenerate.plantUml.ig: onGenerate.plantUml.template: onGenerate.plantUml: onGenerate.copyDataFiles: onGenerate.extend: onGenerate: Template Done (00:00.792 / 02:55.898, 1Gb) Generate HTML Outputs (00:00.000 / 02:55.898, 1Gb) ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console... Generate Summaries (00:27.656 / 03:23.555, 1Gb) Generating Summary Outputs (00:00.000 / 03:23.555, 1Gb) DB Cumulative Time invested: 00:00:34.345 Sending Usage Stats to Server (02:18.189 / 05:41.745, 1Gb) ## Memory (MB): Use = 1088, Free = 17919, Total = 19008, Max = 19008 (00:00.007 / 05:41.752, 1Gb) Reclaiming memory... (00:00.000 / 05:41.752, 1Gb) ## Memory (MB): Use = 875, Free = 18132, Total = 19008, Max = 19008 (00:00.710 / 05:42.463, 883Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.002 / 05:42.465, 883Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 05:42.465, 883Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 05:42.465, 883Mb) * A reference to a manually edited file that hasn't been provided (00:00.003 / 05:42.468, 888Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.452 / 05:42.921, 907Mb) Jekyll: Generating... (00:00.000 / 05:42.921, 907Mb) Jekyll: done in 2.679 seconds. (00:02.678 / 05:45.599, 907Mb) Checking Output HTML (00:01.187 / 05:46.786, 1Gb) found 1392 files (00:00.007 / 05:46.794, 1Gb) ........................................ ........................................ ... 1392 html files, 0 pages invalid xhtml (0%) (00:10.490 / 05:57.284, 4Gb) ... 190422 links, 10 broken links (0%) (00:00.000 / 05:57.284, 4Gb) Build final .zip (00:00.000 / 05:57.285, 4Gb) Final .zip built (00:01.329 / 05:58.614, 4Gb) Built. Times: loading: 00:02.000, generate: 03:48.447, narrative generation: 00:03.782, realm-rules: 00:00.000, previous-version: 00:00.000, jekyll: 00:03.156, validation: 00:10.055 (#75), template: 00:00.792 (#3) (00:01.959 / 06:00.573, 4Gb) Generating QA (00:00.000 / 06:00.573, 4Gb) Validation output in /scratch/repo/output/qa.html Errors: 8, Warnings: 33, Info: 74, Broken Links: 10 (00:00.856 / 06:01.430, 5Gb) Finished. Max Memory Used = 5Gb (00:00.017 / 06:01.448, 5Gb)