INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/IHE/PCC.ODH --branch master repo DEBUG:root:Time to deadline 35879.998215 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 35879.180708 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35877.962152 seconds npm WARN deprecated rimraf@2.6.3: Rimraf versions prior to v4 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 glob@7.2.3: Glob versions prior to v9 are no longer supported added 120 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 -> 10.9.2 npm notice Changelog: npm notice Run `npm install -g npm@10.9.2` 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/IHE/PCC.ODH/ -out /scratch/repo DEBUG:root:Time to deadline 35872.374893 seconds FHIR IG Publisher Version 1.7.5 (Git# 2ec44e6c46a5). Built 2024-11-22T15:37:50.312Z (13 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/IHE/PCC.ODH/ -out /scratch/repo Start Clock @ Thursday, December 5, 2024, 5:11:47 PM Coordinated Universal Time (2024-12-05T17:11:47Z) Build FHIR IG from /scratch/repo (00:00.028 / 00:00.029, 89Mb) API keys loaded from /etc/fhir-settings.json (00:00.004 / 00:00.033, 89Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.036, 89Mb) Run Sushi on /scratch/repo (00:00.006 / 00:00.042, 89Mb) Sushi: info Running SUSHI v3.12.1 (implements FHIR Shorthand specification v3.0.0) (00:00.662 / 00:00.705, 113Mb) Sushi: info Arguments: (00:00.000 / 00:00.705, 113Mb) Sushi: info --require-latest (00:00.000 / 00:00.706, 113Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.706, 113Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.707, 113Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.751 / 00:01.459, 113Mb) Sushi: info Importing FSH text... (00:00.170 / 00:01.630, 113Mb) Sushi: info Preprocessed 5 documents with 11 aliases. (00:02.165 / 00:03.795, 113Mb) Sushi: info Imported 2 definitions and 2 instances. (00:00.228 / 00:04.023, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.tools#current... (00:00.002 / 00:04.026, 113Mb) Sushi: info Did not find hl7.fhir.uv.tools#current in /home/fhiruser/.fhir/packages. (00:00.030 / 00:04.057, 113Mb) Sushi: info Downloading hl7.fhir.uv.tools#current... https://build.fhir.org/ig/FHIR/fhir-tools-ig/branches/master/package.tgz (00:00.120 / 00:04.178, 113Mb) Sushi: info Downloaded hl7.fhir.uv.tools#current (00:00.021 / 00:04.199, 113Mb) Sushi: info Loaded package hl7.fhir.uv.tools#current (00:00.107 / 00:04.306, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.terminology.r4#6.1.0... (00:00.585 / 00:04.892, 113Mb) Sushi: info Did not find hl7.terminology.r4#6.1.0 in /home/fhiruser/.fhir/packages. (00:00.027 / 00:04.919, 113Mb) Sushi: info Downloading hl7.terminology.r4#6.1.0... https://packages.fhir.org/hl7.terminology.r4/6.1.0 (00:00.000 / 00:04.920, 113Mb) Sushi: info Downloaded hl7.terminology.r4#6.1.0 (00:02.302 / 00:07.223, 113Mb) Sushi: info Loaded package hl7.terminology.r4#6.1.0 (00:02.766 / 00:09.989, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.extensions.r4#5.1.0... (00:00.474 / 00:10.464, 113Mb) Sushi: info Did not find hl7.fhir.uv.extensions.r4#5.1.0 in /home/fhiruser/.fhir/packages. (00:00.509 / 00:10.974, 113Mb) Sushi: info Downloading hl7.fhir.uv.extensions.r4#5.1.0... https://packages.fhir.org/hl7.fhir.uv.extensions.r4/5.1.0 (00:00.000 / 00:10.974, 113Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.1.0 (00:02.104 / 00:13.079, 113Mb) Sushi: info Loaded package hl7.fhir.uv.extensions.r4#5.1.0 (00:01.360 / 00:14.439, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for us.cdc.phinvads#0.12.0... (00:00.000 / 00:14.440, 113Mb) Sushi: info Did not find us.cdc.phinvads#0.12.0 in /home/fhiruser/.fhir/packages. (00:00.754 / 00:15.195, 113Mb) Sushi: info Downloading us.cdc.phinvads#0.12.0... https://packages.fhir.org/us.cdc.phinvads/0.12.0 (00:00.000 / 00:15.195, 113Mb) Sushi: info Downloaded us.cdc.phinvads#0.12.0 (00:02.948 / 00:18.143, 113Mb) Sushi: info Loaded package us.cdc.phinvads#0.12.0 (00:06.384 / 00:24.528, 113Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.r4.core#4.0.1... (00:00.000 / 00:24.528, 113Mb) Sushi: info Did not find hl7.fhir.r4.core#4.0.1 in /home/fhiruser/.fhir/packages. (00:05.088 / 00:29.617, 113Mb) Sushi: info Downloading hl7.fhir.r4.core#4.0.1... https://packages.fhir.org/hl7.fhir.r4.core/4.0.1 (00:00.000 / 00:29.617, 113Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:02.645 / 00:32.263, 121Mb) Sushi: info Loaded package hl7.fhir.r4.core#4.0.1 (00:07.643 / 00:39.906, 121Mb) Sushi: info Converting FSH to FHIR resources... (00:00.439 / 00:40.346, 121Mb) Sushi: info Converted 2 FHIR CodeSystems. (00:00.112 / 00:40.458, 121Mb) Sushi: info Converted 2 FHIR instances. (00:12.984 / 00:53.442, 121Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 00:53.443, 121Mb) Sushi: info Exported 4 FHIR resources as JSON. (00:00.046 / 00:53.489, 121Mb) Sushi: info Assembling Implementation Guide sources... (00:00.001 / 00:53.491, 121Mb) Sushi: info Generated ImplementationGuide-ihe.pcc.odh.json (00:00.040 / 00:53.531, 121Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:53.532, 121Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.002 / 00:53.534, 121Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:53.534, 121Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:53.534, 121Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:53.535, 121Mb) Sushi: | | 0 | 0 | 0 | 0 | | (00:00.000 / 00:53.535, 121Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:53.535, 121Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:53.536, 121Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:53.536, 121Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:53.536, 121Mb) Sushi: | | 0 | 2 | 2 | | (00:00.000 / 00:53.537, 121Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:53.537, 121Mb) Sushi: | | (00:00.000 / 00:53.537, 121Mb) Sushi: =================================================================== (00:00.000 / 00:53.537, 121Mb) Sushi: | You're sailing along smoothly. 0 Errors 0 Warnings | (00:00.000 / 00:53.538, 121Mb) Sushi: =================================================================== (00:00.000 / 00:53.538, 121Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.833 / 00:54.372, 37Mb) Load Template from ihe.fhir.template#current (00:00.635 / 00:55.007, 69Mb) Installing ihe.fhir.template#current to the package cache Fetching: Installing ihe.fhir.template#current done. Load Template from fhir.base.template#current (00:01.331 / 00:56.338, 133Mb) 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 (00:04.319 / 01:00.658, 157Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.003 / 01:00.661, 157Mb) Core Package hl7.fhir.r4.core#4.0.1 Running Terminology Log: /tmp/ohfu-fhir-ig-3121032624076227289.log Connect to Terminology Server at http://tx.fhir.org (00:26.067 / 01:26.729, 584Mb) Installing hl7.fhir.pubpack#0.1.9 to the package cache Fetching: Installing hl7.fhir.pubpack#0.1.9 done. Load Package hl7.fhir.pubpack#0.1.9 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#6.1.0 Load Package hl7.fhir.uv.extensions.r4#5.1.0 Load Package us.cdc.phinvads#0.12.0 Installing hl7.fhir.uv.tools.r4#0.3.0 to the package cache Fetching: Installing hl7.fhir.uv.tools.r4#0.3.0 done. 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 (00:23.379 / 01:50.108, 965Mb) Load Content (00:00.000 / 01:50.109, 965Mb) Using en-US as the default narrative language. (no language information in Implementation Guide or command line) (00:00.103 / 01:50.212, 965Mb) 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/data] as /scratch/repo/input/data loadPrePages from FetchedFile[/scratch/repo/input/pagecontent] as /scratch/repo/input/pagecontent Fetch https://profiles.ihe.net/PCC/ODH/package-list.json for version check (00:01.480 / 01:51.693, 1Gb) Processing Conformance Resources (00:00.157 / 01:51.850, 1Gb) Load Dependency Info (00:00.001 / 01:51.852, 1Gb) Load Info (00:00.001 / 01:51.853, 1Gb) Load Resources (00:00.000 / 01:51.854, 1Gb) Load Paths (00:01.244 / 01:53.099, 317Mb) Generating Snapshots (00:00.000 / 01:53.099, 317Mb) Check R4 / R4B (00:01.408 / 01:54.508, 805Mb) Assign Comparison Ids (00:00.116 / 01:54.625, 829Mb) Propagating status (00:00.000 / 01:54.625, 829Mb) Generating Narratives (00:00.000 / 01:54.625, 829Mb) Validating Conformance Resources (00:02.847 / 01:57.472, 654Mb) Check profiles & code systems (00:09.708 / 02:07.181, 585Mb) Check realm rules (00:00.006 / 02:07.188, 585Mb) Previous Version Comparison (00:00.000 / 02:07.188, 585Mb) Installing ihe.pcc.odh#1.0.0 to the package cache Fetching: 2024-12-05 17:13:55.937 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:92] Failed to resolve package ihe.pcc.odh#1.0.0 from server: https://packages.fhir.org (Not Found) Installing ihe.pcc.odh#1.0.0 done. Installing hl7.terminology.r4#5.3.0 to the package cache Fetching: Installing hl7.terminology.r4#5.3.0 done. Installing hl7.fhir.uv.extensions.r4#1.0.0 to the package cache Fetching: Installing hl7.fhir.uv.extensions.r4#1.0.0 done. Validating Resources (00:11.022 / 02:18.210, 1Gb) Processing Provenance Records (00:00.985 / 02:19.196, 1Gb) Generating Outputs in /scratch/repo/output (00:00.000 / 02:19.196, 1Gb) Generate Native Outputs (00:00.185 / 02:19.381, 1Gb) Run Template (00:24.135 / 02:43.517, 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: [mkdir] Created dir: /scratch/repo/input-cache/schemas/R4 [get] Getting: http://hl7.org/fhir/R4/fhir-single.xsd [get] To: /scratch/repo/input-cache/schemas/R4/fhir-single.xsd [get] Getting: http://hl7.org/fhir/R4/fhir-xhtml.xsd [get] To: /scratch/repo/input-cache/schemas/R4/fhir-xhtml.xsd [get] Getting: http://hl7.org/fhir/R4/xml.xsd [get] To: /scratch/repo/input-cache/schemas/R4/xml.xsd [get] Getting: http://hl7.org/fhir/R4/xmldsig-core-schema.xsd [get] To: /scratch/repo/input-cache/schemas/R4/xmldsig-core-schema.xsd 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 19 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 (00:01.208 / 02:44.726, 1Gb) Generate HTML Outputs (00:00.000 / 02:44.726, 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 (00:27.680 / 03:12.407, 1Gb) Generating Summary Outputs (00:00.000 / 03:12.407, 1Gb) DB Cumulative Time invested: 00:00:15.430 Sending Usage Stats to Server (00:04.755 / 03:17.163, 2Gb) ## Memory (MB): Use = 2092, Free = 16915, Total = 19008, Max = 19008 (00:00.008 / 03:17.171, 2Gb) Reclaiming memory... (00:00.000 / 03:17.172, 2Gb) ## Memory (MB): Use = 1476, Free = 17531, Total = 19008, Max = 19008 (00:01.559 / 03:18.731, 1Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 03:18.733, 1Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 03:18.733, 1Gb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 03:18.733, 1Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 03:18.733, 1Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.519 / 03:19.253, 1Gb) Jekyll: Generating... (00:00.000 / 03:19.253, 1Gb) Jekyll: done in 2.022 seconds. (00:02.021 / 03:21.275, 1Gb) onCheck.extend: onCheck: Checking Output HTML (00:04.678 / 03:25.953, 1Gb) found 851 files (00:00.005 / 03:25.959, 1Gb) ........................................ ........................................ ... 851 html files, 0 pages invalid xhtml (0%) (00:26.440 / 03:52.399, 11Gb) ... 253654 links, 0 broken links (0%) (00:00.000 / 03:52.399, 11Gb) Generate fragment-usage-analysis.csv (00:00.000 / 03:52.399, 11Gb) Build final .zip (00:00.008 / 03:52.408, 11Gb) Final .zip built (00:02.977 / 03:55.385, 11Gb) Built. Times: loading: 00:01.740, generate: 02:08.559, narrative generation: 00:02.846, realm-rules: 00:00.000, previous-version: 00:10.978, jekyll: 00:02.561, validation: 00:10.582 (#25), template: 00:01.221 (#3) (00:05.043 / 04:00.428, 12Gb) Generating QA (00:00.000 / 04:00.429, 12Gb) Validation output in /scratch/repo/output/qa.html Errors: 0, Warnings: 0, Info: 0, Broken Links: 0 (00:00.457 / 04:00.886, 12Gb) Finished. Max Memory Used = 12Gb (00:00.015 / 04:00.901, 12Gb)