INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/fhir-cdisc-mapping --branch main repo DEBUG:root:Time to deadline 35879.997972 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 35878.276292 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35877.156574 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 119 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 -> 10.8.2 npm notice Changelog: npm notice Run `npm install -g npm@10.8.2` 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/HL7/fhir-cdisc-mapping/ -out /scratch/repo DEBUG:root:Time to deadline 35871.862817 seconds FHIR IG Publisher Version 1.6.18 (Git# f4d8a040c276). Built 2024-07-17T07:05:28.199Z (12 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-cdisc-mapping/ -out /scratch/repo Start Clock @ Monday, July 29, 2024, 6:50:20 PM Coordinated Universal Time (2024-07-29T18:50:20Z) Build FHIR IG from /scratch/repo (00:00.027 / 00:00.027, 89Mb) API keys loaded from /etc/fhir-settings.json (00:00.004 / 00:00.032, 89Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.035, 89Mb) Load Template from #cdisc-template (00:01.449 / 00:01.484, 69Mb) Load Template from hl7.fhir.template#current (00:00.269 / 00:01.753, 69Mb) Installing hl7.fhir.template#current to the package cache Fetching: Installing hl7.fhir.template#current done. Load Template from hl7.base.template#current (00:01.161 / 00:02.914, 141Mb) Installing hl7.base.template#current to the package cache Fetching: Installing hl7.base.template#current done. Load Template from fhir.base.template#current (00:00.203 / 00:03.118, 141Mb) 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 (00:04.338 / 00:07.457, 135Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.002 / 00:07.459, 135Mb) Core Package hl7.fhir.r4.core#4.0.1 Installing hl7.fhir.r4.core#4.0.1 to the package cache Fetching: Installing hl7.fhir.r4.core#4.0.1 done. Running Terminology Log: /tmp/ohfu-fhir-ig-12805404701271413652.log Connect to Terminology Server at http://tx.fhir.org (00:37.711 / 00:45.171, 731Mb) Installing hl7.fhir.pubpack#0.1.8 to the package cache Fetching: Installing hl7.fhir.pubpack#0.1.8 done. Load Package hl7.fhir.pubpack#0.1.8 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 Installing hl7.terminology.r4#6.0.2 to the package cache Fetching: Installing hl7.terminology.r4#6.0.2 done. Load Package hl7.terminology.r4#6.0.2 Installing hl7.fhir.uv.extensions.r4#5.1.0 to the package cache Fetching: Installing hl7.fhir.uv.extensions.r4#5.1.0 done. Load Package hl7.fhir.uv.extensions.r4#5.1.0 Installing hl7.fhir.uv.tools#0.2.0 to the package cache Fetching: Installing hl7.fhir.uv.tools#0.2.0 done. Version mismatch. This IG is version 4.0.1, while the IG 'hl7.fhir.uv.tools' is from version 5.0.0 (will try to run anyway) (00:09.910 / 00:55.081, 505Mb) Load Package hl7.fhir.uv.tools#0.2.0 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 (00:02.974 / 00:58.056, 1Gb) Load Content (00:00.000 / 00:58.056, 1Gb) Using en-US as the default narrative language. (no language information in Implementation Guide or command line (00:00.061 / 00:58.117, 1Gb) loadPrePages from FetchedFile[/scratch/repo/input/includes] as /scratch/repo/input/includes loadPrePages from FetchedFile[/scratch/repo/input/pagecontent] as /scratch/repo/input/pagecontent Fetch http://hl7.org/fhir/uv/cdisc-mapping/package-list.json for version check (00:00.089 / 00:58.207, 1Gb) Processing Conformance Resources (00:00.183 / 00:58.391, 1Gb) Load Dependency Info (00:00.000 / 00:58.391, 1Gb) Load Info (00:00.000 / 00:58.392, 1Gb) Load Resources (00:00.000 / 00:58.392, 1Gb) Load Paths (00:00.051 / 00:58.444, 1Gb) Generating Snapshots (00:00.000 / 00:58.445, 1Gb) Check R4 / R4B (00:00.010 / 00:58.455, 1Gb) Assign Comparison Ids (00:00.007 / 00:58.463, 1Gb) Propagating status (00:00.000 / 00:58.463, 1Gb) Generating Narratives (00:00.000 / 00:58.463, 1Gb) Validating Conformance Resources (00:00.154 / 00:58.618, 1Gb) Check profiles & code systems (00:04.510 / 01:03.129, 491Mb) Check realm rules (00:00.000 / 01:03.129, 491Mb) Previous Version Comparison (00:00.000 / 01:03.129, 491Mb) Validating Resources (00:00.014 / 01:03.143, 491Mb) Processing Provenance Records (00:00.000 / 01:03.144, 491Mb) Generating Outputs in /scratch/repo/output (00:00.000 / 01:03.144, 491Mb) Generate Native Outputs (00:00.230 / 01:03.375, 499Mb) Run Template (00:00.141 / 01:03.516, 507Mb) 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 onGenerate.r5-schemas: [get] Getting: http://build.fhir.org/fhir-single.xsd [get] To: /scratch/repo/input-cache/schemas/R5/fhir-single.xsd [get] Not modified - so not downloaded [get] Getting: http://build.fhir.org/fhir-xhtml.xsd [get] To: /scratch/repo/input-cache/schemas/R5/fhir-xhtml.xsd [get] Not modified - so not downloaded [get] Getting: http://build.fhir.org/xml.xsd [get] To: /scratch/repo/input-cache/schemas/R5/xml.xsd [get] Not modified - so not downloaded [get] Getting: http://build.fhir.org/xmldsig-core-schema.xsd [get] To: /scratch/repo/input-cache/schemas/R5/xmldsig-core-schema.xsd [get] Not modified - so not downloaded onGenerate.r4-schemas: [get] Getting: http://hl7.org/fhir/R4/fhir-single.xsd [get] To: /scratch/repo/input-cache/schemas/R4/fhir-single.xsd [get] Not modified - so not downloaded [get] Getting: http://hl7.org/fhir/R4/fhir-xhtml.xsd [get] To: /scratch/repo/input-cache/schemas/R4/fhir-xhtml.xsd [get] Not modified - so not downloaded [get] Getting: http://hl7.org/fhir/R4/xml.xsd [get] To: /scratch/repo/input-cache/schemas/R4/xml.xsd [get] Not modified - so not downloaded [get] Getting: http://hl7.org/fhir/R4/xmldsig-core-schema.xsd [get] To: /scratch/repo/input-cache/schemas/R4/xmldsig-core-schema.xsd [get] Not modified - so not downloaded 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.jira.setup: [xslt] Processing /scratch/repo/template/onGenerate-ig-updated.xml to /scratch/repo/template/properties.txt [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.genProperties.xslt [get] Getting: https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/_workgroups.xml [get] To: /scratch/repo/input-cache/workgroups.xml [get] https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/_workgroups.xml moved to https://raw.githubusercontent.com/HL7/JIRA-Spec-Artifacts/master/xml/_workgroups.xml [get] Getting: https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/FHIR-cdisc-mapping.xml [get] To: /scratch/repo/input-cache/jiraspec.xml [get] https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/FHIR-cdisc-mapping.xml moved to https://raw.githubusercontent.com/HL7/JIRA-Spec-Artifacts/master/xml/FHIR-cdisc-mapping.xml onGenerate.jira.packagelistcopy: [copy] Copying 1 file to /scratch/repo/template onGenerate.jira.packagelistget: onGenerate.jira.packagelistProcess: [xslt] Processing /scratch/repo/template/onGenerate.jira.package-list.tmp.xml to /scratch/repo/template/onGenerate.jira.package-list.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.package-list.xslt onGenerate.jira.packagelistSkip: onGenerate.jira.pubrequestProcess: onGenerate.jira.pubrequestSkip: onGenerate.jira.generate: [xslt] Processing /scratch/repo/template/onGenerate.jira.tmp.xml to /scratch/repo/template/onGenerate.jira.tmp2.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.process-pkg-list.xslt [xslt] Processing /scratch/repo/template/onGenerate.jira.tmp2.xml to /scratch/repo/template/onGenerate.jira.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.jira.xslt [xslt] Processing /scratch/repo/template/onGenerate.jira.xml to /scratch/repo/template/jira-new.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.normalize.xslt [xslt] Processing /scratch/repo/input-cache/jiraspec.xml to /scratch/repo/template/jira-current.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.normalize.xslt [copy] Copying 1 file to /scratch/repo onGenerate.jira.check: onGenerate.jira.skip-offline: onGenerate.jira.skip-missing: onGenerate.jira: onGenerate.extend: onGenerate: Template Done (00:01.337 / 01:04.854, 587Mb) Generate HTML Outputs (00:00.000 / 01:04.854, 587Mb) Generate Summaries (00:00.456 / 01:05.311, 619Mb) Generating Summary Outputs (00:00.000 / 01:05.311, 619Mb) ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console... DB Cumulative Time invested: 00:00:00.205 Sending Usage Stats to Server (00:05.729 / 01:11.040, 1Gb) ## Memory (MB): Use = 1200, Free = 17807, Total = 19008, Max = 19008 (00:00.007 / 01:11.048, 1Gb) Reclaiming memory... (00:00.000 / 01:11.048, 1Gb) ## Memory (MB): Use = 578, Free = 18429, Total = 19008, Max = 19008 (00:00.627 / 01:11.676, 586Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.007 / 01:11.684, 588Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.008 / 01:11.692, 588Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 01:11.692, 588Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 01:11.692, 588Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.532 / 01:12.225, 597Mb) Jekyll: Generating... (00:00.000 / 01:12.225, 597Mb) Jekyll: done in 0.297 seconds. (00:00.296 / 01:12.521, 597Mb) Checking Output HTML (00:00.818 / 01:13.340, 667Mb) found 547 files (00:00.004 / 01:13.345, 667Mb) .......................................... .......................................... ... 547 html files, 0 pages invalid xhtml (0%) (00:01.574 / 01:14.919, 1Gb) ... 4283 links, 1 broken links (0%) (00:00.000 / 01:14.920, 1Gb) Generate fragment-usage-analysis.csv (00:00.000 / 01:14.920, 1Gb) Build final .zip (00:00.012 / 01:14.932, 1Gb) Final .zip built (00:00.392 / 01:15.326, 1Gb) Built. Times: loading: 00:00.334, generate: 00:17.857, narrative generation: 00:00.154, validation: 00:04.508, realm-rules: 00:00.000, previous-version: 00:00.000, jekyll: 00:00.852, template: 00:01.337 (#3) (00:00.932 / 01:16.258, 754Mb) Generating QA (00:00.000 / 01:16.258, 754Mb) Validation output in /scratch/repo/output/qa.html Errors: 4, Warnings: 6, Info: 0, Broken Links: 1 (00:00.208 / 01:16.467, 794Mb) Finished. Max Memory Used = 1Gb (00:00.002 / 01:16.469, 794Mb)