INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/fhir-shorthand --branch master repo DEBUG:root:Time to deadline 35879.997976 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 35876.522074 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35875.000918 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-shorthand/ -out /scratch/repo DEBUG:root:Time to deadline 35870.012786 seconds FHIR IG Publisher Version 1.6.20 (Git# 7bbd1ce5defe). Built 2024-08-13T18:33:37.376Z (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-shorthand/ -out /scratch/repo Start Clock @ Monday, August 19, 2024, 3:07:47 PM Coordinated Universal Time (2024-08-19T15:07:47Z) Build FHIR IG from /scratch/repo (00:00.026 / 00:00.027, 89Mb) API keys loaded from /etc/fhir-settings.json (00:00.005 / 00:00.032, 89Mb) Package Cache: /var/lib/.fhir/packages (00:00.004 / 00:00.036, 89Mb) Load Template from hl7.fhir.template#current (00:01.445 / 00:01.482, 69Mb) Installing hl7.fhir.template#current to the package cache Fetching: Installing hl7.fhir.template#current done. Load Template from hl7.base.template#current (00:01.464 / 00:02.947, 141Mb) Installing hl7.base.template#current to the package cache Fetching: Installing hl7.base.template#current done. Load Template from fhir.base.template#current (00:00.180 / 00:03.127, 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 (00:04.345 / 00:07.473, 136Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.002 / 00:07.475, 136Mb) 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-13527661194019579130.log Connect to Terminology Server at http://tx.fhir.org (00:31.231 / 00:38.707, 718Mb) 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) (00:09.539 / 00:48.247, 478Mb) 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 (00:02.965 / 00:51.212, 1Gb) Load Content (00:00.000 / 00:51.213, 1Gb) Using en-US as the default narrative language. (no language information in Implementation Guide or command line (00:00.076 / 00:51.290, 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/shorthand/package-list.json for version check (00:00.072 / 00:51.362, 1Gb) Processing Conformance Resources (00:00.180 / 00:51.542, 1Gb) Load Dependency Info (00:00.000 / 00:51.543, 1Gb) Load Info (00:00.000 / 00:51.544, 1Gb) Load Resources (00:00.000 / 00:51.544, 1Gb) Load Paths (00:00.049 / 00:51.593, 1Gb) Generating Snapshots (00:00.000 / 00:51.594, 1Gb) Check R4 / R4B (00:00.006 / 00:51.601, 1Gb) Assign Comparison Ids (00:00.009 / 00:51.610, 1Gb) Propagating status (00:00.000 / 00:51.610, 1Gb) Generating Narratives (00:00.000 / 00:51.611, 1Gb) Validating Conformance Resources (00:00.133 / 00:51.744, 1Gb) Check profiles & code systems (00:02.129 / 00:53.873, 608Mb) Check realm rules (00:00.000 / 00:53.873, 608Mb) Previous Version Comparison (00:00.000 / 00:53.874, 608Mb) Installing hl7.fhir.uv.shorthand#3.0.0-ballot to the package cache Fetching: Installing hl7.fhir.uv.shorthand#3.0.0-ballot done. Installing hl7.terminology.r4#5.0.0 to the package cache Fetching: Installing hl7.terminology.r4#5.0.0 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 (00:27.750 / 01:21.625, 1Gb) Processing Provenance Records (00:00.000 / 01:21.625, 1Gb) Generating Outputs in /scratch/repo/output (00:00.000 / 01:21.625, 1Gb) Generate Native Outputs (00:00.170 / 01:21.796, 1Gb) Run Template (00:00.108 / 01:21.904, 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.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-shorthand.xml [get] To: /scratch/repo/input-cache/jiraspec.xml [get] https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/FHIR-shorthand.xml moved to https://raw.githubusercontent.com/HL7/JIRA-Spec-Artifacts/master/xml/FHIR-shorthand.xml onGenerate.jira.packagelistcopy: onGenerate.jira.packagelistget: [get] Getting: http://hl7.org/fhir/uv/shorthand/package-list.json [get] To: /scratch/repo/template/onGenerate.jira.workingpackage-list.json 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: [xslt] Processing /scratch/repo/template/onGenerate.jira.pubrequest.tmp.xml to /scratch/repo/template/onGenerate.jira.pubrequest.xml [xslt] Loading stylesheet /scratch/repo/template/scripts/onGenerate.pubrequest.xslt 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 (00:01.837 / 01:23.742, 1Gb) Generate HTML Outputs (00:00.000 / 01:23.742, 1Gb) Generate Summaries (00:00.181 / 01:23.923, 1Gb) Generating Summary Outputs (00:00.000 / 01:23.924, 1Gb) 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: 00:00:00.145 Sending Usage Stats to Server (00:06.407 / 01:30.332, 700Mb) ## Memory (MB): Use = 700, Free = 18307, Total = 19008, Max = 19008 (00:00.007 / 01:30.339, 703Mb) Reclaiming memory... (00:00.000 / 01:30.339, 703Mb) ## Memory (MB): Use = 618, Free = 18389, Total = 19008, Max = 19008 (00:00.642 / 01:30.982, 630Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.006 / 01:30.988, 630Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.007 / 01:30.995, 630Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 01:30.996, 630Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 01:30.996, 630Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.596 / 01:31.593, 634Mb) Jekyll: Generating... (00:00.000 / 01:31.593, 634Mb) Jekyll: done in 1.214 seconds. (00:01.213 / 01:32.806, 634Mb) Checking Output HTML (00:00.799 / 01:33.606, 706Mb) found 538 files (00:00.004 / 01:33.610, 706Mb) ......................................... ......................................... ... 538 html files, 0 pages invalid xhtml (0%) (00:00.926 / 01:34.536, 970Mb) ... 681 links, 0 broken links (0%) (00:00.000 / 01:34.537, 970Mb) Generate fragment-usage-analysis.csv (00:00.000 / 01:34.537, 970Mb) Build final .zip (00:00.010 / 01:34.548, 978Mb) Final .zip built (00:01.185 / 01:35.733, 980Mb) Built. Times: loading: 00:00.328, generate: 00:45.143, narrative generation: 00:00.132, validation: 00:02.128, realm-rules: 00:00.000, previous-version: 00:27.741, jekyll: 00:01.835, template: 00:01.837 (#3) (00:00.979 / 01:36.713, 1Gb) Generating QA (00:00.000 / 01:36.713, 1Gb) Validation output in /scratch/repo/output/qa.html Errors: 1, Warnings: 0, Info: 0, Broken Links: 0 (00:00.139 / 01:36.852, 1Gb) Finished. Max Memory Used = 1Gb (00:00.002 / 01:36.854, 1Gb)