INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/smart-app-launch --branch master repo DEBUG:root:Time to deadline 35879.997703 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 35879.07859 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35877.757812 seconds 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 -> 10.7.0 npm notice Changelog: npm notice Run `npm install -g npm@10.7.0` 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/smart-app-launch/ -out /scratch/repo DEBUG:root:Time to deadline 35872.109288 seconds FHIR IG Publisher Version 1.6.7 (Git# e4b86ee47f9e). Built 2024-05-10T06:19:45.471Z (4 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/smart-app-launch/ -out /scratch/repo Start Clock @ Tuesday, May 14, 2024, 8:28:51 PM Coordinated Universal Time (2024-05-14T20:28:51Z) Build FHIR IG from /scratch/repo (00:00.027 / 00:00.028, 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 / 00:00.036, 89Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.799 / 00:00.836, 37Mb) Load Template from #smart-template (00:00.725 / 00:01.561, 88Mb) Load Template from hl7.fhir.template#current (00:00.258 / 00:01.819, 95Mb) Installing hl7.fhir.template#current to the package cache Fetching: Installing hl7.fhir.template#current done. Load Template from hl7.base.template#current (00:01.215 / 00:03.035, 88Mb) Installing hl7.base.template#current to the package cache Fetching: Installing hl7.base.template#current done. Load Template from fhir.base.template#current (00:00.235 / 00:03.270, 96Mb) 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 (00:04.602 / 00:07.873, 360Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.003 / 00:07.876, 360Mb) 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-9860559745574714013.log Connect to Terminology Server at http://tx.fhir.org (00:44.167 / 00:52.043, 881Mb) 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 Dependency 'hl7.fhir.uv.extensions' has no id, so can't be referred to in markdown in the IG (00:02.472 / 00:54.516, 253Mb) Installing hl7.fhir.uv.extensions#5.1.0-snapshot1 to the package cache Fetching: 2024-05-14 20:29:46.630 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:88] Failed to resolve package hl7.fhir.uv.extensions#5.1.0-snapshot1 from server: https://packages.fhir.org (Not Found) 2024-05-14 20:29:46.824 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:88] Failed to resolve package hl7.fhir.uv.extensions#5.1.0-snapshot1 from server: https://packages2.fhir.org/packages (Not found) Installing hl7.fhir.uv.extensions#5.1.0 done. Version mismatch. This IG is version 4.0.1, while the IG 'hl7.fhir.uv.extensions' is from version 5.0.0 (will try to run anyway) (00:01.452 / 00:55.968, 333Mb) Installing hl7.terminology.r5#5.5.0 to the package cache Fetching: Installing hl7.terminology.r5#5.5.0 done. Ignore Dependency on Core FHIR hl7.fhir.r5.core#5.0.0, from package 'hl7.terminology.r5#5.5.0' (00:01.493 / 00:57.461, 437Mb) Load Package hl7.terminology.r5#5.5.0 Load Package hl7.fhir.uv.extensions#5.1.0 Dependency 'hl7.terminology' has no id, so can't be referred to in markdown in the IG (00:04.263 / 01:01.724, 528Mb) Installing hl7.terminology#5.5.0 to the package cache Fetching: Installing hl7.terminology#5.5.0 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. Load Package hl7.fhir.uv.extensions.r4#1.0.0 Load Package hl7.terminology#5.5.0 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) (00:08.014 / 01:09.739, 816Mb) 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 (00:03.472 / 01:13.211, 555Mb) Fetch http://hl7.org/fhir/smart-app-launch/package-list.json for version check (00:00.003 / 01:13.214, 555Mb) Load Content (00:00.121 / 01:13.336, 555Mb) loadPrePages from FetchedFile[/scratch/repo/input/includes] as /scratch/repo/input/includes loadPrePages from FetchedFile[/scratch/repo/input/pages] as /scratch/repo/input/pages Processing Conformance Resources (00:00.928 / 01:14.264, 587Mb) Load Dependency Info (00:00.001 / 01:14.266, 587Mb) Load Info (00:00.002 / 01:14.268, 587Mb) Load Resources (00:00.001 / 01:14.269, 587Mb) Load Paths (00:00.257 / 01:14.526, 619Mb) Generating Snapshots (00:00.000 / 01:14.527, 619Mb) Check R4 / R4B (00:00.953 / 01:15.480, 862Mb) Assign Comparison Ids (00:00.016 / 01:15.496, 873Mb) Propagating status (00:00.000 / 01:15.497, 873Mb) Generating Narratives (00:00.000 / 01:15.497, 873Mb) Validating Conformance Resources (00:01.137 / 01:16.634, 1Gb) Check profiles & code systems (00:15.780 / 01:32.414, 1Gb) Check realm rules (00:00.002 / 01:32.417, 1Gb) Previous Version Comparison (00:00.000 / 01:32.417, 1Gb) Validating Resources (00:00.022 / 01:32.439, 1Gb) Processing Provenance Records (00:01.727 / 01:34.167, 1Gb) Generating Outputs in /scratch/repo/output (00:00.000 / 01:34.168, 1Gb) Generate Native Outputs (00:00.324 / 01:34.492, 1Gb) Run Template (00:04.042 / 01:38.535, 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-smart.xml [get] To: /scratch/repo/input-cache/jiraspec.xml [get] https://github.com/HL7/JIRA-Spec-Artifacts/raw/master/xml/FHIR-smart.xml moved to https://raw.githubusercontent.com/HL7/JIRA-Spec-Artifacts/master/xml/FHIR-smart.xml onGenerate.jira.packagelistcopy: onGenerate.jira.packagelistget: [get] Getting: http://hl7.org/fhir/smart-app-launch/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 (00:03.213 / 01:41.748, 1Gb) Generate HTML Outputs (00:00.000 / 01:41.748, 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 (00:21.264 / 02:03.013, 1Gb) Generating Summary Outputs (00:00.000 / 02:03.013, 1Gb) Installing hl7.fhir.uv.extensions#5.1.0-snapshot1 to the package cache Fetching: 2024-05-14 20:30:57.550 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:88] Failed to resolve package hl7.fhir.uv.extensions#5.1.0-snapshot1 from server: https://packages.fhir.org (Not Found) 2024-05-14 20:30:57.682 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:88] Failed to resolve package hl7.fhir.uv.extensions#5.1.0-snapshot1 from server: https://packages2.fhir.org/packages (Not found) Installing hl7.fhir.uv.extensions#5.1.0Installing hl7.fhir.uv.extensions#5.1.0-snapshot1 to the package cache Fetching: 2024-05-14 20:31:02.022 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:88] Failed to resolve package hl7.fhir.uv.extensions#5.1.0-snapshot1 from server: https://packages.fhir.org (Not Found) 2024-05-14 20:31:02.058 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:88] Failed to resolve package hl7.fhir.uv.extensions#5.1.0-snapshot1 from server: https://packages2.fhir.org/packages (Not found) Installing hl7.fhir.uv.extensions#5.1.0DB Cumulative Time invested: 00:00:00.679 Sending Usage Stats to Server (00:08.640 / 02:11.654, 1Gb) ## Memory (MB): Use = 1936, Free = 17071, Total = 19008, Max = 19008 (00:00.009 / 02:11.663, 1Gb) Reclaiming memory... (00:00.000 / 02:11.664, 1Gb) ## Memory (MB): Use = 1117, Free = 17890, Total = 19008, Max = 19008 (00:01.380 / 02:13.045, 1Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.008 / 02:13.053, 1Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.007 / 02:13.060, 1Gb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 02:13.060, 1Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 02:13.060, 1Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.711 / 02:13.772, 1Gb) Jekyll: Generating... (00:00.000 / 02:13.772, 1Gb) Jekyll: done in 2.186 seconds. (00:02.185 / 02:15.958, 1Gb) Checking Output HTML (00:02.044 / 02:18.002, 1Gb) found 789 files (00:00.005 / 02:18.007, 1Gb) ......................................... ......................................... ... 789 html files, 0 pages invalid xhtml (0%) (00:08.153 / 02:26.161, 4Gb) ... 80032 links, 0 broken links (0%) (00:00.000 / 02:26.162, 4Gb) Generate fragment-usage-analysis.csv (00:00.000 / 02:26.162, 4Gb) Build final .zip (00:00.007 / 02:26.169, 4Gb) Final .zip built (00:00.871 / 02:27.041, 4Gb) Installing hl7.fhir.uv.extensions#5.1.0-snapshot1 to the package cache Fetching: 2024-05-14 20:31:19.574 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:88] Failed to resolve package hl7.fhir.uv.extensions#5.1.0-snapshot1 from server: https://packages.fhir.org (Not Found) 2024-05-14 20:31:19.684 [main] INFO o.h.f.u.npm.BasePackageCacheManager [BasePackageCacheManager.java:88] Failed to resolve package hl7.fhir.uv.extensions#5.1.0-snapshot1 from server: https://packages2.fhir.org/packages (Not found) Installing hl7.fhir.uv.extensions#5.1.0Built. Times: loading: 00:00.927, generate: 01:17.829, narrative generation: 00:01.137, realm-rules: 00:00.000, previous-version: 00:00.000, jekyll: 00:02.933, validation: 00:17.504 (#19), template: 00:03.212 (#3) (00:05.057 / 02:32.099, 1Gb) Generating QA (00:00.000 / 02:32.099, 1Gb) Validation output in /scratch/repo/output/qa.html Errors: 0, Warnings: 0, Info: 0, Broken Links: 0 (00:00.983 / 02:33.082, 1Gb) Finished. Max Memory Used = 4Gb (00:00.010 / 02:33.092, 1Gb)