INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/IHE/pharm-supply --branch master repo DEBUG:root:Time to deadline 35879.997839 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 35878.075378 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35876.754995 seconds 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 rimraf@2.6.3: Rimraf versions prior to v4 are no longer supported 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 -> 10.8.1 npm notice Changelog: npm notice Run `npm install -g npm@10.8.1` 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/pharm-supply/ -out /scratch/repo DEBUG:root:Time to deadline 35871.715396 seconds FHIR IG Publisher Version 1.6.11 (Git# c24a6a19351a). Built 2024-06-07T06:35:31.259Z (11 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/pharm-supply/ -out /scratch/repo Start Clock @ Tuesday, June 18, 2024, 9:00:20 PM Coordinated Universal Time (2024-06-18T21:00:20Z) Build FHIR IG from /scratch/repo (00:00.021 / 00:00.022, 89Mb) API keys loaded from /etc/fhir-settings.json (00:00.003 / 00:00.025, 89Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.028, 89Mb) Run Sushi on /scratch/repo (00:00.004 / 00:00.033, 89Mb) Sushi: info Running SUSHI v3.11.0 (implements FHIR Shorthand specification v3.0.0-ballot) (00:00.516 / 00:00.550, 97Mb) Sushi: info Arguments: (00:00.000 / 00:00.551, 97Mb) Sushi: info --require-latest (00:00.000 / 00:00.551, 97Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.551, 97Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.552, 97Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.605 / 00:01.157, 97Mb) Sushi: warn Configuration property pages/volume2.md contains unexpected property: title:"Volume 2. Check that this property is spelled, capitalized, and indented correctly. If this is a page, it should end with .md, .xml, or .html. (00:00.172 / 00:01.330, 97Mb) Sushi: info Importing FSH text... (00:00.000 / 00:01.330, 97Mb) Sushi: info Preprocessed 6 documents with 0 aliases. (00:00.227 / 00:01.557, 97Mb) Sushi: info Imported 18 definitions and 5 instances. (00:00.020 / 00:01.578, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.tools#current... (00:00.001 / 00:01.580, 97Mb) Sushi: info Did not find hl7.fhir.uv.tools#current in /home/fhiruser/.fhir/packages. (00:00.025 / 00:01.606, 97Mb) Sushi: info Downloading hl7.fhir.uv.tools#current... https://build.fhir.org/ig/FHIR/fhir-tools-ig/branches/master/package.tgz (00:00.113 / 00:01.719, 97Mb) Sushi: info Downloaded hl7.fhir.uv.tools#current (00:00.018 / 00:01.737, 97Mb) Sushi: info Loaded package hl7.fhir.uv.tools#current (00:00.107 / 00:01.844, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.terminology.r5#5.5.0... (00:00.521 / 00:02.366, 97Mb) Sushi: info Did not find hl7.terminology.r5#5.5.0 in /home/fhiruser/.fhir/packages. (00:00.022 / 00:02.388, 97Mb) Sushi: info Downloading hl7.terminology.r5#5.5.0... https://packages.fhir.org/hl7.terminology.r5/5.5.0 (00:00.000 / 00:02.388, 97Mb) Sushi: info Downloaded hl7.terminology.r5#5.5.0 (00:02.234 / 00:04.623, 97Mb) Sushi: info Loaded package hl7.terminology.r5#5.5.0 (00:01.848 / 00:06.472, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.uv.extensions.r5#5.1.0... (00:00.443 / 00:06.916, 97Mb) Sushi: info Did not find hl7.fhir.uv.extensions.r5#5.1.0 in /home/fhiruser/.fhir/packages. (00:00.361 / 00:07.277, 97Mb) Sushi: info Downloading hl7.fhir.uv.extensions.r5#5.1.0... https://packages.fhir.org/hl7.fhir.uv.extensions.r5/5.1.0 (00:00.000 / 00:07.278, 97Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r5#5.1.0 (00:02.094 / 00:09.372, 97Mb) Sushi: info Loaded package hl7.fhir.uv.extensions.r5#5.1.0 (00:01.162 / 00:10.535, 97Mb) Sushi: info Checking /home/fhiruser/.fhir/packages for hl7.fhir.r5.core#5.0.0... (00:00.000 / 00:10.536, 97Mb) Sushi: info Did not find hl7.fhir.r5.core#5.0.0 in /home/fhiruser/.fhir/packages. (00:00.524 / 00:11.061, 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 / 00:11.061, 97Mb) Sushi: info Downloaded hl7.fhir.r5.core#5.0.0 (00:02.879 / 00:13.940, 97Mb) Sushi: info Loaded package hl7.fhir.r5.core#5.0.0 (00:02.431 / 00:16.372, 97Mb) Sushi: info Found 4 files in input/* resource folders that were neither XML nor JSON. These files were not processed as resources by SUSHI. To see the unprocessed files in the logs, run SUSHI with the "--log-level debug" flag. (00:00.043 / 00:16.416, 97Mb) Sushi: info Converting FSH to FHIR resources... (00:00.001 / 00:16.417, 97Mb) Sushi: info Converted 14 FHIR StructureDefinitions. (00:01.088 / 00:17.506, 97Mb) Sushi: info Converted 2 FHIR CodeSystems. (00:00.053 / 00:17.559, 97Mb) Sushi: info Converted 2 FHIR ValueSets. (00:00.096 / 00:17.656, 97Mb) Sushi: info Converted 5 FHIR instances. (00:00.075 / 00:17.732, 97Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.001 / 00:17.733, 97Mb) Sushi: info Exported 23 FHIR resources as JSON. (00:00.045 / 00:17.779, 97Mb) Sushi: info Assembling Implementation Guide sources... (00:00.001 / 00:17.781, 97Mb) Sushi: info Generated ImplementationGuide-ihe.pharm.supply.json (00:00.010 / 00:17.792, 97Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:17.792, 97Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:17.794, 97Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:17.794, 97Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:17.795, 97Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:17.795, 97Mb) Sushi: | | 5 | 1 | 8 | 0 | | (00:00.000 / 00:17.795, 97Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:17.796, 97Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:17.796, 97Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:17.796, 97Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:17.796, 97Mb) Sushi: | | 2 | 2 | 5 | | (00:00.000 / 00:17.796, 97Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:17.797, 97Mb) Sushi: | | (00:00.000 / 00:17.797, 97Mb) Sushi: =================================================================== (00:00.000 / 00:17.797, 97Mb) Sushi: | Not bad, but you cod do batter! 0 Errors 1 Warning | (00:00.000 / 00:17.797, 97Mb) Sushi: =================================================================== (00:00.000 / 00:17.797, 97Mb) Load Template from ihe.fhir.template#current (00:00.637 / 00:18.435, 37Mb) Installing ihe.fhir.template#current to the package cache Fetching: Installing ihe.fhir.template#current done. Load Template from fhir.base.template#current (00:01.128 / 00:19.564, 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 (00:03.705 / 00:23.269, 127Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.002 / 00:23.271, 127Mb) Core Package hl7.fhir.r5.core#5.0.0 Running Terminology Log: /tmp/ohfu-fhir-ig-3378323820886363343.log Connect to Terminology Server at http://tx.fhir.org (00:04.598 / 00:27.870, 575Mb) 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.r5#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. Load Package hl7.fhir.uv.tools#0.2.0 Initialization complete (00:05.169 / 00:33.040, 1Gb) Load Content (00:00.000 / 00:33.040, 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/data] as /scratch/repo/input/data loadPrePages from FetchedFile[/scratch/repo/input/pagecontent] as /scratch/repo/input/pagecontent Fetch http://profiles.ihe.net/PHARM/supply/package-list.json for version check (00:00.993 / 00:34.033, 414Mb) Processing Conformance Resources (00:00.143 / 00:34.177, 414Mb) Load Dependency Info (00:00.001 / 00:34.178, 414Mb) Load Info (00:00.001 / 00:34.180, 414Mb) Load Resources (00:00.000 / 00:34.180, 418Mb) Load Paths (00:00.125 / 00:34.305, 438Mb) Generating Snapshots (00:00.000 / 00:34.306, 438Mb) Check R4 / R4B (00:00.377 / 00:34.683, 550Mb) Assign Comparison Ids (00:00.007 / 00:34.691, 550Mb) Propagating status (00:00.000 / 00:34.691, 550Mb) Generating Narratives (00:00.000 / 00:34.691, 550Mb) Validating Conformance Resources (00:00.933 / 00:35.624, 934Mb) Check profiles & code systems (00:04.013 / 00:39.637, 1Gb) Check realm rules (00:00.002 / 00:39.640, 1Gb) Previous Version Comparison (00:00.000 / 00:39.640, 1Gb) Validating Resources (00:00.013 / 00:39.653, 1Gb) Processing Provenance Records (00:00.162 / 00:39.816, 1Gb) Generating Outputs in /scratch/repo/output (00:00.005 / 00:39.821, 1Gb) Generate Native Outputs (00:00.247 / 00:40.069, 1Gb) Run Template (00:03.129 / 00:43.199, 765Mb) 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 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 (00:03.318 / 00:46.517, 822Mb) Generate HTML Outputs (00:00.000 / 00:46.517, 822Mb) 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 (00:09.340 / 00:55.858, 2Gb) Generating Summary Outputs (00:00.000 / 00:55.858, 2Gb) DB Cumulative Time invested: 00:00:00.466 Sending Usage Stats to Server (00:02.570 / 00:58.429, 2Gb) ## Memory (MB): Use = 2792, Free = 16215, Total = 19008, Max = 19008 (00:00.006 / 00:58.435, 2Gb) Reclaiming memory... (00:00.000 / 00:58.435, 2Gb) ## Memory (MB): Use = 819, Free = 18184, Total = 19008, Max = 19008 (00:00.764 / 00:59.200, 831Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 00:59.202, 833Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 00:59.202, 833Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 00:59.202, 833Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 00:59.202, 833Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.435 / 00:59.637, 851Mb) Jekyll: Generating... (00:00.000 / 00:59.638, 851Mb) Jekyll: done in 2.068 seconds. (00:02.067 / 01:01.705, 867Mb) Checking Output HTML (00:00.471 / 01:02.176, 1Gb) found 949 files (00:00.005 / 01:02.182, 1Gb) ......................................... ......................................... ... 949 html files, 0 pages invalid xhtml (0%) (00:06.299 / 01:08.481, 1Gb) ... 79661 links, 11 broken links (0%) (00:00.000 / 01:08.481, 1Gb) Generate fragment-usage-analysis.csv (00:00.000 / 01:08.481, 1Gb) Build final .zip (00:00.007 / 01:08.489, 1Gb) Final .zip built (00:00.669 / 01:09.158, 1Gb) Built. Times: loading: 00:01.135, generate: 00:36.101, narrative generation: 00:00.933, realm-rules: 00:00.000, previous-version: 00:00.000, jekyll: 00:02.523, validation: 00:04.167 (#25), template: 00:03.318 (#3) (00:01.130 / 01:10.289, 2Gb) Generating QA (00:00.000 / 01:10.289, 2Gb) Validation output in /scratch/repo/output/qa.html Errors: 14, Warnings: 21, Info: 27, Broken Links: 11 (00:00.576 / 01:10.865, 2Gb) Finished. Max Memory Used = 2Gb (00:00.010 / 01:10.876, 2Gb)