INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/costateixeira/smart-anc --branch add-workflows repo DEBUG:root:Time to deadline 35879.997582 seconds Cloning into 'repo'... 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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 35771.303698 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35770.232826 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 -> 10.8.3 npm notice Changelog: npm notice Run `npm install -g npm@10.8.3` 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/costateixeira/smart-anc/ -out /scratch/repo DEBUG:root:Time to deadline 35765.188794 seconds FHIR IG Publisher Version 1.6.23 (Git# 7018cc10a866). Built 2024-09-09T19:42:44.328Z (9 hours 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/costateixeira/smart-anc/ -out /scratch/repo Start Clock @ Tuesday, September 10, 2024, 4:53:32 AM Coordinated Universal Time (2024-09-10T04:53:32Z) Build FHIR IG from /scratch/repo (00:00.033 / 00:00.034, 89Mb) API keys loaded from /etc/fhir-settings.json (00:00.003 / 00:00.037, 89Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.041, 89Mb) Load Template from cqf.fhir.template#0.4.0 (00:01.150 / 00:01.191, 69Mb) Installing cqf.fhir.template#0.4.0 to the package cache Fetching: Installing cqf.fhir.template#0.4.0 done. Load Template from fhir.base.template#0.6.0 (00:01.378 / 00:02.570, 101Mb) Installing fhir.base.template#0.6.0 to the package cache Fetching: Installing fhir.base.template#0.6.0 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 (00:05.743 / 00:08.313, 128Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.003 / 00:08.316, 128Mb) 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-5996066868704864491.log Connect to Terminology Server at http://tx.fhir.org (00:53.175 / 01:01.491, 743Mb) 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.cpg#1.0.0 to the package cache Fetching: Installing hl7.fhir.uv.cpg#1.0.0 done. Load Package hl7.fhir.uv.cpg#1.0.0 Installing hl7.fhir.us.cqfmeasures#current to the package cache Fetching: Installing hl7.fhir.us.cqfmeasures#current done. Installing fhir.cqf.common#4.0.1 to the package cache Fetching: Installing fhir.cqf.common#4.0.1 done. Load Package fhir.cqf.common#4.0.1 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.crmi#1.0.0 to the package cache Fetching: Installing hl7.fhir.uv.crmi#1.0.0 done. Load Package hl7.fhir.uv.crmi#1.0.0 Installing hl7.fhir.uv.cql#1.0.0 to the package cache Fetching: Installing hl7.fhir.uv.cql#1.0.0 done. Load Package hl7.fhir.uv.cql#1.0.0 Load Package hl7.fhir.us.cqfmeasures#current 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) (00:25.141 / 01:26.633, 1Gb) 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 (00:02.668 / 01:29.302, 937Mb) Load Content (00:00.000 / 01:29.302, 937Mb) Using en-US as the default narrative language. (no language information in Implementation Guide or command line (00:00.091 / 01:29.393, 945Mb) loadPrePages from FetchedFile[/scratch/repo/input/includes] as /scratch/repo/input/includes loadPrePages from FetchedFile[/scratch/repo/input/pagecontent] as /scratch/repo/input/pagecontent loadPrePages from FetchedFile[/scratch/repo/input/pagecontent/assets] as /scratch/repo/input/pagecontent loadPrePages from FetchedFile[/scratch/repo/input/pagecontent/assets/images] as /scratch/repo/input/pagecontent Fetch http://fhir.org/guides/who/anc-cds/package-list.json for version check (00:19.053 / 01:48.447, 1Gb) Processing Conformance Resources (00:00.594 / 01:49.042, 869Mb) Load Dependency Info (00:00.027 / 01:49.070, 877Mb) Load Info (00:00.004 / 01:49.074, 877Mb) Load Resources (00:00.002 / 01:49.077, 881Mb) Load Paths (00:15.190 / 02:04.268, 4Gb) Generating Snapshots (00:00.003 / 02:04.271, 4Gb) Unable to generate snapshot @3 for http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-patient: Attempt to fetch the profile http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-base-patient|0.3.0 while generating the snapshot for it Unable to generate snapshot @3 for http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-patient: Profile ANCPatient (http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-patient), element StructureDefinition-anc-patient.html. Error generating snapshot: Error sorting Differential: The element Patient.identifier @diff[1] is out of order (and maybe others after it) Unable to generate snapshot @3 for http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-encounter: Attempt to fetch the profile http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-base-encounter|0.3.0 while generating the snapshot for it Unable to generate snapshot @3 for http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-encounter: Attempt to use a snapshot on profile 'http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-base-encounter' as Base for generating a snapshot for the profile http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-encounter before it is generated Unable to generate snapshot @3 for http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-encounter: Attempt to use a snapshot on profile 'http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-base-encounter' as Base for generating a snapshot for the profile http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-encounter before it is generated Unable to generate snapshot @3 for http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-encounter: Attempt to use a snapshot on profile 'http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-base-encounter' as Base for generating a snapshot for the profile http://fhir.org/guides/who/anc-cds/StructureDefinition/anc-encounter before it is generated Check R4 / R4B (00:12.959 / 02:17.231, 11Gb) Assign Comparison Ids (00:00.238 / 02:17.469, 11Gb) Propagating status (00:00.002 / 02:17.472, 11Gb) Generating Narratives (00:00.000 / 02:17.472, 11Gb) Validating Conformance Resources (00:22.324 / 02:39.797, 2Gb) Check profiles & code systems (02:26.274 / 05:06.071, 6Gb) Check realm rules (00:00.036 / 05:06.108, 6Gb) Previous Version Comparison (00:00.002 / 05:06.110, 6Gb) Validating Resources (00:00.231 / 05:06.342, 6Gb) Processing Provenance Records (00:11.846 / 05:18.189, 7Gb) Generating Outputs in /scratch/repo/output (00:00.001 / 05:18.190, 7Gb) Generate Native Outputs (00:00.823 / 05:19.014, 8Gb) Run Template (04:57.533 / 10:16.547, 3Gb) 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 20 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 (00:03.361 / 10:19.909, 3Gb) Generate HTML Outputs (00:00.003 / 10:19.912, 3Gb) ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console... Error from http://tx.fhir.org/r4: Unable to provide support for code system http://fhir.org/guides/who/anc-cds/CodeSystem/anc-custom [x-request-id: 154-7333022] Error from http://tx.fhir.org/r4: Unable to provide support for code system http://fhir.org/guides/who/anc-cds/CodeSystem/anc-custom [x-request-id: 154-7333025] Error from http://tx.fhir.org/r4: Unable to provide support for code system http://unitsofmeasure.org/ [x-request-id: 154-7333074] Error from http://tx.fhir.org/r4: Unable to provide support for code system http://unitsofmeasure.org/ [x-request-id: 154-7333082] XSLT Error: Error reported by XML parser: Invalid byte 1 of 1-byte UTF-8 sequence. Exception generating xslt page /scratch/repo/temp/pages/_includes/assets/images/data-element-processing.jpg for _includes/assets/images/data-element-processing.jpg in /scratch/repo/temp/pages: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Invalid byte 1 of 1-byte UTF-8 sequence. (05:11.449 / 15:31.361, 11Gb) XSLT Error: Error reported by XML parser: Invalid byte 1 of 1-byte UTF-8 sequence. Exception generating xslt page /scratch/repo/temp/pages/_includes/assets/images/test-case-processing.jpg for _includes/assets/images/test-case-processing.jpg in /scratch/repo/temp/pages: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Invalid byte 1 of 1-byte UTF-8 sequence. (00:00.023 / 15:31.384, 11Gb) XSLT Error: Error reported by XML parser: Invalid byte 1 of 1-byte UTF-8 sequence. Exception generating xslt page /scratch/repo/temp/pages/_includes/assets/images/dak-to-cpg.jpg for _includes/assets/images/dak-to-cpg.jpg in /scratch/repo/temp/pages: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Invalid byte 1 of 1-byte UTF-8 sequence. (00:00.045 / 15:31.430, 11Gb) XSLT Error: Error reported by XML parser: Invalid byte 1 of 1-byte UTF-8 sequence. Exception generating xslt page /scratch/repo/temp/pages/_includes/assets/images/decision-table-processing.jpg for _includes/assets/images/decision-table-processing.jpg in /scratch/repo/temp/pages: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Invalid byte 1 of 1-byte UTF-8 sequence. (00:00.020 / 15:31.451, 11Gb) Generate Summaries (00:12.953 / 15:44.404, 5Gb) Generating Summary Outputs (00:00.000 / 15:44.404, 5Gb) Installing hl7.fhir.uv.extensions#5.1.0 to the package cache Fetching: Installing hl7.fhir.uv.extensions#5.1.0 done. Installing hl7.terminology.r5#5.5.0 to the package cache Fetching: Installing hl7.terminology.r5#5.5.0 done. Table of contents has a section with more than 222 entries. Collapsing will not work reliably DB Cumulative Time invested: 00:00:53.386 Sending Usage Stats to Server (02:06.619 / 17:51.023, 4Gb) ## Memory (MB): Use = 5058, Free = 13949, Total = 19008, Max = 19008 (00:00.021 / 17:51.044, 4Gb) Reclaiming memory... (00:00.000 / 17:51.044, 4Gb) ## Memory (MB): Use = 3923, Free = 15084, Total = 19008, Max = 19008 (00:03.394 / 17:54.439, 3Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.005 / 17:54.444, 3Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.005 / 17:54.450, 3Gb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 17:54.451, 3Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 17:54.451, 3Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.573 / 17:55.025, 3Gb) Jekyll: Generating... (00:00.000 / 17:55.025, 3Gb) Jekyll: done in 57.141 seconds. (00:57.140 / 18:52.165, 3Gb) Checking Output HTML (00:49.634 / 19:41.800, 5Gb) found 16129 files (00:00.082 / 19:41.882, 5Gb) ....Sending usage stats failed: Connection timed out .................................... ........................................ Publishing Content Failed: The