INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/HL7/fhir-bfdr --branch master repo DEBUG:root:Time to deadline 35879.997685 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 35861.90207 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35860.832557 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 140 packages in 7s 15 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 11.5.2 npm notice Changelog: npm notice Run `npm install -g npm@11.5.2` 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-bfdr/ -out /scratch/repo DEBUG:root:Time to deadline 35853.628932 seconds FHIR IG Publisher Version 2.0.12 (Git# 1e7f5af908a3). Built 2025-07-27T20:11:20.240Z (9 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-bfdr/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Wednesday, August 6, 2025, 2:22:02 PM Coordinated Universal Time (2025-08-06T14:22:02Z) Build FHIR IG from /scratch/repo (00:00.033 / 00:00.033, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.002 / 00:00.036, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.039, 97Mb) Found dependency on hl7.fhir.us.core#5.0.1 in Sushi config. Pre-installing (00:00.007 / 00:00.046, 97Mb) Installing hl7.fhir.us.core#5.0.1 to the package cache  Fetching:  Installing hl7.fhir.us.core#5.0.1  done. Found dependency on us.nlm.vsac#0.19.0 in Sushi config. Pre-installing (00:03.785 / 00:03.832, 97Mb) Installing us.nlm.vsac#0.19.0 to the package cache  Fetching:  Installing us.nlm.vsac#0.19.0  done. Found dependency on us.cdc.phinvads#0.12.0 in Sushi config. Pre-installing (00:08.264 / 00:12.096, 593Mb) Installing us.cdc.phinvads#0.12.0 to the package cache  Fetching:  Installing us.cdc.phinvads#0.12.0  done. Found dependency on hl7.fhir.us.vr-common-library#2.0.0 in Sushi config. Pre-installing (00:12.033 / 00:24.129, 921Mb) Installing hl7.fhir.us.vr-common-library#2.0.0 to the package cache  Fetching:  Installing hl7.fhir.us.vr-common-library#2.0.0  done. Found dependency on hl7.fhir.us.odh#1.3.0 in Sushi config. Pre-installing (00:01.907 / 00:26.036, 921Mb) Installing hl7.fhir.us.odh#1.3.0 to the package cache  Fetching:  Installing hl7.fhir.us.odh#1.3.0  done. Run Sushi on /scratch/repo (00:00.650 / 00:26.686, 933Mb) Sushi: info Running SUSHI v3.16.3 (implements FHIR Shorthand specification v3.0.0) (00:00.747 / 00:27.434, 937Mb) Sushi: info Arguments: (00:00.000 / 00:27.434, 937Mb) Sushi: info --require-latest (00:00.000 / 00:27.434, 937Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:27.435, 937Mb) Sushi: info /scratch/repo (00:00.000 / 00:27.435, 937Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.777 / 00:28.213, 937Mb) Sushi: info Importing FSH text... (00:00.178 / 00:28.392, 937Mb) Sushi: warn RuleSet UnmatchedMapConcept contains unused parameters: targetcode, targetdisplay (00:00.277 / 00:28.669, 937Mb) Sushi: File: /scratch/repo/input/fsh/conceptmaps/DEF_ConceptMapRuleSets.fsh (00:00.000 / 00:28.669, 937Mb) Sushi: Line: 28 - 34 (00:00.000 / 00:28.669, 937Mb) Sushi: warn RuleSet RequireMetaProfile contains unused parameter: profile (00:00.578 / 00:29.248, 937Mb) Sushi: File: /scratch/repo/input/fsh/rulesets/DEF_Rulesets.fsh (00:00.000 / 00:29.248, 937Mb) Sushi: Line: 36 - 47 (00:00.000 / 00:29.249, 937Mb) Sushi: info Preprocessed 326 documents with 59 aliases. (00:00.031 / 00:29.280, 937Mb) Sushi: info Imported 126 definitions and 201 instances. (00:00.715 / 00:29.996, 937Mb) Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.183 / 00:30.179, 937Mb) Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.7.1 (00:00.644 / 00:30.824, 937Mb) Sushi: info Attempting to download hl7.fhir.uv.tools.r4#0.7.1 from https://packages.fhir.org/hl7.fhir.uv.tools.r4/0.7.1 (00:00.001 / 00:30.825, 937Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.7.1 (00:00.850 / 00:31.676, 937Mb) Sushi: info Cached hl7.fhir.uv.tools.r4#0.7.1 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.tools.r4#0.7.1 (00:00.003 / 00:31.680, 937Mb) Sushi: info Loaded hl7.fhir.uv.tools.r4#0.7.1 with 105 resources (00:00.080 / 00:31.760, 937Mb) Sushi: info Resolved hl7.terminology.r4#latest to concrete version 6.5.0 (00:00.477 / 00:32.238, 937Mb) Sushi: info Attempting to download hl7.terminology.r4#6.5.0 from https://packages.fhir.org/hl7.terminology.r4/6.5.0 (00:00.000 / 00:32.238, 937Mb) Sushi: info Downloaded hl7.terminology.r4#6.5.0 (00:02.506 / 00:34.745, 937Mb) Sushi: info Cached hl7.terminology.r4#6.5.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#6.5.0 (00:00.001 / 00:34.746, 937Mb) Sushi: info Loaded hl7.terminology.r4#6.5.0 with 4392 resources (00:01.906 / 00:36.653, 937Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.458 / 00:37.112, 937Mb) Sushi: info Attempting to download hl7.fhir.uv.extensions.r4#5.2.0 from https://packages.fhir.org/hl7.fhir.uv.extensions.r4/5.2.0 (00:00.000 / 00:37.112, 937Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.530 / 00:38.643, 937Mb) Sushi: info Cached hl7.fhir.uv.extensions.r4#5.2.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.extensions.r4#5.2.0 (00:00.002 / 00:38.645, 937Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.397 / 00:39.043, 937Mb) Sushi: info Loaded hl7.fhir.us.core#5.0.1 with 194 resources (00:00.122 / 00:39.166, 937Mb) Sushi: info Loaded us.nlm.vsac#0.19.0 with 15332 resources (00:11.634 / 00:50.800, 937Mb) Sushi: info Loaded us.cdc.phinvads#0.12.0 with 1967 resources (00:02.600 / 00:53.401, 937Mb) Sushi: info Loaded hl7.fhir.us.vr-common-library#2.0.0 with 91 resources (00:00.172 / 00:53.573, 937Mb) Sushi: info Loaded hl7.fhir.us.odh#1.3.0 with 10 resources (00:00.026 / 00:53.599, 937Mb) Sushi: info Attempting to download hl7.fhir.r4.core#4.0.1 from https://packages.fhir.org/hl7.fhir.r4.core/4.0.1 (00:00.000 / 00:53.600, 937Mb) Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:02.893 / 00:56.493, 937Mb) Sushi: info Cached hl7.fhir.r4.core#4.0.1 to /home/fhiruser/.fhir/packages/hl7.fhir.r4.core#4.0.1 (00:00.002 / 00:56.495, 937Mb) Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.662 / 00:58.158, 937Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.014 / 00:58.172, 937Mb) Sushi: info Converting FSH to FHIR resources... (00:00.062 / 00:58.235, 937Mb) Sushi: info Converted 101 FHIR StructureDefinitions. (00:20.176 / 01:18.412, 937Mb) Sushi: info Converted 2 FHIR CodeSystems. (00:00.052 / 01:18.465, 937Mb) Sushi: info Converted 23 FHIR ValueSets. (00:00.682 / 01:19.147, 937Mb) Sushi: info Converted 201 FHIR instances. (00:38.845 / 01:57.993, 937Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.008 / 01:58.001, 937Mb) Sushi: info Exported 327 FHIR resources as JSON. (00:00.652 / 01:58.654, 937Mb) Sushi: info Assembling Implementation Guide sources... (00:00.018 / 01:58.673, 937Mb) Sushi: warn Files not in the supported file types (.md and .xml) were detected. These files will be included without any processing. (00:01.060 / 01:59.734, 937Mb) Sushi: File: /scratch/repo/input/pagecontent (00:00.000 / 01:59.734, 937Mb) Sushi: info Generated ImplementationGuide-hl7.fhir.us.bfdr.json (00:00.006 / 01:59.741, 937Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 01:59.741, 937Mb) Sushi: info The sample-ig located at https://github.com/FHIR/sample-ig contains scripts useful for downloading and running the IG Publisher. (00:00.000 / 01:59.741, 937Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.002 / 01:59.744, 937Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:59.744, 937Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 01:59.744, 937Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:59.745, 937Mb) Sushi: | | 96 | 5 | 0 | 0 | | (00:00.000 / 01:59.745, 937Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:59.745, 937Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:59.745, 937Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 01:59.745, 937Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 01:59.745, 937Mb) Sushi: | | 23 | 2 | 201 | | (00:00.000 / 01:59.746, 937Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 01:59.746, 937Mb) Sushi: | | (00:00.000 / 01:59.746, 937Mb) Sushi: =================================================================== (00:00.000 / 01:59.746, 937Mb) Sushi: | You should gut it out. 0 Errors 3 Warnings | (00:00.000 / 01:59.746, 937Mb) Sushi: =================================================================== (00:00.000 / 01:59.746, 937Mb) Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.912 / 02:00.659, 57Mb) Load Template from hl7.fhir.template#current (00:00.761 / 02:01.420, 65Mb) Installing hl7.fhir.template#current to the package cache  Fetching:  Installing hl7.fhir.template#current  done.  Load Template from hl7.base.template#current (00:00.615 / 02:02.035, 113Mb) Installing hl7.base.template#current to the package cache  Fetching:  Installing hl7.base.template#current  done.  Load Template from fhir.base.template#current (00:00.126 / 02:02.162, 113Mb) Installing fhir.base.template#current to the package cache  Fetching:  Installing fhir.base.template#current  done. Root directory: /scratch/repo (00:04.144 / 02:06.308, 425Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.003 / 02:06.311, 425Mb) Core Package hl7.fhir.r4.core#4.0.1 Running Terminology Log: /tmp/ohfu-fhir-ig-6548774851444430334.html Connect to Terminology Server at http://tx.fhir.org (00:22.573 / 02:28.884, 630Mb) Installing hl7.fhir.pubpack#0.2.3 to the package cache  Fetching:  Installing hl7.fhir.pubpack#0.2.3  done. Load Package hl7.fhir.pubpack#0.2.3 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.r4#6.5.0 Installing hl7.fhir.uv.extensions.r4#5.3.0-ballot-tc1 to the package cache  Fetching:  Installing hl7.fhir.uv.extensions.r4#5.3.0-ballot-tc1  done. Load Package hl7.fhir.uv.extensions.r4#5.3.0-ballot-tc1 Installing hl7.terminology.r4#3.1.0 to the package cache  Fetching:  Installing hl7.terminology.r4#3.1.0  done. Load Package hl7.terminology.r4#3.1.0 Installing hl7.fhir.uv.bulkdata#2.0.0 to the package cache  Fetching:  Installing hl7.fhir.uv.bulkdata#2.0.0  done. Load Package hl7.fhir.uv.bulkdata#2.0.0 Installing hl7.fhir.uv.smart-app-launch#2.0.0 to the package cache  Fetching:  Installing hl7.fhir.uv.smart-app-launch#2.0.0  done. Load Package hl7.fhir.uv.smart-app-launch#2.0.0 Installing us.nlm.vsac#0.7.0 to the package cache  Fetching:  Installing us.nlm.vsac#0.7.0  done. Load Package us.nlm.vsac#0.7.0 Installing hl7.fhir.uv.sdc#3.0.0 to the package cache  Fetching:  Installing hl7.fhir.uv.sdc#3.0.0  done. Ignore Dependency on Core FHIR hl7.fhir.r4.examples#4.0.1, from package 'hl7.fhir.uv.sdc#3.0.0' (01:33.943 / 04:02.828, 420Mb) Load Package hl7.fhir.uv.sdc#3.0.0 Load Package hl7.fhir.us.core#5.0.1 Load Package us.nlm.vsac#0.19.0 Load Package us.cdc.phinvads#0.12.0 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 Load Package hl7.fhir.us.vr-common-library#2.0.0 Installing hl7.terminology.r4#5.0.0 to the package cache  Fetching:  Installing hl7.terminology.r4#5.0.0  done. Load Package hl7.terminology.r4#5.0.0 Load Package hl7.fhir.us.odh#1.3.0 Load Package hl7.fhir.uv.tools.r4#0.7.1 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 (00:40.919 / 04:43.747, 1Gb) Load IG (00:00.000 / 04:43.748, 1Gb) Load Content (00:00.001 / 04:43.749, 1Gb) Using en-US as the default narrative language. (no language information in Implementation Guide) (00:00.215 / 04:43.964, 1Gb) Process Loaded Resources (00:05.145 / 04:49.109, 812Mb) Generating Snapshots (00:01.741 / 04:50.851, 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/pagecontent] as /scratch/repo/input/pagecontent Signing Certificate: RSA key for Subject: OU=IG Publisher, L=Ann Arbor, CN=hl7.org, O=HL7, ST=Missouri, C=us from: OU=IG Publisher, L=Ann Arbor, CN=hl7.org, O=HL7, ST=Missouri, C=us Fetch http://hl7.org/fhir/us/bfdr/package-list.json for version check (00:10.179 / 05:01.031, 1Gb) Processing Conformance Resources (00:00.304 / 05:01.335, 1Gb) Checking Language (00:00.000 / 05:01.336, 1Gb) Load Dependency Info (00:00.007 / 05:01.344, 1Gb) Load Info (00:00.003 / 05:01.347, 1Gb) Load Paths (00:00.002 / 05:01.349, 1Gb) Check R4 / R4B (00:00.001 / 05:01.350, 1Gb) Assign Comparison Ids (00:00.189 / 05:01.540, 1Gb) Propagating status (00:00.000 / 05:01.541, 1Gb) Generating Narratives (00:00.550 / 05:02.091, 800Mb) Validating Conformance Resources (00:12.926 / 05:15.018, 1Gb) Check profiles & code systems (01:58.342 / 07:13.361, 2Gb) Check realm rules (00:00.026 / 07:13.387, 2Gb) Installing hl7.fhir.us.core#8.0.0 to the package cache  Fetching:  Installing hl7.fhir.us.core#8.0.0  done. US Core Comparisons Finished Previous Version Comparison (01:56.985 / 09:10.372, 12Gb) Checking for Bundles to sign (00:00.148 / 09:10.521, 12Gb) Validating Resources (00:00.000 / 09:10.521, 12Gb) Processing Provenance Records (01:21.113 / 10:31.635, 7Gb) Generating Outputs in /scratch/repo/output (00:00.001 / 10:31.636, 7Gb) Generate Native Outputs (00:00.380 / 10:32.017, 7Gb) Run Template (00:34.502 / 11:06.519, 4Gb) Generate HTML Outputs (00:03.938 / 11:10.457, 4Gb) XSLT Error: Error reported by XML parser: Content is not allowed in prolog. Exception generating xslt page /scratch/repo/temp/pages/_includes/ije_mapping.md.save for _includes/ije_mapping.md.save in /scratch/repo/temp/pages: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. (01:26.309 / 12:36.767, 5Gb) XSLT Error: Error reported by XML parser: Content is not allowed in prolog. Exception generating xslt page /scratch/repo/temp/pages/_includes/ihe_specification_relationship_and_guidance.md.save for _includes/ihe_specification_relationship_and_guidance.md.save in /scratch/repo/temp/pages: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. (00:00.037 / 12:36.804, 5Gb) XSLT Error: Error reported by XML parser: Content is not allowed in prolog. Exception generating xslt page /scratch/repo/temp/pages/_includes/terminology.md.save for _includes/terminology.md.save in /scratch/repo/temp/pages: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. (00:00.042 / 12:36.846, 5Gb) Generate Spreadsheets (00:00.012 / 12:36.859, 5Gb) Generate Summaries (00:24.081 / 13:00.940, 4Gb) Generating Summary Outputs (00:00.000 / 13:00.941, 4Gb) Table of contents has a section with more than 222 entries. Collapsing will not work reliably DB Cumulative Time invested: 00:00:02.699 Sending Usage Stats to Server (00:34.049 / 13:34.990, 11Gb) ## Memory (MB): Use = 11581, Free = 7426, Total = 19008, Max = 19008 (00:00.016 / 13:35.006, 11Gb) Reclaiming memory... (00:00.000 / 13:35.006, 11Gb) ## Memory (MB): Use = 1419, Free = 17578, Total = 19008, Max = 19008 (00:02.261 / 13:37.268, 1Gb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 13:37.270, 1Gb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 13:37.270, 1Gb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 13:37.270, 1Gb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 13:37.270, 1Gb) Jekyll: Source: /scratch/repo/temp/pages (00:00.641 / 13:37.912, 1Gb) Jekyll: Generating... (00:00.000 / 13:37.912, 1Gb) Jekyll: done in 24.065 seconds. (00:24.064 / 14:01.977, 1Gb) Checking Output HTML (00:14.899 / 14:16.876, 8Gb) found 4187 files (00:00.025 / 14:16.901, 8Gb) ........................................ .................Sending usage stats failed: Connection timed out ....................... ... 4187 html files, 0 pages invalid xhtml (0%) (02:09.820 / 16:26.721, 4Gb) ... 1581004 links, 0 broken links (0%) (00:00.000 / 16:26.722, 4Gb) Generate fragment-usage-analysis.csv (00:00.000 / 16:26.722, 4Gb) Build final .zip (00:00.010 / 16:26.732, 4Gb) Final .zip built (00:34.308 / 17:01.041, 4Gb) Installing hl7.fhir.r4.examples#4.0.1 to the package cache  Fetching:  Installing hl7.fhir.r4.examples#4.0.1  done. Built. Times: loading: 00:17.587, generate: 12:45.607, propagating status: 00:00.549, narrative generation: 00:12.925, realm-rules: 01:56.985, previous-version: 00:00.000, jekyll: 00:24.810, validation: 03:18.848 (#328), template: 00:03.948 (#3) (00:45.902 / 17:46.943, 7Gb) Generating QA (00:00.000 / 17:46.944, 7Gb) Validation output in /scratch/repo/output/qa.html Errors: 0, Warnings: 287, Info: 75, Broken Links: 0 (00:01.318 / 17:48.262, 7Gb) Finished @ 8/6/25, 2:39 PM. Max Memory Used = 12Gb (00:00.105 / 17:48.367, 7Gb)