INFO:root:about to clone! DEBUG:root:running: git clone --recursive https://github.com/IHE/pharm-mpd --branch master repo DEBUG:root:Time to deadline 35879.99812 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 35873.211257 seconds DEBUG:root:running: npm -g install fsh-sushi DEBUG:root:Time to deadline 35872.09188 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 4s 15 packages are looking for funding run `npm fund` for details npm notice npm notice New major version of npm available! 9.8.1 -> 11.4.1 npm notice Changelog: npm notice Run `npm install -g npm@11.4.1` 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-mpd/ -out /scratch/repo DEBUG:root:Time to deadline 35867.404565 seconds FHIR IG Publisher Version 2.0.5 (Git# 0c838e691608). Built 2025-06-05T00:58:33.148Z (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/IHE/pharm-mpd/ -out /scratch/repo Character encoding = UTF-8 / UTF-8 Start Clock @ Monday, June 9, 2025, 7:25:27 AM Coordinated Universal Time (2025-06-09T07:25:27Z) Build FHIR IG from /scratch/repo (00:00.025 / 00:00.025, 97Mb) API keys loaded from /etc/fhir-settings.json (00:00.003 / 00:00.028, 97Mb) Package Cache: /var/lib/.fhir/packages (00:00.002 / 00:00.030, 97Mb) Run Sushi on /scratch/repo (00:00.005 / 00:00.036, 97Mb) Sushi: info Running SUSHI v3.16.0 (implements FHIR Shorthand specification v3.0.0) (00:00.856 / 00:00.893, 113Mb) Sushi: info Arguments: (00:00.000 / 00:00.894, 113Mb) Sushi: info --require-latest (00:00.000 / 00:00.894, 113Mb) Sushi: info --out /scratch/repo (00:00.000 / 00:00.894, 113Mb) Sushi: info /scratch/repo (00:00.000 / 00:00.894, 113Mb) Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.580 / 00:01.475, 113Mb) Sushi: info Importing FSH text... (00:00.133 / 00:01.609, 113Mb) Sushi: info Preprocessed 38 documents with 13 aliases. (00:00.315 / 00:01.924, 113Mb) Sushi: info Imported 21 definitions and 55 instances. (00:00.045 / 00:01.970, 113Mb) Sushi: info Resolved hl7.fhir.uv.tools.r5#latest to concrete version 0.5.0 (00:00.703 / 00:02.673, 113Mb) Sushi: info Attempting to download hl7.fhir.uv.tools.r5#0.5.0 from https://packages.fhir.org/hl7.fhir.uv.tools.r5/0.5.0 (00:00.110 / 00:02.786, 113Mb) Sushi: info Downloaded hl7.fhir.uv.tools.r5#0.5.0 (00:00.796 / 00:03.580, 113Mb) Sushi: info Cached hl7.fhir.uv.tools.r5#0.5.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.tools.r5#0.5.0 (00:00.002 / 00:03.582, 113Mb) Sushi: info Loaded hl7.fhir.uv.tools.r5#0.5.0 with 96 resources (00:00.105 / 00:03.688, 113Mb) Sushi: info Resolved hl7.terminology.r5#latest to concrete version 6.4.0 (00:00.477 / 00:04.165, 113Mb) Sushi: info Attempting to download hl7.terminology.r5#6.4.0 from https://packages.fhir.org/hl7.terminology.r5/6.4.0 (00:00.000 / 00:04.165, 113Mb) Sushi: info Downloaded hl7.terminology.r5#6.4.0 (00:02.424 / 00:06.589, 113Mb) Sushi: info Cached hl7.terminology.r5#6.4.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r5#6.4.0 (00:00.001 / 00:06.591, 113Mb) Sushi: info Loaded hl7.terminology.r5#6.4.0 with 4381 resources (00:01.262 / 00:07.853, 113Mb) Sushi: info Resolved hl7.fhir.uv.extensions.r5#latest to concrete version 5.2.0 (00:00.449 / 00:08.303, 113Mb) Sushi: info Attempting to download hl7.fhir.uv.extensions.r5#5.2.0 from https://packages.fhir.org/hl7.fhir.uv.extensions.r5/5.2.0 (00:00.000 / 00:08.303, 113Mb) Sushi: info Downloaded hl7.fhir.uv.extensions.r5#5.2.0 (00:01.482 / 00:09.786, 113Mb) Sushi: info Cached hl7.fhir.uv.extensions.r5#5.2.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.extensions.r5#5.2.0 (00:00.002 / 00:09.788, 113Mb) Sushi: info Loaded hl7.fhir.uv.extensions.r5#5.2.0 with 759 resources (00:00.215 / 00:10.004, 113Mb) Sushi: info Attempting to download hl7.fhir.r5.core#5.0.0 from https://packages.fhir.org/hl7.fhir.r5.core/5.0.0 (00:00.000 / 00:10.004, 113Mb) Sushi: info Downloaded hl7.fhir.r5.core#5.0.0 (00:03.489 / 00:13.494, 113Mb) Sushi: info Cached hl7.fhir.r5.core#5.0.0 to /home/fhiruser/.fhir/packages/hl7.fhir.r5.core#5.0.0 (00:00.001 / 00:13.495, 113Mb) Sushi: info Loaded hl7.fhir.r5.core#5.0.0 with 2968 resources (00:00.956 / 00:14.452, 113Mb) Sushi: info Found 1 non-JSON / non-XML file(s) in directory: /scratch/repo/input/examples. Only resource files with JSON or XML extensions are supported. To see the skipped files in the logs, use debug logging. (00:00.026 / 00:14.478, 113Mb) Sushi: info Found 1 non-JSON / non-XML file(s) in directory: /scratch/repo/input/extensions. Only resource files with JSON or XML extensions are supported. To see the skipped files in the logs, use debug logging. (00:00.000 / 00:14.479, 113Mb) Sushi: info Found 1 non-JSON / non-XML file(s) in directory: /scratch/repo/input/models. Only resource files with JSON or XML extensions are supported. To see the skipped files in the logs, use debug logging. (00:00.000 / 00:14.479, 113Mb) Sushi: info Found 3 non-JSON / non-XML file(s) in directory: /scratch/repo/input/profiles. Only resource files with JSON or XML extensions are supported. To see the skipped files in the logs, use debug logging. (00:00.000 / 00:14.479, 113Mb) Sushi: info Found 1 non-JSON / non-XML file(s) in directory: /scratch/repo/input/resources. Only resource files with JSON or XML extensions are supported. To see the skipped files in the logs, use debug logging. (00:00.000 / 00:14.479, 113Mb) Sushi: info Found 1 non-JSON / non-XML file(s) in directory: /scratch/repo/input/vocabulary. Only resource files with JSON or XML extensions are supported. To see the skipped files in the logs, use debug logging. (00:00.000 / 00:14.479, 113Mb) Sushi: info Loaded virtual package sushi-local#LOCAL with 0 resources (00:00.000 / 00:14.480, 113Mb) Sushi: info Converting FSH to FHIR resources... (00:00.016 / 00:14.496, 113Mb) Sushi: info Converted 21 FHIR StructureDefinitions. (00:03.493 / 00:17.990, 113Mb) Sushi: info Converted 55 FHIR instances. (00:03.717 / 00:21.708, 113Mb) Sushi: info Exporting FHIR resources as JSON... (00:00.000 / 00:21.709, 113Mb) Sushi: info Exported 74 FHIR resources as JSON. (00:00.041 / 00:21.750, 113Mb) Sushi: info Assembling Implementation Guide sources... (00:00.002 / 00:21.753, 113Mb) Sushi: info Generated ImplementationGuide-ihe.pharm.mpd.json (00:00.015 / 00:21.768, 113Mb) Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:21.768, 113Mb) Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:21.769, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:21.770, 113Mb) Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:21.770, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:21.770, 113Mb) Sushi: | | 3 | 11 | 7 | 0 | | (00:00.000 / 00:21.770, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:21.770, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:21.770, 113Mb) Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:21.771, 113Mb) Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:21.771, 113Mb) Sushi: | | 0 | 0 | 55 | | (00:00.000 / 00:21.771, 113Mb) Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:21.771, 113Mb) Sushi: | | (00:00.000 / 00:21.771, 113Mb) Sushi: =================================================================== (00:00.000 / 00:21.772, 113Mb) Sushi: | You're sailing along smoothly. 0 Errors 0 Warnings | (00:00.000 / 00:21.772, 113Mb) Sushi: =================================================================== (00:00.000 / 00:21.772, 113Mb) Load Template from ihe.fhir.template#current (00:00.590 / 00:22.363, 38Mb) Installing ihe.fhir.template#current to the package cache Fetching: Installing ihe.fhir.template#current done. Load Template from fhir.base.template#current (00:01.174 / 00:23.537, 102Mb) Installing fhir.base.template#current to the package cache Fetching: Installing fhir.base.template#current done. Root directory: /scratch/repo (00:03.616 / 00:27.154, 171Mb) Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.001 / 00:27.155, 171Mb) Core Package hl7.fhir.r5.core#5.0.0 Running Terminology Log: /tmp/ohfu-fhir-ig-12313723575213319443.html Connect to Terminology Server at http://tx.fhir.org (00:03.720 / 00:30.876, 709Mb) 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.r5#6.4.0 Load Package hl7.fhir.uv.extensions.r5#5.2.0 Load Package hl7.fhir.uv.tools.r5#0.5.0 Initialization complete (00:06.135 / 00:37.012, 648Mb) Load IG (00:00.000 / 00:37.012, 648Mb) Load Content (00:00.000 / 00:37.013, 648Mb) Using en-US as the default narrative language. (no language information in Implementation Guide) (00:00.067 / 00:37.081, 656Mb) Error loading /scratch/repo/input/profiles/prescription.fsh as XML: Content is not allowed in prolog. at line 0 col 0 (00:00.525 / 00:37.607, 688Mb) Error loading /scratch/repo/input/profiles/prescription.fsh as JSON: Error parsing JSON source: Unexpected content at start of JSON: String at Line 1 (path=[Profile]) (00:00.001 / 00:37.609, 688Mb) Error loading /scratch/repo/input/profiles/prescription.fsh as Turtle: Unknown prefix Profile (00:00.005 / 00:37.615, 688Mb) ADL Error loading /scratch/repo/input/profiles/prescription.fsh: Error @1, 8: Found "Profile" expecting "group" (00:00.008 / 00:37.623, 688Mb) Error loading /scratch/repo/input/profiles/dispense.fsh as XML: Content is not allowed in prolog. at line 0 col 0 (00:00.004 / 00:37.627, 688Mb) Error loading /scratch/repo/input/profiles/dispense.fsh as JSON: Error parsing JSON source: Unexpected content at start of JSON: String at Line 1 (path=[Profile]) (00:00.001 / 00:37.629, 688Mb) Error loading /scratch/repo/input/profiles/dispense.fsh as Turtle: Unknown prefix Profile (00:00.004 / 00:37.634, 688Mb) ADL Error loading /scratch/repo/input/profiles/dispense.fsh: Error @1, 8: Found "Profile" expecting "group" (00:00.006 / 00:37.640, 688Mb) Process Loaded Resources (00:00.641 / 00:38.281, 760Mb) Generating Snapshots (00:00.225 / 00:38.506, 808Mb) 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 https://profiles.ihe.net/PHARM/MPD/package-list.json for version check (00:00.657 / 00:39.164, 968Mb) Processing Conformance Resources (00:00.149 / 00:39.314, 976Mb) Checking Language (00:00.000 / 00:39.314, 976Mb) Load Dependency Info (00:00.002 / 00:39.317, 976Mb) Load Info (00:00.001 / 00:39.318, 976Mb) Load Paths (00:00.000 / 00:39.319, 980Mb) Check R4 / R4B (00:00.000 / 00:39.319, 980Mb) Installing hl7.fhir.r4.core#4.0.1 to the package cache Fetching: Installing hl7.fhir.r4.core#4.0.1 done. Assign Comparison Ids (00:27.736 / 01:07.056, 1Gb) Propagating status (00:00.000 / 01:07.056, 1Gb) Generating Narratives (00:00.000 / 01:07.057, 1Gb) Validating Conformance Resources (00:02.620 / 01:09.677, 842Mb) Check profiles & code systems (00:11.579 / 01:21.256, 758Mb) Check realm rules (00:00.002 / 01:21.259, 758Mb) Previous Version Comparison (00:00.000 / 01:21.259, 758Mb) Validating Resources (00:00.021 / 01:21.281, 758Mb) Processing Provenance Records (00:03.158 / 01:24.439, 926Mb) Generating Outputs in /scratch/repo/output (00:00.000 / 01:24.439, 926Mb) Generate Native Outputs (00:00.160 / 01:24.600, 934Mb) Run Template (00:03.161 / 01:27.761, 1Gb) Generate HTML Outputs (00:05.452 / 01:33.214, 724Mb) Generate Spreadsheets (00:05.193 / 01:38.408, 2Gb) Generate Summaries (00:04.352 / 01:42.761, 1Gb) Generating Summary Outputs (00:00.000 / 01:42.761, 1Gb) DB Cumulative Time invested: 00:00:00.533 Sending Usage Stats to Server (00:03.166 / 01:45.928, 1Gb) ## Memory (MB): Use = 1928, Free = 17079, Total = 19008, Max = 19008 (00:00.006 / 01:45.935, 1Gb) Reclaiming memory... (00:00.000 / 01:45.935, 1Gb) ## Memory (MB): Use = 567, Free = 18440, Total = 19008, Max = 19008 (00:00.474 / 01:46.410, 575Mb) Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.001 / 01:46.411, 583Mb) Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 01:46.411, 583Mb) * A failure to produce a fragment that is already logged in the output above (00:00.000 / 01:46.411, 583Mb) * A reference to a manually edited file that hasn't been provided (00:00.000 / 01:46.411, 583Mb) Jekyll: Source: /scratch/repo/temp/pages (00:00.427 / 01:46.839, 599Mb) Jekyll: Generating... (00:00.000 / 01:46.839, 599Mb) Jekyll: done in 2.526 seconds. (00:02.525 / 01:49.364, 599Mb) Checking Output HTML (00:00.532 / 01:49.897, 1Gb) found 1479 files (00:00.007 / 01:49.905, 1Gb) ......................................... ......................................... ... 1479 html files, 0 pages invalid xhtml (0%) (00:12.526 / 02:02.432, 966Mb) ... 133309 links, 0 broken links (0%) (00:00.001 / 02:02.433, 966Mb) Generate fragment-usage-analysis.csv (00:00.000 / 02:02.433, 966Mb) Build final .zip (00:00.008 / 02:02.442, 966Mb) Final .zip built (00:01.263 / 02:03.705, 974Mb) Built. Times: loading: 00:02.301, generate: 01:25.486, narrative generation: 00:02.620, realm-rules: 00:00.000, previous-version: 00:00.000, jekyll: 00:02.972, validation: 00:14.661 (#75), template: 00:05.461 (#3) (00:01.096 / 02:04.801, 1Gb) Generating QA (00:00.000 / 02:04.801, 1Gb) Validation output in /scratch/repo/output/qa.html Errors: 0, Warnings: 5, Info: 1, Broken Links: 0 (00:00.226 / 02:05.028, 1Gb) Finished. Max Memory Used = 2Gb (00:00.016 / 02:05.044, 1Gb)