INFO:root:about to clone!
DEBUG:root:running: git clone --recursive https://github.com/HL7/VhDir --branch master repo
DEBUG:root:Time to deadline 35879.998028 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 35875.869406 seconds
DEBUG:root:running: npm -g install fsh-sushi
DEBUG:root:Time to deadline 35874.499515 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 177 packages in 7s
28 packages are looking for funding
run `npm fund` for details
npm notice
npm notice New major version of npm available! 9.8.1 -> 11.1.0
npm notice Changelog: <https://github.com/npm/cli/releases/tag/v11.1.0>
npm notice Run `npm install -g npm@11.1.0` 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/VhDir/ -out /scratch/repo
DEBUG:root:Time to deadline 35866.806929 seconds
FHIR IG Publisher Version 1.8.13 (Git# e89cdedc7f58). Built 2025-02-17T04:21:57.376Z (20 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/HL7/VhDir/ -out /scratch/repo
Start Clock @ Tuesday, February 18, 2025, 1:13:29 AM Coordinated Universal Time (2025-02-18T01:13:29Z)
Build FHIR IG from /scratch/repo (00:00.028 / 00:00.029, 97Mb)
API keys loaded from /etc/fhir-settings.json (00:00.003 / 00:00.032, 97Mb)
Package Cache: /var/lib/.fhir/packages (00:00.003 / 00:00.035, 97Mb)
Run Sushi on /scratch/repo (00:00.004 / 00:00.040, 97Mb)
Sushi: info Running SUSHI v3.14.0 (implements FHIR Shorthand specification v3.0.0) (00:00.719 / 00:00.759, 113Mb)
Sushi: info Arguments: (00:00.000 / 00:00.760, 113Mb)
Sushi: info --require-latest (00:00.000 / 00:00.760, 113Mb)
Sushi: info --out /scratch/repo (00:00.000 / 00:00.761, 113Mb)
Sushi: info /scratch/repo (00:00.000 / 00:00.761, 113Mb)
Sushi: info Using configuration file: /scratch/repo/sushi-config.yaml (00:00.955 / 00:01.717, 113Mb)
Sushi: info Importing FSH text... (00:00.162 / 00:01.879, 113Mb)
Sushi: info Preprocessed 0 documents with 0 aliases. (00:00.000 / 00:01.880, 113Mb)
Sushi: info Imported 0 definitions and 0 instances. (00:00.000 / 00:01.880, 113Mb)
Sushi: info Loaded virtual package sushi-r5forR4#1.0.0 with 7 resources (00:00.135 / 00:02.016, 113Mb)
Sushi: info Resolved hl7.fhir.uv.tools.r4#latest to concrete version 0.3.0 (00:00.657 / 00:02.673, 113Mb)
Sushi: info Attempting to download hl7.fhir.uv.tools.r4#0.3.0 from https://packages.fhir.org/hl7.fhir.uv.tools.r4/0.3.0 (00:00.001 / 00:02.675, 113Mb)
Sushi: info Downloaded hl7.fhir.uv.tools.r4#0.3.0 (00:01.021 / 00:03.696, 113Mb)
Sushi: info Cached hl7.fhir.uv.tools.r4#0.3.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.tools.r4#0.3.0 (00:00.002 / 00:03.699, 113Mb)
Sushi: info Loaded hl7.fhir.uv.tools.r4#0.3.0 with 75 resources (00:00.064 / 00:03.764, 113Mb)
Sushi: info Resolved hl7.terminology.r4#latest to concrete version 6.2.0 (00:00.450 / 00:04.215, 113Mb)
Sushi: info Attempting to download hl7.terminology.r4#6.2.0 from https://packages.fhir.org/hl7.terminology.r4/6.2.0 (00:00.000 / 00:04.215, 113Mb)
Sushi: info Downloaded hl7.terminology.r4#6.2.0 (00:03.079 / 00:07.295, 113Mb)
Sushi: info Cached hl7.terminology.r4#6.2.0 to /home/fhiruser/.fhir/packages/hl7.terminology.r4#6.2.0 (00:00.002 / 00:07.297, 113Mb)
Sushi: info Loaded hl7.terminology.r4#6.2.0 with 4323 resources (00:01.825 / 00:09.122, 113Mb)
Sushi: info Resolved hl7.fhir.uv.extensions.r4#latest to concrete version 5.2.0 (00:00.457 / 00:09.580, 113Mb)
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 / 00:09.580, 113Mb)
Sushi: info Downloaded hl7.fhir.uv.extensions.r4#5.2.0 (00:01.467 / 00:11.048, 113Mb)
Sushi: info Cached hl7.fhir.uv.extensions.r4#5.2.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.extensions.r4#5.2.0 (00:00.003 / 00:11.052, 113Mb)
Sushi: info Loaded hl7.fhir.uv.extensions.r4#5.2.0 with 759 resources (00:00.347 / 00:11.399, 113Mb)
Sushi: info Attempting to download hl7.fhir.uv.bulkdata#2.0.0 from https://packages.fhir.org/hl7.fhir.uv.bulkdata/2.0.0 (00:00.000 / 00:11.400, 113Mb)
Sushi: info Downloaded hl7.fhir.uv.bulkdata#2.0.0 (00:00.477 / 00:11.877, 113Mb)
Sushi: info Cached hl7.fhir.uv.bulkdata#2.0.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.bulkdata#2.0.0 (00:00.001 / 00:11.878, 113Mb)
Sushi: info Loaded hl7.fhir.uv.bulkdata#2.0.0 with 8 resources (00:00.004 / 00:11.883, 113Mb)
Sushi: info Attempting to download hl7.fhir.uv.smart-app-launch#2.1.0 from https://packages.fhir.org/hl7.fhir.uv.smart-app-launch/2.1.0 (00:00.000 / 00:11.883, 113Mb)
Sushi: info Downloaded hl7.fhir.uv.smart-app-launch#2.1.0 (00:00.744 / 00:12.627, 113Mb)
Sushi: info Cached hl7.fhir.uv.smart-app-launch#2.1.0 to /home/fhiruser/.fhir/packages/hl7.fhir.uv.smart-app-launch#2.1.0 (00:00.001 / 00:12.628, 113Mb)
Sushi: info Loaded hl7.fhir.uv.smart-app-launch#2.1.0 with 8 resources (00:00.006 / 00:12.635, 113Mb)
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 / 00:12.635, 113Mb)
Sushi: info Downloaded hl7.fhir.r4.core#4.0.1 (00:03.267 / 00:15.903, 113Mb)
Sushi: info Cached hl7.fhir.r4.core#4.0.1 to /home/fhiruser/.fhir/packages/hl7.fhir.r4.core#4.0.1 (00:00.001 / 00:15.904, 113Mb)
Sushi: info Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources (00:01.793 / 00:17.697, 113Mb)
Sushi: info Loaded virtual package sushi-local#LOCAL with 263 resources (00:00.431 / 00:18.129, 113Mb)
Sushi: info Converting FSH to FHIR resources... (00:00.023 / 00:18.153, 113Mb)
Sushi: info Exporting FHIR resources as JSON... (00:00.006 / 00:18.159, 113Mb)
Sushi: info Exported 0 FHIR resources as JSON. (00:00.156 / 00:18.316, 113Mb)
Sushi: info Assembling Implementation Guide sources... (00:00.001 / 00:18.317, 113Mb)
Sushi: warn The following files were not added to the ImplementationGuide JSON because they are not in one of the supported input folders or are nested too deep in one of those folders. While SUSHI automatically supports resources in sub-folders, the IG Publisher does not, unless the folder is explicitly added via the template or an IG parameter. To fix any issues you may encounter due to this, adjust your IG parameters or template accordingly or move these files so they are directly under a supported input folder (e.g., input/resources, input/profiles, etc.): (00:00.246 / 00:18.564, 113Mb)
Sushi: - /scratch/repo/input/examples/draft/location-example-ffcardiology.xml (00:00.000 / 00:18.564, 113Mb)
Sushi: - /scratch/repo/input/resources/draft/boundary.structuredefinition.xml (00:00.000 / 00:18.565, 113Mb)
Sushi: - /scratch/repo/input/resources/draft/capabilitystatement-server.xml (00:00.000 / 00:18.565, 113Mb)
Sushi: - /scratch/repo/input/resources/draft/validation.structuredefinition.xml (00:00.000 / 00:18.565, 113Mb)
Sushi: info Generated ImplementationGuide-hl7.fhir.uv.vhdir.json (00:00.012 / 00:18.578, 113Mb)
Sushi: info Assembled Implementation Guide sources; ready for IG Publisher. (00:00.000 / 00:18.578, 113Mb)
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 / 00:18.579, 113Mb)
Sushi: ========================= SUSHI RESULTS =========================== (00:00.001 / 00:18.580, 113Mb)
Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:18.581, 113Mb)
Sushi: | | Profiles | Extensions | Logicals | Resources | | (00:00.000 / 00:18.581, 113Mb)
Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:18.581, 113Mb)
Sushi: | | 0 | 0 | 0 | 0 | | (00:00.000 / 00:18.581, 113Mb)
Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:18.582, 113Mb)
Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:18.582, 113Mb)
Sushi: | | ValueSets | CodeSystems | Instances | | (00:00.000 / 00:18.582, 113Mb)
Sushi: | |-------------------------------------------------------------| | (00:00.000 / 00:18.582, 113Mb)
Sushi: | | 0 | 0 | 0 | | (00:00.000 / 00:18.583, 113Mb)
Sushi: | ------------------------------------------------------------- | (00:00.000 / 00:18.583, 113Mb)
Sushi: | | (00:00.000 / 00:18.583, 113Mb)
Sushi: =================================================================== (00:00.000 / 00:18.583, 113Mb)
Sushi: | You seem to be casting about. 0 Errors 1 Warning | (00:00.000 / 00:18.583, 113Mb)
Sushi: =================================================================== (00:00.000 / 00:18.584, 113Mb)
Unable to load IG as an r5 IG - try R4 (property code is a class com.google.gson.JsonPrimitive looking for an object) (00:00.824 / 00:19.408, 37Mb)
Load Template from hl7.fhir.template#current (00:00.727 / 00:20.136, 93Mb)
Installing hl7.fhir.template#current to the package cache
Fetching:
Installing hl7.fhir.template#current
done.
Load Template from hl7.base.template#current (00:01.372 / 00:21.508, 87Mb)
Installing hl7.base.template#current to the package cache
Fetching:
Installing hl7.base.template#current
done.
Load Template from fhir.base.template#current (00:00.166 / 00:21.675, 95Mb)
Installing fhir.base.template#current to the package cache
Fetching:
Installing fhir.base.template#current
done.
Root directory: /scratch/repo (00:06.396 / 00:28.072, 391Mb)
Terminology Cache is at /scratch/repo/input-cache/txcache. Trimming now (00:00.003 / 00:28.075, 391Mb)
Core Package hl7.fhir.r4.core#4.0.1
Running Terminology Log: /tmp/ohfu-fhir-ig-2246200862745609985.log
Connect to Terminology Server at http://tx.fhir.org (00:28.434 / 00:56.510, 261Mb)
Installing hl7.fhir.pubpack#0.2.1 to the package cache
Fetching:
Installing hl7.fhir.pubpack#0.2.1
done.
Load Package hl7.fhir.pubpack#0.2.1
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#6.2.0
Load Package hl7.fhir.uv.extensions.r4#5.2.0
Load Package hl7.fhir.uv.bulkdata#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.uv.smart-app-launch#2.1.0
Load Package hl7.fhir.uv.tools.r4#0.3.0
Installing ihe.formatcode.fhir#1.1.0 to the package cache
Fetching:
Installing ihe.formatcode.fhir#1.1.0
done.
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 (00:33.856 / 01:30.366, 823Mb)
Load Content (00:00.000 / 01:30.367, 823Mb)
Using en-US as the default narrative language. (no language information in Implementation Guide) (00:00.146 / 01:30.513, 847Mb)
Process Loaded Resources (00:03.379 / 01:33.893, 364Mb)
Generating Snapshots (00:02.237 / 01:36.130, 596Mb)
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/intro-notes] as /scratch/repo/input/intro-notes
loadPrePages from FetchedFile[/scratch/repo/input/pages] as /scratch/repo/input/pages
Fetch http://hl7.org/fhir/uv/vhdir/package-list.json for version check (00:01.354 / 01:37.485, 1Gb)
Processing Conformance Resources (00:00.161 / 01:37.646, 1Gb)
Checking Language (00:00.000 / 01:37.647, 1Gb)
Load Dependency Info (00:00.007 / 01:37.655, 1Gb)
Load Info (00:00.003 / 01:37.658, 1Gb)
Load Paths (00:00.001 / 01:37.659, 1Gb)
Check R4 / R4B (00:00.000 / 01:37.659, 1Gb)
Assign Comparison Ids (00:00.080 / 01:37.740, 1Gb)
Propagating status (00:00.000 / 01:37.741, 1Gb)
Generating Narratives (00:00.134 / 01:37.875, 1Gb)
Validating Conformance Resources (00:04.672 / 01:42.548, 843Mb)
Check profiles & code systems (00:15.694 / 01:58.242, 1Gb)
Check realm rules (00:00.008 / 01:58.251, 1Gb)
Previous Version Comparison (00:00.000 / 01:58.251, 1Gb)
Installing hl7.fhir.uv.vhdir#0.2.0 to the package cache
Fetching:
Installing hl7.fhir.uv.vhdir#0.2.0
done.
Installing null#3.5.0 to the package cache
Fetching:
java.io.IOException: Error reading https://packages2.fhir.org/packages/3.5.0: Input is not in the .gz format
at org.hl7.fhir.utilities.npm.NpmPackage.extractFromTgz(NpmPackage.java:550)
at org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.lambda$addPackageToCache$5(FilesystemPackageCacheManager.java:535)
at org.hl7.fhir.utilities.npm.FilesystemPackageCacheManagerLocks$PackageLock.doWriteWithLock(FilesystemPackageCacheManagerLocks.java:263)
at org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.addPackageToCache(FilesystemPackageCacheManager.java:531)
at org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.loadPackage(FilesystemPackageCacheManager.java:694)
at org.hl7.fhir.igtools.publisher.comparators.PreviousVersionComparator.startChecks(PreviousVersionComparator.java:206)
at org.hl7.fhir.igtools.publisher.Publisher.checkConformanceResources(Publisher.java:6254)
at org.hl7.fhir.igtools.publisher.Publisher.loadConformance2(Publisher.java:6086)
at org.hl7.fhir.igtools.publisher.Publisher.createIg(Publisher.java:1184)
at org.hl7.fhir.igtools.publisher.Publisher.execute(Publisher.java:1020)
at org.hl7.fhir.igtools.publisher.Publisher.main(Publisher.java:14543)
Caused by: java.io.IOException: Input is not in the .gz format
at org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream.init(GzipCompressorInputStream.java:219)
at org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream.<init>(GzipCompressorInputStream.java:168)
at org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream.<init>(GzipCompressorInputStream.java:142)
at org.hl7.fhir.utilities.npm.NpmPackage.extractFromTgz(NpmPackage.java:548)
... 10 more
Validating Resources (00:01.975 / 02:00.226, 1Gb)
Processing Provenance Records (00:04.236 / 02:04.463, 634Mb)
Generating Outputs in /scratch/repo/output (00:00.000 / 02:04.464, 634Mb)
Generate Native Outputs (00:00.258 / 02:04.723, 666Mb)
Run Template (00:16.289 / 02:21.012, 1Gb)
Generate HTML Outputs (00:03.085 / 02:24.098, 1Gb)
Generate Spreadsheets (00:31.940 / 02:56.039, 4Gb)
Generate Summaries (00:06.739 / 03:02.778, 6Gb)
Generating Summary Outputs (00:00.000 / 03:02.778, 6Gb)
Table of contents has a section with more than 222 entries. Collapsing will not work reliably
DB Cumulative Time invested: 00:00:04.551
Sending Usage Stats to Server (00:11.021 / 03:13.800, 7Gb)
## Memory (MB): Use = 8094, Free = 10913, Total = 19008, Max = 19008 (00:00.011 / 03:13.811, 7Gb)
Reclaiming memory... (00:00.000 / 03:13.812, 7Gb)
## Memory (MB): Use = 854, Free = 18153, Total = 19008, Max = 19008 (00:01.510 / 03:15.323, 862Mb)
Run jekyll: jekyll build --destination "/scratch/repo/output" (in folder /scratch/repo/temp/pages) (00:00.003 / 03:15.326, 874Mb)
Troubleshooting Note: usual cases for Jekyll to fail are: (00:00.000 / 03:15.326, 874Mb)
* A failure to produce a fragment that is already logged in the output above (00:00.000 / 03:15.326, 874Mb)
* A reference to a manually edited file that hasn't been provided (00:00.000 / 03:15.326, 874Mb)
Jekyll: Source: /scratch/repo/temp/pages (00:00.478 / 03:15.805, 886Mb)
Jekyll: Generating... (00:00.000 / 03:15.805, 886Mb)
Jekyll: done in 7.846 seconds. (00:07.845 / 03:23.651, 886Mb)
Checking Output HTML (00:06.088 / 03:29.739, 3Gb)
found 3264 files (00:00.016 / 03:29.756, 3Gb)
........................................
........................................
... 3264 html files, 0 pages invalid xhtml (0%) (00:36.254 / 04:06.010, 10Gb)
... 386616 links, 0 broken links (0%) (00:00.000 / 04:06.011, 10Gb)
Generate fragment-usage-analysis.csv (00:00.000 / 04:06.011, 10Gb)
Build final .zip (00:00.013 / 04:06.024, 10Gb)
Final .zip built (00:04.187 / 04:10.211, 10Gb)
Built. Times: loading: 00:07.279, generate: 02:35.297, propagating status: 00:00.134, narrative generation: 00:04.672, realm-rules: 00:00.000, previous-version: 00:01.931, jekyll: 00:08.435, validation: 00:19.515 (#260), template: 00:03.095 (#3) (00:02.753 / 04:12.965, 11Gb)
Generating QA (00:00.000 / 04:12.965, 11Gb)
Validation output in /scratch/repo/output/qa.html
Errors: 0, Warnings: 0, Info: 0, Broken Links: 0 (00:02.798 / 04:15.763, 11Gb)
Finished. Max Memory Used = 11Gb (00:00.081 / 04:15.845, 11Gb)