Vincent Carey
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/BiocFHIR |
| git_branch: RELEASE_3_17 |
| git_last_commit: eae34c1 |
| git_last_commit_date: 2023-04-25 11:41:10 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:58 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 174/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocFHIR 1.2.0 (landing page) Vincent Carey
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the BiocFHIR package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BiocFHIR |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocFHIR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocFHIR_1.2.0.tar.gz |
| StartedAt: 2023-10-17 05:22:21 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 05:24:34 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 133.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocFHIR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocFHIR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocFHIR_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BiocFHIR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocFHIR/DESCRIPTION’ ... OK
* this is package ‘BiocFHIR’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiocFHIR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
Note: found 630 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BiocFHIR.Rcheck/00check.log’
for details.
BiocFHIR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocFHIR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘BiocFHIR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocFHIR)
BiocFHIR.Rcheck/tests/test.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(BiocFHIR)
>
> test_check("BiocFHIR")
prcs__> testf = system.file("json/Vince741_Rogahn59_6fa3d4ab-c0b6-424a-89d8-7d9105129296.json",
prcs__+ package="BiocFHIR")
prcs__> tbun = process_fhir_bundle(testf)
prcs__> tbun
BiocFHIR FHIR.bundle instance.
resource types are:
AllergyIntolerance CarePlan ... Patient Procedure
[1] 231 10
id system code
1 3eae0267-0426-439c-a616-04c1dea70dd1 http://snomed.info/sct 409002
2 3eae0267-0426-439c-a616-04c1dea70dd1 http://snomed.info/sct 58332002
3 3eae0267-0426-439c-a616-04c1dea70dd1 http://snomed.info/sct 58332002
4 86d99438-bcfe-4149-b581-555f4e8243bb http://snomed.info/sct 386463000
5 86d99438-bcfe-4149-b581-555f4e8243bb http://snomed.info/sct 413473000
6 86d99438-bcfe-4149-b581-555f4e8243bb http://snomed.info/sct 1151000175103
display status
1 Food allergy diet in-progress
2 Allergy education in-progress
3 Allergy education in-progress
4 Prescribed activity/exercise education in-progress
5 Counseling about alcohol consumption in-progress
6 Dietary approaches to stop hypertension diet in-progress
location category.system category.code
1 HALLMARK HEALTH SYSTEM http://snomed.info/sct 326051000000105
2 HALLMARK HEALTH SYSTEM http://snomed.info/sct 326051000000105
3 HALLMARK HEALTH SYSTEM http://snomed.info/sct 326051000000105
4 RIVERBEND MEDICAL GROUP INC http://snomed.info/sct 443402002
5 RIVERBEND MEDICAL GROUP INC http://snomed.info/sct 443402002
6 RIVERBEND MEDICAL GROUP INC http://snomed.info/sct 443402002
category.display
1 Self care
2 Self care
3 Self care
4 Lifestyle education regarding hypertension
5 Lifestyle education regarding hypertension
6 Lifestyle education regarding hypertension
subject.reference
1 urn:uuid:15e20922-0f51-47a0-9345-225906c35fbf
2 urn:uuid:15e20922-0f51-47a0-9345-225906c35fbf
3 urn:uuid:15e20922-0f51-47a0-9345-225906c35fbf
4 urn:uuid:aef6dabb-9372-44bc-abf1-f3111812eec7
5 urn:uuid:aef6dabb-9372-44bc-abf1-f3111812eec7
6 urn:uuid:aef6dabb-9372-44bc-abf1-f3111812eec7
[1] 1423 9
[1] 247 5
[1] 1032 9
[1] 406 6
[1] 391 8
[1] 6860 11
[1] 30 40
[1] 881 8
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ]
>
> proc.time()
user system elapsed
23.858 0.659 35.802
BiocFHIR.Rcheck/BiocFHIR-Ex.timings
| name | user | system | elapsed | |
| FHIR_ResourceTypes | 0.001 | 0.000 | 0.000 | |
| FHIR_retention_schemas | 0.001 | 0.001 | 0.001 | |
| FHIRtabs | 0.000 | 0.000 | 0.001 | |
| add_procedures | 1.023 | 0.056 | 1.585 | |
| allin | 0.463 | 0.014 | 0.705 | |
| available_retention_schemas | 0 | 0 | 0 | |
| build_proccond_igraph | 0.810 | 0.034 | 1.094 | |
| display_proccond_igraph | 0.780 | 0.016 | 1.116 | |
| freq_app | 0.000 | 0.000 | 0.001 | |
| getHumanName | 0.501 | 0.010 | 0.729 | |
| make_condition_graph | 0.588 | 0.013 | 0.908 | |
| make_test_json_set | 0.057 | 0.151 | 0.305 | |
| print.BiocFHIR.FHIRgraph | 0.583 | 0.012 | 0.883 | |
| process_AllergyIntolerance | 0.493 | 0.009 | 0.744 | |
| process_CarePlan | 0.465 | 0.006 | 0.693 | |
| process_Claim | 0.481 | 0.009 | 0.748 | |
| process_Condition | 0.472 | 0.007 | 0.736 | |
| process_Encounter | 0.484 | 0.009 | 0.738 | |
| process_Immunization | 0.476 | 0.006 | 0.741 | |
| process_MedicationRequest | 0.481 | 0.007 | 0.747 | |
| process_Observation | 0.676 | 0.025 | 1.052 | |
| process_Patient | 0.455 | 0.007 | 0.707 | |
| process_Procedure | 0.453 | 0.007 | 0.720 | |
| process_fhir_bundle | 0.442 | 0.006 | 0.682 | |
| stack_fhir | 1.473 | 0.094 | 2.390 | |