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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 178/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocFHIR 1.6.0  (landing page)
Vincent Carey
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/BiocFHIR
git_branch: RELEASE_3_19
git_last_commit: 11ce6e3
git_last_commit_date: 2024-04-30 11:45:41 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for BiocFHIR on nebbiolo1

To the developers/maintainers of the BiocFHIR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocFHIR.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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.

raw results


Summary

Package: BiocFHIR
Version: 1.6.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BiocFHIR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BiocFHIR_1.6.0.tar.gz
StartedAt: 2024-06-19 20:57:51 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 20:59:30 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 98.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocFHIR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BiocFHIR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BiocFHIR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BiocFHIR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BiocFHIR/DESCRIPTION’ ... OK
* this is package ‘BiocFHIR’ version ‘1.6.0’
* 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 code 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 loading without being on the library search path ... 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/BiocFHIR.Rcheck/00check.log’
for details.


Installation output

BiocFHIR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BiocFHIR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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)

Tests output

BiocFHIR.Rcheck/tests/test.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 17.720   0.347  18.057 

Example timings

BiocFHIR.Rcheck/BiocFHIR-Ex.timings

nameusersystemelapsed
FHIR_ResourceTypes0.0010.0000.001
FHIR_retention_schemas0.0010.0000.001
FHIRtabs000
add_procedures0.8160.0640.880
allin0.3830.0200.403
available_retention_schemas000
build_proccond_igraph0.6500.0320.682
display_proccond_igraph0.6010.0240.624
freq_app000
getHumanName0.4260.0040.429
make_condition_graph0.4530.0080.461
make_test_json_set0.0910.0310.125
print.BiocFHIR.FHIRgraph0.4760.0120.488
process_AllergyIntolerance0.3670.0000.367
process_CarePlan0.3700.0330.403
process_Claim0.3600.0130.374
process_Condition0.3600.0040.363
process_Encounter0.3700.0010.370
process_Immunization0.4290.0070.437
process_MedicationRequest0.3680.0040.372
process_Observation0.4100.0050.414
process_Patient0.3690.0440.413
process_Procedure0.3690.0000.369
process_fhir_bundle0.3830.0000.383
stack_fhir1.3060.0761.437