Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 179/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocFHIR 1.9.0 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: BiocFHIR |
Version: 1.9.0 |
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_1.9.0.tar.gz |
StartedAt: 2024-12-23 18:19:25 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 18:20:11 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 46.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BiocFHIR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BiocFHIR.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocFHIR/DESCRIPTION’ ... OK * this is package ‘BiocFHIR’ version ‘1.9.0’ * 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 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 ... OK * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
BiocFHIR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocFHIR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 8.968 0.241 13.512
BiocFHIR.Rcheck/BiocFHIR-Ex.timings
name | user | system | elapsed | |
FHIR_ResourceTypes | 0 | 0 | 0 | |
FHIR_retention_schemas | 0.000 | 0.000 | 0.001 | |
FHIRtabs | 0 | 0 | 0 | |
add_procedures | 0.497 | 0.019 | 0.797 | |
allin | 0.236 | 0.006 | 0.364 | |
available_retention_schemas | 0.001 | 0.000 | 0.000 | |
build_proccond_igraph | 0.445 | 0.014 | 0.690 | |
display_proccond_igraph | 0.284 | 0.005 | 0.303 | |
freq_app | 0.000 | 0.001 | 0.000 | |
getHumanName | 0.137 | 0.002 | 0.165 | |
make_condition_graph | 0.213 | 0.002 | 0.357 | |
make_test_json_set | 0.029 | 0.052 | 0.095 | |
print.BiocFHIR.FHIRgraph | 0.284 | 0.004 | 0.405 | |
process_AllergyIntolerance | 0.226 | 0.002 | 0.367 | |
process_CarePlan | 0.231 | 0.002 | 0.359 | |
process_Claim | 0.284 | 0.012 | 0.484 | |
process_Condition | 0.149 | 0.002 | 0.220 | |
process_Encounter | 0.176 | 0.003 | 0.291 | |
process_Immunization | 0.155 | 0.002 | 0.240 | |
process_MedicationRequest | 0.163 | 0.002 | 0.283 | |
process_Observation | 0.174 | 0.005 | 0.287 | |
process_Patient | 0.166 | 0.002 | 0.265 | |
process_Procedure | 0.209 | 0.002 | 0.310 | |
process_fhir_bundle | 0.172 | 0.001 | 0.252 | |
stack_fhir | 0.622 | 0.036 | 1.061 | |