| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:22 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 174/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocFHIR 1.1.5 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
| Package: BiocFHIR |
| Version: 1.1.5 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BiocFHIR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BiocFHIR_1.1.5.tar.gz |
| StartedAt: 2023-04-11 18:50:13 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 18:51:30 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 77.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BiocFHIR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BiocFHIR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BiocFHIR_1.1.5.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BiocFHIR.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BiocFHIR/DESCRIPTION’ ... OK
* this is package ‘BiocFHIR’ version ‘1.1.5’
* 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘A_upper.Rmd’ using ‘UTF-8’... OK
‘B_handling.Rmd’ using ‘UTF-8’... OK
‘BiocFHIR.Rmd’ using ‘UTF-8’... OK
‘C_tables.Rmd’ using ‘UTF-8’... OK
‘D_linking.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘A_upper.Rmd’ using rmarkdown
Error: processing vignette 'A_upper.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘A_upper.Rmd’
--- re-building ‘B_handling.Rmd’ using rmarkdown
Error: processing vignette 'B_handling.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘B_handling.Rmd’
--- re-building ‘BiocFHIR.Rmd’ using rmarkdown
Error: processing vignette 'BiocFHIR.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘BiocFHIR.Rmd’
--- re-building ‘C_tables.Rmd’ using rmarkdown
Error: processing vignette 'C_tables.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘C_tables.Rmd’
--- re-building ‘D_linking.Rmd’ using rmarkdown
Error: processing vignette 'D_linking.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘D_linking.Rmd’
SUMMARY: processing the following files failed:
‘A_upper.Rmd’ ‘B_handling.Rmd’ ‘BiocFHIR.Rmd’ ‘C_tables.Rmd’
‘D_linking.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BiocFHIR.Rcheck/00check.log’
for details.
BiocFHIR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BiocFHIR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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)
BiocFHIR.Rcheck/tests/test.Rout
R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
19.727 0.346 20.061
BiocFHIR.Rcheck/BiocFHIR-Ex.timings
| name | user | system | elapsed | |
| FHIR_ResourceTypes | 0.001 | 0.000 | 0.001 | |
| FHIR_retention_schemas | 0.001 | 0.000 | 0.001 | |
| FHIRtabs | 0 | 0 | 0 | |
| add_procedures | 0.882 | 0.064 | 0.946 | |
| allin | 0.364 | 0.028 | 0.392 | |
| available_retention_schemas | 0.001 | 0.000 | 0.001 | |
| build_proccond_igraph | 0.681 | 0.015 | 0.697 | |
| display_proccond_igraph | 0.620 | 0.012 | 0.632 | |
| freq_app | 0.000 | 0.000 | 0.001 | |
| getHumanName | 0.467 | 0.000 | 0.468 | |
| make_condition_graph | 0.491 | 0.000 | 0.491 | |
| make_test_json_set | 0.069 | 0.055 | 0.126 | |
| print.BiocFHIR.FHIRgraph | 0.508 | 0.004 | 0.512 | |
| process_AllergyIntolerance | 0.406 | 0.000 | 0.406 | |
| process_CarePlan | 0.417 | 0.000 | 0.417 | |
| process_Claim | 0.419 | 0.028 | 0.447 | |
| process_Condition | 0.396 | 0.008 | 0.405 | |
| process_Encounter | 0.429 | 0.004 | 0.434 | |
| process_Immunization | 0.462 | 0.011 | 0.474 | |
| process_MedicationRequest | 0.431 | 0.000 | 0.432 | |
| process_Observation | 0.407 | 0.016 | 0.423 | |
| process_Patient | 0.416 | 0.000 | 0.417 | |
| process_Procedure | 0.419 | 0.000 | 0.419 | |
| process_fhir_bundle | 0.428 | 0.020 | 0.447 | |
| stack_fhir | 1.473 | 0.088 | 1.562 | |