| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:17 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 cbpManager package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/cbpManager.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 255/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cbpManager 1.2.2 (landing page) Arsenij Ustjanzew
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: cbpManager |
| Version: 1.2.2 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:cbpManager.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cbpManager_1.2.2.tar.gz |
| StartedAt: 2022-04-12 16:54:13 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 16:56:11 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 118.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cbpManager.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:cbpManager.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cbpManager_1.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cbpManager.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cbpManager/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cbpManager' version '1.2.2'
* 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 whether package 'cbpManager' can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cbpManager.Rcheck/00install.out' for details.
* 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 ... WARNING
'::' or ':::' import not declared from: 'rlang'
Namespace in Imports field not imported from: 'markdown'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cbpManager: no visible binding for '<<-' assignment to
'cbpManager.options'
shinyAppServer: no visible binding for '<<-' assignment to 'study_dir'
shinyAppServer: no visible binding for '<<-' assignment to 'logDir'
shinyAppServer: no visible binding for '<<-' assignment to 'oncotree'
shinyAppServer: no visible binding for '<<-' assignment to
'tumor_tissue_site'
shinyAppServer: no visible binding for '<<-' assignment to
'cancer_type'
shinyAppServer: no visible binding for '<<-' assignment to
'oncotree_code'
shinyAppServer: no visible binding for '<<-' assignment to
'cancer_type_detailed'
* 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 line endings in shell scripts ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
setupConda_cbpManager 0.16 0.15 16.38
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.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 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/cbpManager.Rcheck/00check.log'
for details.
cbpManager.Rcheck/00install.out
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch cbpManager
###
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* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
* installing *source* package 'cbpManager' ...
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cbpManager'
finding HTML links ... done
IsDate html
ValidationDependencies html
addColumn_Server html
addColumn_UI html
addRowRc_Server html
addRowRc_UI html
addRow_Server html
addRow_UI html
cBioPortalToDataFrame html
cbpManager-pkg html
cbpManager html
check_input_dates html
convertDataFrame html
create_name html
deleteColumn_Server html
deleteColumn_UI html
deleteRowRc_Server html
deleteRowRc_UI html
deleteRow_Server html
deleteRow_UI html
editRowRc_Server html
editRowRc_UI html
editRow_Server html
editRow_UI html
fncols html
generateOncotreeUIwidgets html
generateUIwidgets html
getSampleIDs html
importPatientData html
saveResource_Server html
saveResource_UI html
saveTimeline_Server html
saveTimeline_UI html
setupConda_cbpManager html
shinyAppServer html
shinyAppUI html
updateOncotreeUIwidgets html
validateResourceDefinition html
validateResourcePatient html
validateResourceSample html
validateResourceStudy html
writeLogfile html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cbpManager)
Making 'packages.html' ... done
cbpManager.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(cbpManager)
Loading required package: shiny
Loading required package: shinydashboard
Attaching package: 'shinydashboard'
The following object is masked from 'package:graphics':
box
>
> test_check("cbpManager")
##---------------------------------------------------------------------------##
## Launching cbpManager
##---------------------------------------------------------------------------##
##---------------------------------------------------------------------------##
## Launching cbpManager
##---------------------------------------------------------------------------##
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 19 ]
== Skipped tests ===============================================================
* On CRAN (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 19 ]
>
> proc.time()
user system elapsed
3.34 0.37 3.70
cbpManager.Rcheck/cbpManager-Ex.timings
| name | user | system | elapsed | |
| IsDate | 0.00 | 0.02 | 0.01 | |
| cBioPortalToDataFrame | 0 | 0 | 0 | |
| cbpManager | 0 | 0 | 0 | |
| check_input_dates | 0 | 0 | 0 | |
| convertDataFrame | 0 | 0 | 0 | |
| create_name | 0 | 0 | 0 | |
| fncols | 0 | 0 | 0 | |
| generateOncotreeUIwidgets | 0.12 | 0.02 | 0.16 | |
| generateUIwidgets | 0 | 0 | 0 | |
| getSampleIDs | 0 | 0 | 0 | |
| setupConda_cbpManager | 0.16 | 0.15 | 16.38 | |
| writeLogfile | 0.02 | 0.00 | 0.02 | |