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).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (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

CHECK results for cbpManager on tokay2


To the developers/maintainers of the cbpManager package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org: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.

raw results

Package 255/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cbpManager 1.2.2  (landing page)
Arsenij Ustjanzew
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/cbpManager
git_branch: RELEASE_3_14
git_last_commit: fd7d9e9
git_last_commit_date: 2021-12-02 07:21:43 -0400 (Thu, 02 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.



Installation output

cbpManager.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch cbpManager
###
##############################################################################
##############################################################################


* 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

Tests output

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 

Example timings

cbpManager.Rcheck/cbpManager-Ex.timings

nameusersystemelapsed
IsDate0.000.020.01
cBioPortalToDataFrame000
cbpManager000
check_input_dates000
convertDataFrame000
create_name000
fncols000
generateOncotreeUIwidgets0.120.020.16
generateUIwidgets000
getSampleIDs000
setupConda_cbpManager 0.16 0.1516.38
writeLogfile0.020.000.02