Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-06 13:05:50 -0500 (Mon, 06 Dec 2021).

CHECK results for bioCancer on machv2

To the developers/maintainers of the bioCancer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bioCancer.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 155/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioCancer 1.22.0  (landing page)
Karim Mezhoud
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/bioCancer
git_branch: RELEASE_3_14
git_last_commit: bd61aa9
git_last_commit_date: 2021-10-26 12:28:03 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: bioCancer
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bioCancer_1.22.0.tar.gz
StartedAt: 2021-12-05 12:12:44 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 12:17:14 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 270.4 seconds
RetCode: 0
Status:   OK  
CheckDir: bioCancer.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bioCancer_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/bioCancer.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bioCancer/DESCRIPTION’ ... OK
* this is package ‘bioCancer’ version ‘1.22.0’
* 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 ‘bioCancer’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    app       3.3Mb
    extdata   1.6Mb
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘AlgDesign’ ‘GO.db’ ‘import’ ‘methods’ ‘org.Bt.eg.db’ ‘shinythemes’
  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 ... 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 LazyData ... 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 ‘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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/bioCancer.Rcheck/00check.log’
for details.



Installation output

bioCancer.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bioCancer
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘bioCancer’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (bioCancer)

Tests output

bioCancer.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(bioCancer)
Loading required package: radiant.data
Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

Loading required package: ggplot2
Loading required package: lubridate

Attaching package: 'lubridate'

The following objects are masked from 'package:base':

    date, intersect, setdiff, union

Loading required package: tidyr

Attaching package: 'tidyr'

The following object is masked from 'package:magrittr':

    extract

The following object is masked from 'package:testthat':

    matches

Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'radiant.data'

The following objects are masked from 'package:lubridate':

    month, wday

The following object is masked from 'package:ggplot2':

    diamonds

The following object is masked from 'package:magrittr':

    set_attr

The following object is masked from 'package:testthat':

    describe

The following object is masked from 'package:base':

    date

Loading required package: cgdsr
Please send questions to cbioportal@googlegroups.com
Loading required package: XML


> 
> test_check("bioCancer")
getCancerStudies...  OK
getCaseLists (1/2) ...  OK
getCaseLists (2/2) ...  OK
getGeneticProfiles (1/2) ...  OK
getGeneticProfiles (2/2) ...  OK
getClinicalData (1/1) ...  OK
getProfileData (1/6) ...  OK
getProfileData (2/6) ...  OK
getProfileData (3/6) ...  OK
getProfileData (4/6) ...  OK
getProfileData (5/6) ...  OK
getProfileData (6/6) ...  OK
ReactomeFI connection...  OK
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 13.407   0.716  15.266 

Example timings

bioCancer.Rcheck/bioCancer-Ex.timings

nameusersystemelapsed
AnnotationFuncs-package0.5910.0280.624
Edges_Diseases_obj0.0020.0000.003
Mutation_obj0.0040.0000.004
Node_Diseases_obj0.0030.0010.003
Node_df_FreqIn0.0000.0010.002
Node_obj_CNA_ProfData0.0010.0010.002
Node_obj_FreqIn0.0010.0010.001
Node_obj_Met_ProfData0.0000.0010.002
Node_obj_mRNA_Classifier0.0020.0010.002
Studies_obj0.0070.0010.008
UnifyRowNames0.0010.0010.002
attriColorGene0.0010.0000.002
attriColorValue0.0010.0010.002
attriColorVector0.0010.0010.001
attriShape2Gene0.0000.0000.001
attriShape2Node0.0010.0000.001
bioCancer0.0000.0010.000
checkDimensions0.0020.0000.001
coffeewheel0.0010.0000.000
coffeewheelOutput0.0000.0000.001
displayTable0.0690.0050.189
findPhantom000
getEvidenceCodes0.0000.0000.001
getFreqMutData0.0010.0010.002
getGenesClassification0.0130.0010.057
getListProfData0.0010.0010.001
getList_Cases0.0180.0010.124
getList_GenProfs0.0170.0010.060
getMegaProfData0.0010.0010.001
getOrthologs000
getSequensed_SampleSize000
grepRef0.0000.0010.001
mapLists0.0000.0010.002
metabologram0.0000.0010.001
metabologramOutput000
pickGO0.2140.0110.228
pickRefSeq0.3320.0090.345
reStrColorGene0.0020.0010.002
reStrDimension0.0010.0010.001
reStrDisease0.0010.0000.001
removeNAs0.0000.0000.001
renderCoffeewheel0.0000.0010.000
renderMetabologram000
returnTextAreaInput000
translate0.2390.0090.249
whichGeneList0.0000.0000.001
widgetThumbnail0.0000.0000.001