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CHECK report for bioCancer on tokay1

This page was generated on 2020-08-13 11:41:02 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE bioCancer PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 147/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioCancer 1.17.0
Karim Mezhoud
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/bioCancer
Branch: master
Last Commit: 9ab1d92
Last Changed Date: 2020-04-27 14:57:51 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: bioCancer
Version: 1.17.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bioCancer.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings bioCancer_1.17.0.tar.gz
StartedAt: 2020-08-13 03:21:31 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 03:26:55 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 324.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: bioCancer.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bioCancer.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings bioCancer_1.17.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/bioCancer.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bioCancer/DESCRIPTION' ... OK
* this is package 'bioCancer' version '1.17.0'
* 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 whether package 'bioCancer' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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' 'import' 'methods' '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 ... WARNING
checkRd: (5) bioCancer.Rd:0-20: Must have a \description
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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-3.12-bioc/meat/bioCancer.Rcheck/00check.log'
for details.



Installation output

bioCancer.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/bioCancer_1.17.0.tar.gz && rm -rf bioCancer.buildbin-libdir && mkdir bioCancer.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bioCancer.buildbin-libdir bioCancer_1.17.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL bioCancer_1.17.0.zip && rm bioCancer_1.17.0.tar.gz bioCancer_1.17.0.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 6695k  100 6695k    0     0  35.1M      0 --:--:-- --:--:-- --:--:-- 35.9M

install for i386

* 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
  converting help for package 'bioCancer'
    finding HTML links ... done
    Edges_Diseases_obj                      html  
    Mutation_obj                            html  
    Node_Diseases_obj                       html  
    Node_df_FreqIn                          html  
    Node_obj_CNA_ProfData                   html  
    Node_obj_FreqIn                         html  
    Node_obj_Met_ProfData                   html  
    Node_obj_mRNA_Classifier                html  
    Studies_obj                             html  
    UnifyRowNames                           html  
    attriColorGene                          html  
    attriColorValue                         html  
    attriColorVector                        html  
    attriShape2Gene                         html  
    attriShape2Node                         html  
    bioCancer                               html  
    checkDimensions                         html  
    coffeewheel                             html  
    coffeewheelOutput                       html  
    displayTable                            html  
    epiGenomics                             html  
    findPhantom                             html  
    getFreqMutData                          html  
    getGenesClassification                  html  
    getListProfData                         html  
    getList_Cases                           html  
    getList_GenProfs                        html  
    getMegaProfData                         html  
    getSequensed_SampleSize                 html  
    grepRef                                 html  
    metabologram                            html  
    metabologramOutput                      html  
    reStrColorGene                          html  
    reStrDimension                          html  
    reStrDisease                            html  
    renderCoffeewheel                       html  
    renderMetabologram                      html  
    returnTextAreaInput                     html  
    switchButton                            html  
    user_CNA                                html  
    user_MetHM27                            html  
    user_MetHM450                           html  
    user_Mut                                html  
    user_mRNA                               html  
    whichGeneList                           html  
    widgetThumbnail                         html  
** 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

install for x64

* installing *source* package 'bioCancer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bioCancer' as bioCancer_1.17.0.zip
* DONE (bioCancer)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'bioCancer' successfully unpacked and MD5 sums checked

Tests output

bioCancer.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: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
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   8.73    0.84   10.43 

bioCancer.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(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: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
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.32    0.79   14.67 

Example timings

bioCancer.Rcheck/examples_i386/bioCancer-Ex.timings

nameusersystemelapsed
Edges_Diseases_obj0.020.000.01
Mutation_obj000
Node_Diseases_obj000
Node_df_FreqIn000
Node_obj_CNA_ProfData000
Node_obj_FreqIn000
Node_obj_Met_ProfData000
Node_obj_mRNA_Classifier000
Studies_obj0.020.000.02
UnifyRowNames000
attriColorGene000
attriColorValue000
attriColorVector000
attriShape2Gene000
attriShape2Node000
bioCancer000
checkDimensions000
coffeewheel000
coffeewheelOutput000
displayTable0.110.000.15
findPhantom000
getFreqMutData000
getGenesClassification0.030.000.05
getListProfData000
getList_Cases0.030.000.05
getList_GenProfs0.020.010.04
getMegaProfData000
getSequensed_SampleSize000
grepRef000
metabologram000
metabologramOutput000
reStrColorGene000
reStrDimension000
reStrDisease000
renderCoffeewheel000
renderMetabologram000
returnTextAreaInput000
whichGeneList000
widgetThumbnail000

bioCancer.Rcheck/examples_x64/bioCancer-Ex.timings

nameusersystemelapsed
Edges_Diseases_obj0.020.000.02
Mutation_obj000
Node_Diseases_obj0.020.000.02
Node_df_FreqIn000
Node_obj_CNA_ProfData000
Node_obj_FreqIn000
Node_obj_Met_ProfData000
Node_obj_mRNA_Classifier0.010.000.01
Studies_obj000
UnifyRowNames0.020.000.02
attriColorGene000
attriColorValue000
attriColorVector000
attriShape2Gene000
attriShape2Node000
bioCancer000
checkDimensions000
coffeewheel000
coffeewheelOutput000
displayTable0.050.000.10
findPhantom000
getFreqMutData000
getGenesClassification0.040.000.07
getListProfData000
getList_Cases0.050.000.06
getList_GenProfs0.050.000.06
getMegaProfData000
getSequensed_SampleSize000
grepRef000
metabologram000
metabologramOutput0.000.020.02
reStrColorGene000
reStrDimension000
reStrDisease000
renderCoffeewheel000
renderMetabologram000
returnTextAreaInput000
whichGeneList000
widgetThumbnail000