Back to Multiple platform build/check report for BioC 3.14
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-26 14:06:53 -0400 (Tue, 26 Oct 2021).

CHECK results for bioCancer on riesling1

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 1.21.02  (landing page)
Karim Mezhoud
Snapshot Date: 2021-10-25 14:50:11 -0400 (Mon, 25 Oct 2021)
git_url: https://git.bioconductor.org/packages/bioCancer
git_branch: master
git_last_commit: 0153dc8
git_last_commit_date: 2021-06-28 09:03:47 -0400 (Mon, 28 Jun 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: bioCancer
Version: 1.21.02
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bioCancer.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings bioCancer_1.21.02.tar.gz
StartedAt: 2021-10-26 00:30:02 -0400 (Tue, 26 Oct 2021)
EndedAt: 2021-10-26 00:36:23 -0400 (Tue, 26 Oct 2021)
EllapsedTime: 381.0 seconds
RetCode: 0
Status:   OK  
CheckDir: bioCancer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bioCancer.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings bioCancer_1.21.02.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/bioCancer.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.21.02'
* 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  5.8Mb
  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' '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 ...
** 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/bioCancer.Rcheck/00check.log'
for details.



Installation output

bioCancer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/bioCancer_1.21.02.tar.gz && rm -rf bioCancer.buildbin-libdir && mkdir bioCancer.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bioCancer.buildbin-libdir bioCancer_1.21.02.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL bioCancer_1.21.02.zip && rm bioCancer_1.21.02.tar.gz bioCancer_1.21.02.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 30 6715k   30 2021k    0     0  4175k      0  0:00:01 --:--:--  0:00:01 4175k
100 6715k  100 6715k    0     0  6217k      0  0:00:01  0:00:01 --:--:-- 6217k

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
    AnnotationFuncs-package                 html  
    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  
    dot-dbEscapeString                      html  
    dot-getTableName                        html  
    dot-pickRef                             html  
    epiGenomics                             html  
    findPhantom                             html  
    getEvidenceCodes                        html  
    getFreqMutData                          html  
    getGenesClassification                  html  
    getListProfData                         html  
    getList_Cases                           html  
    getList_GenProfs                        html  
    getMegaProfData                         html  
    getOrthologs                            html  
    getSequensed_SampleSize                 html  
    grepRef                                 html  
    mapLists                                html  
    metabologram                            html  
    metabologramOutput                      html  
    pickGO                                  html  
    pickRefSeq                              html  
    reStrColorGene                          html  
    reStrDimension                          html  
    reStrDisease                            html  
    removeNAs                               html  
    renderCoffeewheel                       html  
    renderMetabologram                      html  
    returnTextAreaInput                     html  
    switchButton                            html  
    translate                               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_1.21.02.zip
* DONE (bioCancer)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'bioCancer' successfully unpacked and MD5 sums checked

Tests output

bioCancer.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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: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 
   6.21    0.53    8.57 

bioCancer.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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: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 
   7.10    0.82    8.75 

Example timings

bioCancer.Rcheck/examples_i386/bioCancer-Ex.timings

nameusersystemelapsed
AnnotationFuncs-package0.340.030.96
Edges_Diseases_obj000
Mutation_obj0.020.000.01
Node_Diseases_obj000
Node_df_FreqIn000
Node_obj_CNA_ProfData000
Node_obj_FreqIn000
Node_obj_Met_ProfData000
Node_obj_mRNA_Classifier000
Studies_obj000
UnifyRowNames000
attriColorGene000
attriColorValue0.010.000.02
attriColorVector000
attriShape2Gene000
attriShape2Node000
bioCancer000
checkDimensions000
coffeewheel000
coffeewheelOutput000
displayTable0.100.020.25
findPhantom000
getEvidenceCodes000
getFreqMutData000
getGenesClassification0.010.000.06
getListProfData000
getList_Cases0.030.000.06
getList_GenProfs0.020.000.07
getMegaProfData000
getOrthologs000
getSequensed_SampleSize000
grepRef000
mapLists000
metabologram000
metabologramOutput000
pickGO0.090.010.17
pickRefSeq0.090.000.10
reStrColorGene000
reStrDimension000
reStrDisease000
removeNAs000
renderCoffeewheel000
renderMetabologram000
returnTextAreaInput000
translate0.150.050.21
whichGeneList000
widgetThumbnail000

bioCancer.Rcheck/examples_x64/bioCancer-Ex.timings

nameusersystemelapsed
AnnotationFuncs-package0.250.020.27
Edges_Diseases_obj000
Mutation_obj0.020.000.01
Node_Diseases_obj000
Node_df_FreqIn000
Node_obj_CNA_ProfData000
Node_obj_FreqIn000
Node_obj_Met_ProfData000
Node_obj_mRNA_Classifier000
Studies_obj000
UnifyRowNames000
attriColorGene000
attriColorValue0.020.000.02
attriColorVector000
attriShape2Gene000
attriShape2Node000
bioCancer000
checkDimensions000
coffeewheel000
coffeewheelOutput000
displayTable0.030.020.14
findPhantom000
getEvidenceCodes000
getFreqMutData000
getGenesClassification0.010.000.06
getListProfData000
getList_Cases0.020.000.07
getList_GenProfs0.000.000.04
getMegaProfData000
getOrthologs000
getSequensed_SampleSize000
grepRef000
mapLists000
metabologram000
metabologramOutput000
pickGO0.110.000.11
pickRefSeq0.070.030.09
reStrColorGene000
reStrDimension000
reStrDisease000
removeNAs000
renderCoffeewheel000
renderMetabologram000
returnTextAreaInput000
translate0.110.010.12
whichGeneList000
widgetThumbnail000