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CHECK report for cBioPortalData on tokay1

This page was generated on 2020-08-07 12:20:49 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cBioPortalData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 232/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cBioPortalData 2.1.23
Marcel Ramos
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/cBioPortalData
Branch: master
Last Commit: 06a601a
Last Changed Date: 2020-08-05 23:49:47 -0400 (Wed, 05 Aug 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK YES, new version is higher than in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: cBioPortalData
Version: 2.1.23
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cBioPortalData.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings cBioPortalData_2.1.23.tar.gz
StartedAt: 2020-08-07 06:25:55 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 06:34:10 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 494.5 seconds
RetCode: 0
Status:  OK  
CheckDir: cBioPortalData.Rcheck
Warnings: 0

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:cBioPortalData.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings cBioPortalData_2.1.23.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/cBioPortalData.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 'cBioPortalData/DESCRIPTION' ... OK
* this is package 'cBioPortalData' version '2.1.23'
* 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 'cBioPortalData' can be installed ... OK
* 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
* 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 ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
cBioDataPack   15.75   0.93   20.68
cBioPortal     12.33   0.41   13.63
cBioPortalData 10.88   0.36   11.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
cBioPortalData 15.37   0.39   15.92
cBioDataPack   13.27   0.20   16.33
cBioPortal     10.08   0.34   10.55
* 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: OK


Installation output

cBioPortalData.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/cBioPortalData_2.1.23.tar.gz && rm -rf cBioPortalData.buildbin-libdir && mkdir cBioPortalData.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cBioPortalData.buildbin-libdir cBioPortalData_2.1.23.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL cBioPortalData_2.1.23.zip && rm cBioPortalData_2.1.23.tar.gz cBioPortalData_2.1.23.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 65276  100 65276    0     0  1498k      0 --:--:-- --:--:-- --:--:-- 1677k

install for i386

* installing *source* package 'cBioPortalData' ...
** 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 'cBioPortalData'
    finding HTML links ... done
    cBioCache                               html  
    cBioDataPack                            html  
    finding level-2 HTML links ... done

    cBioPortal-class                        html  
    cBioPortal                              html  
    cBioPortalData                          html  
    downloadStudy                           html  
    studiesTable                            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 'cBioPortalData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cBioPortalData' as cBioPortalData_2.1.23.zip
* DONE (cBioPortalData)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'cBioPortalData' successfully unpacked and MD5 sums checked

Tests output

cBioPortalData.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(cBioPortalData)
Loading required package: AnVIL
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

Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    combine, intersect, setdiff, union

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    first, rename

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    collapse, desc, slice

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

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

    count


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

> 
> test_check("cBioPortalData")
trying URL 'https://www.cbioportal.org/api/api-docs'
Content type 'application/json' length 95785 bytes (93 KB)
==================================================
downloaded 93 KB

== testthat results  ===========================================================
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  11.70    1.18   13.07 

cBioPortalData.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(cBioPortalData)
Loading required package: AnVIL
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

Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    combine, intersect, setdiff, union

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    first, rename

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    collapse, desc, slice

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

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

    count


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

> 
> test_check("cBioPortalData")
trying URL 'https://www.cbioportal.org/api/api-docs'
Content type 'application/json' length 95785 bytes (93 KB)
==================================================
downloaded 93 KB

== testthat results  ===========================================================
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.54    0.53   14.28 

Example timings

cBioPortalData.Rcheck/examples_i386/cBioPortalData-Ex.timings

nameusersystemelapsed
cBioCache0.000.000.06
cBioDataPack15.75 0.9320.68
cBioPortal-class0.400.010.53
cBioPortal12.33 0.4113.63
cBioPortalData10.88 0.3611.53
downloadStudy0.610.030.64

cBioPortalData.Rcheck/examples_x64/cBioPortalData-Ex.timings

nameusersystemelapsed
cBioCache000
cBioDataPack13.27 0.2016.33
cBioPortal-class0.410.020.53
cBioPortal10.08 0.3410.55
cBioPortalData15.37 0.3915.92
downloadStudy0.470.020.49