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CHECK report for RTCGA on tokay2

This page was generated on 2020-10-17 11:57:42 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RTCGA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1548/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCGA 1.18.0
Marcin Kosinski
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/RTCGA
Branch: RELEASE_3_11
Last Commit: 04b4767
Last Changed Date: 2020-04-27 14:51:10 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RTCGA
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RTCGA_1.18.0.tar.gz
StartedAt: 2020-10-17 07:49:39 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:56:11 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 392.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RTCGA.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RTCGA_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/RTCGA.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTCGA/DESCRIPTION' ... OK
* this is package 'RTCGA' version '1.18.0'
* 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 'RTCGA' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/convertTCGA.Rd:23: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/convertTCGA.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/convertTCGA.Rd:13: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/convertTCGA.Rd:13: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/convertTCGA.Rd:18: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/convertTCGA.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/installTCGA.Rd:16: file link 'install_github' in package 'devtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/RTCGA.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
* 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 ... NOTE
availableDates: no visible binding for global variable '.'
downloadTCGA: no visible binding for global variable '.'
ggbiplot: no visible binding for global variable 'xvar'
ggbiplot: no visible binding for global variable 'yvar'
ggbiplot: no visible global function definition for 'muted'
ggbiplot: no visible binding for global variable 'varname'
ggbiplot: no visible binding for global variable 'angle'
ggbiplot: no visible binding for global variable 'hjust'
read.mutations: no visible binding for global variable '.'
read.rnaseq: no visible binding for global variable '.'
survivalTCGA: no visible binding for global variable 'times'
whichDateToUse: no visible binding for global variable '.'
Undefined global functions or variables:
  . angle hjust muted times varname xvar yvar
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
boxplotTCGA     16.97   3.46   69.94
expressionsTCGA 14.64   3.13   62.94
heatmapTCGA      6.58   1.07    7.66
kmTCGA           6.09   0.02    6.59
survivalTCGA     5.04   0.00    5.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
boxplotTCGA     16.34   0.99   17.33
expressionsTCGA 12.45   1.00   13.58
heatmapTCGA      8.94   0.28    9.22
kmTCGA           7.54   0.08    7.62
survivalTCGA     6.86   0.02    6.87
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/RTCGA.Rcheck/00check.log'
for details.



Installation output

RTCGA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/RTCGA_1.18.0.tar.gz && rm -rf RTCGA.buildbin-libdir && mkdir RTCGA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTCGA.buildbin-libdir RTCGA_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL RTCGA_1.18.0.zip && rm RTCGA_1.18.0.tar.gz RTCGA_1.18.0.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
100 2434k  100 2434k    0     0  25.5M      0 --:--:-- --:--:-- --:--:-- 27.6M

install for i386

* installing *source* package 'RTCGA' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RTCGA'
    finding HTML links ... done
    RTCGA-package                           html  
    boxplotTCGA                             html  
    finding level-2 HTML links ... done

    checkTCGA                               html  
    convertTCGA                             html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/convertTCGA.Rd:23: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/convertTCGA.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/convertTCGA.Rd:13: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/convertTCGA.Rd:13: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/convertTCGA.Rd:18: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/convertTCGA.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    datasetsTCGA                            html  
    downloadTCGA                            html  
    expressionsTCGA                         html  
    heatmapTCGA                             html  
    infoTCGA                                html  
    installTCGA                             html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp0EU041/R.INSTALLf3092f7dcb/RTCGA/man/installTCGA.Rd:16: file link 'install_github' in package 'devtools' does not exist and so has been treated as a topic
    kmTCGA                                  html  
    mutationsTCGA                           html  
    pcaTCGA                                 html  
    readTCGA                                html  
    survivalTCGA                            html  
    theme_RTCGA                             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 'RTCGA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCGA' as RTCGA_1.18.0.zip
* DONE (RTCGA)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'RTCGA' successfully unpacked and MD5 sums checked

Tests output

RTCGA.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(RTCGA)
Welcome to the RTCGA (version: 1.18.0).
> library(RTCGA.rnaseq)
> library(Biobase)
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: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, which.max, which.min

Welcome to Bioconductor

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

> library(GenomicRanges)
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
> #library(RTCGA.CNV)
> #library(RTCGA.PANCAN12)
> 
> test_check("RTCGA")
trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601/gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
Content type 'application/x-gzip' length 151456 bytes (147 KB)
==================================================
downloaded 147 KB

trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601/gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
Content type 'application/x-gzip' length 151456 bytes (147 KB)
==================================================
downloaded 147 KB

== testthat results  ===========================================================
[ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  14.26    1.59   17.12 

RTCGA.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(RTCGA)
Welcome to the RTCGA (version: 1.18.0).
> library(RTCGA.rnaseq)
> library(Biobase)
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: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, which.max, which.min

Welcome to Bioconductor

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

> library(GenomicRanges)
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
> #library(RTCGA.CNV)
> #library(RTCGA.PANCAN12)
> 
> test_check("RTCGA")
trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601/gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
Content type 'application/x-gzip' length 151456 bytes (147 KB)
==================================================
downloaded 147 KB

trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601/gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
Content type 'application/x-gzip' length 151456 bytes (147 KB)
==================================================
downloaded 147 KB

== testthat results  ===========================================================
[ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  12.79    1.12   14.87 

Example timings

RTCGA.Rcheck/examples_i386/RTCGA-Ex.timings

nameusersystemelapsed
RTCGA-package000
boxplotTCGA16.97 3.4669.94
checkTCGA0.610.061.82
convertTCGA1.490.141.62
datasetsTCGA000
downloadTCGA0.010.002.39
expressionsTCGA14.64 3.1362.94
heatmapTCGA6.581.077.66
infoTCGA1.080.001.23
installTCGA000
kmTCGA6.090.026.59
mutationsTCGA2.670.012.69
pcaTCGA000
readTCGA000
survivalTCGA5.040.005.03
theme_RTCGA2.230.002.24

RTCGA.Rcheck/examples_x64/RTCGA-Ex.timings

nameusersystemelapsed
RTCGA-package000
boxplotTCGA16.34 0.9917.33
checkTCGA0.440.060.88
convertTCGA1.890.202.09
datasetsTCGA000
downloadTCGA0.050.000.48
expressionsTCGA12.45 1.0013.58
heatmapTCGA8.940.289.22
infoTCGA1.050.001.24
installTCGA000
kmTCGA7.540.087.62
mutationsTCGA3.350.003.34
pcaTCGA000
readTCGA0.010.000.02
survivalTCGA6.860.026.87
theme_RTCGA2.500.012.52