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CHECK report for RTCGA on tokay1

This page was generated on 2018-04-12 13:26:50 -0400 (Thu, 12 Apr 2018).

Package 1223/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCGA 1.8.0
Marcin Kosinski
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/RTCGA
Branch: RELEASE_3_6
Last Commit: c502417
Last Changed Date: 2017-10-30 12:40:54 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RTCGA
Version: 1.8.0
Command: rm -rf RTCGA.buildbin-libdir RTCGA.Rcheck && mkdir RTCGA.buildbin-libdir RTCGA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTCGA.buildbin-libdir RTCGA_1.8.0.tar.gz >RTCGA.Rcheck\00install.out 2>&1 && cp RTCGA.Rcheck\00install.out RTCGA-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RTCGA.buildbin-libdir --install="check:RTCGA-install.out" --force-multiarch --no-vignettes --timings RTCGA_1.8.0.tar.gz
StartedAt: 2018-04-12 02:53:33 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:19:22 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 1548.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RTCGA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RTCGA.buildbin-libdir RTCGA.Rcheck && mkdir RTCGA.buildbin-libdir RTCGA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTCGA.buildbin-libdir RTCGA_1.8.0.tar.gz >RTCGA.Rcheck\00install.out 2>&1 && cp RTCGA.Rcheck\00install.out RTCGA-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RTCGA.buildbin-libdir --install="check:RTCGA-install.out" --force-multiarch --no-vignettes --timings RTCGA_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/RTCGA.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.8.0'
* 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-3.6-bioc/tmpdir/RtmpKGaf4I/R.INSTALL1e3c6fd228a9/RTCGA/man/convertTCGA.Rd:23: missing file link 'ExpressionSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKGaf4I/R.INSTALL1e3c6fd228a9/RTCGA/man/convertTCGA.Rd:23: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKGaf4I/R.INSTALL1e3c6fd228a9/RTCGA/man/convertTCGA.Rd:13: missing file link 'ExpressionSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKGaf4I/R.INSTALL1e3c6fd228a9/RTCGA/man/convertTCGA.Rd:13: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKGaf4I/R.INSTALL1e3c6fd228a9/RTCGA/man/convertTCGA.Rd:18: missing file link 'ExpressionSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKGaf4I/R.INSTALL1e3c6fd228a9/RTCGA/man/convertTCGA.Rd:18: missing file link 'GRanges'
See 'C:/Users/biocbuild/bbs-3.6-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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
expressionsTCGA 295.09   3.50  302.32
heatmapTCGA     174.72   4.89  179.69
boxplotTCGA     141.21   5.61  150.01
kmTCGA           27.39   0.04   27.93
survivalTCGA     24.58   0.03   24.61
mutationsTCGA    13.97   0.03   14.01
theme_RTCGA       8.66   0.05    8.71
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
expressionsTCGA 292.56   0.72  293.28
heatmapTCGA     187.88   0.25  188.13
boxplotTCGA     163.14   1.19  164.32
kmTCGA           17.97   0.03   18.00
survivalTCGA     14.75   0.00   14.75
mutationsTCGA     7.42   0.00    7.42
theme_RTCGA       6.70   0.00    6.70
* 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-3.6-bioc/meat/RTCGA.Rcheck/00check.log'
for details.



Installation output

RTCGA.Rcheck/00install.out


install for i386

* installing *source* package 'RTCGA' ...
** R
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpKGaf4I/R.INSTALL1e3c6fd228a9/RTCGA/man/convertTCGA.Rd:23: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKGaf4I/R.INSTALL1e3c6fd228a9/RTCGA/man/convertTCGA.Rd:23: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKGaf4I/R.INSTALL1e3c6fd228a9/RTCGA/man/convertTCGA.Rd:13: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKGaf4I/R.INSTALL1e3c6fd228a9/RTCGA/man/convertTCGA.Rd:13: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKGaf4I/R.INSTALL1e3c6fd228a9/RTCGA/man/convertTCGA.Rd:18: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKGaf4I/R.INSTALL1e3c6fd228a9/RTCGA/man/convertTCGA.Rd:18: missing file link 'GRanges'
    datasetsTCGA                            html  
    downloadTCGA                            html  
    expressionsTCGA                         html  
    heatmapTCGA                             html  
    infoTCGA                                html  
    installTCGA                             html  
    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
In R CMD INSTALL

install for x64

* installing *source* package 'RTCGA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCGA' as RTCGA_1.8.0.zip
* DONE (RTCGA)
In R CMD INSTALL
In R CMD INSTALL

Tests output

RTCGA.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 1.8.0).
> 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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  14.59    1.65   18.03 

RTCGA.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 1.8.0).
> 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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  12.31    1.28   14.98 

Example timings

RTCGA.Rcheck/examples_i386/RTCGA-Ex.timings

nameusersystemelapsed
RTCGA-package000
boxplotTCGA141.21 5.61150.01
checkTCGA0.420.041.36
convertTCGA1.110.331.43
datasetsTCGA000
downloadTCGA0.470.080.93
expressionsTCGA295.09 3.50302.32
heatmapTCGA174.72 4.89179.69
infoTCGA1.350.011.52
installTCGA000
kmTCGA27.39 0.0427.93
mutationsTCGA13.97 0.0314.01
pcaTCGA000
readTCGA000
survivalTCGA24.58 0.0324.61
theme_RTCGA8.660.058.71

RTCGA.Rcheck/examples_x64/RTCGA-Ex.timings

nameusersystemelapsed
RTCGA-package000
boxplotTCGA163.14 1.19164.32
checkTCGA0.540.031.54
convertTCGA1.990.202.19
datasetsTCGA000
downloadTCGA0.170.010.56
expressionsTCGA292.56 0.72293.28
heatmapTCGA187.88 0.25188.13
infoTCGA1.120.001.26
installTCGA000
kmTCGA17.97 0.0318.00
mutationsTCGA7.420.007.42
pcaTCGA000
readTCGA0.020.000.02
survivalTCGA14.75 0.0014.75
theme_RTCGA6.70.06.7