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CHECK report for RTCGA on malbec1

This page was generated on 2019-04-16 11:51:34 -0400 (Tue, 16 Apr 2019).

Package 1360/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCGA 1.12.1
Marcin Kosinski
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/RTCGA
Branch: RELEASE_3_8
Last Commit: 06aa512
Last Changed Date: 2019-01-04 13:12:18 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RTCGA
Version: 1.12.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RTCGA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RTCGA_1.12.1.tar.gz
StartedAt: 2019-04-16 02:47:21 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:54:34 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 432.6 seconds
RetCode: 0
Status:  OK 
CheckDir: RTCGA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RTCGA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RTCGA_1.12.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/RTCGA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTCGA/DESCRIPTION’ ... OK
* this is package ‘RTCGA’ version ‘1.12.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RTCGA’ 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
expressionsTCGA 124.572  0.664 126.723
heatmapTCGA     106.872  0.184 109.916
boxplotTCGA      70.440  1.300  73.527
kmTCGA           14.504  0.000  14.723
survivalTCGA     12.864  0.004  12.881
mutationsTCGA     7.964  0.004   7.975
theme_RTCGA       5.068  0.000   5.075
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/RTCGA.Rcheck/00check.log’
for details.



Installation output

RTCGA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL RTCGA
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘RTCGA’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RTCGA)

Tests output

RTCGA.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: 1.12.1).
> 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, colMeans, colSums, colnames,
    dirname, 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 
 13.056   1.048  16.061 

Example timings

RTCGA.Rcheck/RTCGA-Ex.timings

nameusersystemelapsed
RTCGA-package000
boxplotTCGA70.440 1.30073.527
checkTCGA0.3360.0081.253
convertTCGA1.6240.3001.928
datasetsTCGA000
downloadTCGA0.1040.1520.637
expressionsTCGA124.572 0.664126.723
heatmapTCGA106.872 0.184109.916
infoTCGA1.7080.0042.089
installTCGA000
kmTCGA14.504 0.00014.723
mutationsTCGA7.9640.0047.975
pcaTCGA000
readTCGA0.0040.0000.001
survivalTCGA12.864 0.00412.881
theme_RTCGA5.0680.0005.075