Package: TCGAutils

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TCGAutils_1.6.2.tar.gz

StartedAt: 2020-04-15 06:06:24 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:13:53 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 449.7 seconds

RetCode: 0

Status:  OK

CheckDir: TCGAutils.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TCGAutils_1.6.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/TCGAutils.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAutils/DESCRIPTION’ ... OK
* this is package ‘TCGAutils’ version ‘1.6.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘TCGAutils’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’ ‘GenomicRanges:::.normarg_field’
  See the note in ?`:::` about the use of this operator.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
simplifyTCGA                       41.549  2.176  44.942
TCGAprimaryTumors                  28.404  0.976  30.898
makeSummarizedExperimentFromGISTIC 17.482  9.212  13.110
imputeAssay                        21.412  0.367  22.939
trimColData                        19.929  0.761  21.992
curatedTCGAData-helpers            19.618  0.362  21.262
oncoPrintTCGA                      16.685  0.441  17.904
* 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
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/TCGAutils.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TCGAutils
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘TCGAutils’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (TCGAutils)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(TCGAutils)
> 
> test_check("TCGAutils")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 44 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 15.284   0.728  17.924 

name	user	system	elapsed
ID-translation	1.709	0.047	3.769
TCGAbarcode	0.001	0.000	0.001
TCGAbiospec	0.022	0.002	0.024
TCGAprimaryTumors	28.404	0.976	30.898
TCGAsampleSelect	0.010	0.001	0.011
builds	0.031	0.001	0.032
curatedTCGAData-helpers	19.618	0.362	21.262
findGRangesCols	0.004	0.000	0.004
generateMap	0.044	0.000	0.044
getFileName	0.507	0.001	0.705
imputeAssay	21.412	0.367	22.939
makeGRangesListFromCopyNumber	1.216	0.037	2.239
makeGRangesListFromExonFiles	0.146	0.001	0.149
makeSummarizedExperimentFromGISTIC	17.482	9.212	13.110
mergeColData	0.407	0.009	0.418
oncoPrintTCGA	16.685	0.441	17.904
simplifyTCGA	41.549	2.176	44.942
trimColData	19.929	0.761	21.992