Package: TCGAutils

Version: 1.2.2

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TCGAutils_1.2.2.tar.gz

StartedAt: 2019-04-16 03:22:36 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:28:05 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 328.5 seconds

RetCode: 0

Status:  OK

CheckDir: TCGAutils.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TCGAutils_1.2.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/TCGAutils.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 ‘TCGAutils/DESCRIPTION’ ... OK
* this is package ‘TCGAutils’ version ‘1.2.2’
* 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                       30.852  0.520  32.800
qreduceTCGA                        27.544  0.652  29.111
makeSummarizedExperimentFromGISTIC 19.016  2.644  29.178
imputeAssay                         9.316  0.312  11.045
symbolsToRanges                     9.208  0.028   9.244
mirToRanges                         6.488  0.216   7.662
* 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/TCGAutils.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL TCGAutils
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘TCGAutils’ ...
** 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
* DONE (TCGAutils)

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(TCGAutils)
> 
> #test_check("TCGAutils")
> 
> proc.time()
   user  system elapsed 
  0.264   0.040   0.297 

name	user	system	elapsed
ID-translation	1.204	0.040	3.235
TCGAbarcode	0.000	0.000	0.001
TCGAbiospec	0.028	0.004	0.046
TCGAsampleSelect	0.008	0.004	0.012
builds	0.052	0.004	0.057
curatedTCGAData-helpers	0.016	0.000	0.013
findGRangesCols	0.004	0.000	0.004
generateMap	0.092	0.000	0.094
getFileNames	0.084	0.000	0.281
imputeAssay	9.316	0.312	11.045
makeGRangesListFromCopyNumber	0.628	0.028	1.522
makeGRangesListFromExonFiles	0.160	0.000	0.172
makeSummarizedExperimentFromGISTIC	19.016	2.644	29.178
mergeColData	0.408	0.008	0.417
mirToRanges	6.488	0.216	7.662
qreduceTCGA	27.544	0.652	29.111
simplifyTCGA	30.852	0.520	32.800
symbolsToRanges	9.208	0.028	9.244