Package: readat

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:readat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings readat_1.11.0.tar.gz

StartedAt: 2019-07-31 04:27:23 -0400 (Wed, 31 Jul 2019)

EndedAt: 2019-07-31 04:30:43 -0400 (Wed, 31 Jul 2019)

EllapsedTime: 199.5 seconds

RetCode: 0

Status:  OK

CheckDir: readat.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:readat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings readat_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/readat.Rcheck’
* using R version 3.6.0 (2019-04-26)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘readat/DESCRIPTION’ ... OK
* this is package ‘readat’ version ‘1.11.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘readat’ 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
sfread: no visible binding for global variable ‘header’
sfread: no visible binding for global variable ‘nrows’
Undefined global functions or variables:
  header nrows
* 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
as.ExpressionSet 4.237  1.615   3.338
* 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/readat.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 readat
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘readat’ ...
** 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 (readat)

R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 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(readat)
> library(testthat)
> 
> test_check("readat")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 62 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 13.976   3.213  10.319 

name	user	system	elapsed
WideSomaLogicData	0.024	0.009	0.032
WideSomaLogicDataAttributes	1.028	1.152	0.423
aptamers	0.051	0.069	0.017
as.ExpressionSet	4.237	1.615	3.338
as.SummarizedExperiment	0.784	0.780	0.300
chromosomalPositions	0.407	0.463	0.156
colnamesStartWithSeqId	0.684	0.668	0.297
convertSeqIdToAptamer	0.002	0.003	0.000
ensemblIds	0.009	0.010	0.002
extractSampleData	0.040	0.060	0.015
getChromosomalPositions	0.145	0.182	0.048
getEnsemblIds	0.014	0.014	0.005
getGoMolecularFunctions	0.543	0.394	0.338
getKeggDefinitions	0.027	0.002	0.029
getPfam	0.010	0.001	0.010
getUniProtKeywords	0.016	0.002	0.019
goMolecularFunction	0.789	0.018	0.813
keggDefinitions	0.045	0.002	0.048
pfam	0.018	0.001	0.018
readAdat	0.958	0.830	0.363
readComments	0.101	0.094	0.033
readControls	0.596	0.527	0.191
readSamples	0.734	0.519	0.290
readSlides	0.110	0.102	0.040
sub-.WideSomaLogicData	1.077	0.942	0.345
uniprotKeywords	0.097	0.075	0.029
writeSampleSubmissionForm	0.374	0.320	0.118