Package: readat

Version: 1.8.0

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_1.8.0.tar.gz

StartedAt: 2019-04-16 02:15:02 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:18:06 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 183.6 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/readat.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.0’
* 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 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 4.507  1.103   3.625
* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘readat’ ...
** 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 (readat)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 13.602   4.076   9.978 

name	user	system	elapsed
WideSomaLogicData	0.029	0.007	0.036
WideSomaLogicDataAttributes	1.230	1.039	0.505
aptamers	0.050	0.054	0.018
as.ExpressionSet	4.507	1.103	3.625
as.SummarizedExperiment	0.890	0.814	0.337
chromosomalPositions	0.341	0.380	0.126
colnamesStartWithSeqId	0.626	0.535	0.265
convertSeqIdToAptamer	0.002	0.002	0.000
ensemblIds	0.009	0.013	0.003
extractSampleData	0.040	0.054	0.016
getChromosomalPositions	0.156	0.158	0.047
getEnsemblIds	0.013	0.019	0.005
getGoMolecularFunctions	0.576	0.425	0.367
getKeggDefinitions	0.033	0.003	0.037
getPfam	0.015	0.001	0.016
getUniProtKeywords	0.024	0.001	0.026
goMolecularFunction	0.819	0.014	0.844
keggDefinitions	0.041	0.002	0.043
pfam	0.016	0.000	0.017
readAdat	0.935	0.917	0.339
readComments	0.180	0.225	0.059
readControls	0.437	0.506	0.137
readSamples	0.775	0.726	0.293
readSlides	0.314	0.367	0.103
sub-.WideSomaLogicData	0.935	0.857	0.288
uniprotKeywords	0.104	0.086	0.030
writeSampleSubmissionForm	0.455	0.362	0.130