Package: readat

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings readat_1.4.0.tar.gz

StartedAt: 2018-04-12 08:26:50 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 08:29:39 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 168.8 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 --no-vignettes --timings readat_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/readat.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.6-bioc/meat/readat.Rcheck/00check.log’
for details.

* installing *source* package ‘readat’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (readat)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 
  8.273   0.398   8.295 

name	user	system	elapsed
WideSomaLogicData	0.018	0.002	0.020
WideSomaLogicDataAttributes	1.005	0.065	0.909
aptamers	0.010	0.003	0.013
as.ExpressionSet	3.570	0.141	3.919
as.SummarizedExperiment	0.636	0.051	0.520
chromosomalPositions	0.210	0.003	0.214
colnamesStartWithSeqId	0.325	0.011	0.333
convertSeqIdToAptamer	0.002	0.000	0.001
ensemblIds	0.004	0.001	0.003
extractSampleData	0.013	0.004	0.010
getChromosomalPositions	0.254	0.037	0.148
getEnsemblIds	0.007	0.002	0.004
getGoMolecularFunctions	0.531	0.020	0.554
getKeggDefinitions	0.032	0.001	0.035
getPfam	0.010	0.001	0.012
getUniProtKeywords	0.017	0.002	0.019
goMolecularFunction	0.571	0.010	0.592
keggDefinitions	0.033	0.002	0.034
pfam	0.011	0.001	0.011
readAdat	0.449	0.027	0.395
readComments	0.059	0.011	0.036
readControls	0.509	0.019	0.478
readSamples	0.154	0.000	0.161
readSlides	0.497	0.003	0.516
sub-.WideSomaLogicData	0.354	0.016	0.343
uniprotKeywords	0.035	0.007	0.022
writeSampleSubmissionForm	0.230	0.056	0.166