BioC 3.5: CHECK report for readat on oaxaca

Package: readat

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings readat_1.1.0.tar.gz

StartedAt: 2017-03-04 07:53:13 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:56:13 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 180.0 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/readat.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘readat/DESCRIPTION’ ... OK
* this is package ‘readat’ version ‘1.1.0’
* 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 ... 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 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: OK

* 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)

name	user	system	elapsed
WideSomaLogicData	0.013	0.001	0.014
WideSomaLogicDataAttributes	0.767	0.013	0.782
aptamers	0.009	0.002	0.012
as.ExpressionSet	3.411	0.072	3.796
as.SummarizedExperiment	0.507	0.005	0.513
chromosomalPositions	0.178	0.001	0.179
colnamesStartWithSeqId	0.349	0.006	0.355
convertSeqIdToAptamer	0.001	0.000	0.000
ensemblIds	0.002	0.000	0.002
extractSampleData	0.005	0.002	0.008
getChromosomalPositions	0.157	0.000	0.158
getEnsemblIds	0.004	0.000	0.004
getGoMolecularFunctions	0.529	0.017	0.546
getKeggDefinitions	0.021	0.001	0.023
getPfam	0.011	0.001	0.011
getUniProtKeywords	0.023	0.003	0.026
goMolecularFunction	0.216	0.009	0.224
keggDefinitions	0.408	0.004	0.413
pfam	0.014	0.000	0.014
readAdat	0.371	0.009	0.380
readComments	0.012	0.002	0.036
readControls	0.035	0.001	0.035
readSamples	0.407	0.030	0.437
readSlides	0.011	0.001	0.011
sub-.WideSomaLogicData	0.368	0.006	0.374
uniprotKeywords	0.021	0.001	0.022
writeSampleSubmissionForm	0.119	0.019	0.172