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CHECK report for readat on malbec2

This page was generated on 2019-04-09 11:46:44 -0400 (Tue, 09 Apr 2019).

Package 1315/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
readat 1.9.0
Richard Cotton
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/readat
Branch: master
Last Commit: 68aeadc
Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: readat
Version: 1.9.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:readat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings readat_1.9.0.tar.gz
StartedAt: 2019-04-09 03:07:00 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:10:59 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 239.2 seconds
RetCode: 0
Status:  OK 
CheckDir: readat.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:readat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings readat_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/readat.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘readat/DESCRIPTION’ ... OK
* this is package ‘readat’ version ‘1.9.0’
* 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
WideSomaLogicDataAttributes 38.647  0.133   6.368
sub-.WideSomaLogicData      34.975  0.173   6.820
readAdat                    34.763  0.117   6.787
colnamesStartWithSeqId      34.512  0.183   6.714
as.SummarizedExperiment     31.861  0.126   6.083
as.ExpressionSet            10.329  0.104   3.118
* 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-3.9-bioc/meat/readat.Rcheck/00check.log’
for details.



Installation output

readat.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL readat
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

Tests output

readat.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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(readat)
> library(testthat)
> 
> test_check("readat")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 62 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
145.398   0.978  33.679 

Example timings

readat.Rcheck/readat-Ex.timings

nameusersystemelapsed
WideSomaLogicData0.0170.0080.025
WideSomaLogicDataAttributes38.647 0.133 6.368
aptamers0.4040.0040.408
as.ExpressionSet10.329 0.104 3.118
as.SummarizedExperiment31.861 0.126 6.083
chromosomalPositions0.1040.0000.104
colnamesStartWithSeqId34.512 0.183 6.714
convertSeqIdToAptamer000
ensemblIds0.0030.0000.002
extractSampleData0.0060.0040.055
getChromosomalPositions0.0420.0000.042
getEnsemblIds0.0030.0000.003
getGoMolecularFunctions0.9290.0200.950
getKeggDefinitions0.030.000.03
getPfam0.0120.0000.013
getUniProtKeywords0.0230.0000.023
goMolecularFunction0.2400.0240.264
keggDefinitions0.0410.0000.041
pfam0.0150.0000.015
readAdat34.763 0.117 6.787
readComments0.1260.0000.046
readControls0.2100.0000.136
readSamples0.3420.0000.263
readSlides0.1240.0000.069
sub-.WideSomaLogicData34.975 0.173 6.820
uniprotKeywords0.0240.0000.024
writeSampleSubmissionForm0.3970.0000.142