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BioC 3.4: CHECK report for bioassayR on morelia

This page was generated on 2017-04-15 16:25:00 -0400 (Sat, 15 Apr 2017).

Package 107/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioassayR 1.12.1
Tyler Backman
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/bioassayR
Last Changed Rev: 123183 / Revision: 128728
Last Changed Date: 2016-10-29 12:59:02 -0400 (Sat, 29 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: bioassayR
Version: 1.12.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioassayR_1.12.1.tar.gz
StartedAt: 2017-04-14 23:08:23 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:09:50 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 86.7 seconds
RetCode: 0
Status:  OK 
CheckDir: bioassayR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioassayR_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/bioassayR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bioassayR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bioassayR’ version ‘1.12.1’
* 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 ‘bioassayR’ 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
crossReactivityPrior: no visible global function definition for ‘sd’
crossReactivityProbability : <anonymous>: no visible global function
  definition for ‘pbeta’
Undefined global functions or variables:
  pbeta sd
Consider adding
  importFrom("stats", "pbeta", "sd")
to your NAMESPACE file.
* 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-3.4-bioc/meat/bioassayR.Rcheck/00check.log’
for details.


bioassayR.Rcheck/00install.out:

* installing *source* package ‘bioassayR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘organism’ in package ‘bioassayR’
Creating a new generic function for ‘organism<-’ in package ‘bioassayR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bioassayR)

bioassayR.Rcheck/bioassayR-Ex.timings:

nameusersystemelapsed
BioAssayDB-class0.0010.0000.001
activeAgainst0.0150.0010.017
activeTargets0.0120.0010.014
addBioassayIndex0.0170.0050.025
addDataSource0.0270.0040.033
allCids0.0050.0010.005
allTargets0.0050.0000.005
assaySetTargets0.0450.0000.045
bioactivityFingerprint0.2480.0020.250
bioassay-class0.0220.0030.025
bioassaySet-class0.0010.0010.001
connectBioassayDB0.0130.0020.017
crossReactivityProbability0.2800.0010.282
disconnectBioassayDB0.0120.0030.014
dropBioassay0.0550.0070.069
dropBioassayIndex0.0280.0090.041
getAssay0.0100.0010.012
getAssays0.0320.0000.034
getBioassaySetByCids0.2420.0010.244
inactiveTargets0.0100.0010.011
loadBioassay0.0370.0040.042
loadIdMapping0.0150.0040.021
newBioassayDB0.0080.0020.011
parsePubChemBioassay0.0200.0000.021
perTargetMatrix0.2980.0010.300
queryBioassayDB0.0240.0110.035
samplebioassay0.0030.0010.005
scaleBioassaySet0.0430.0010.044
screenedAtLeast0.0170.0010.018
selectiveAgainst0.1710.0040.175
targetSelectivity0.0330.0010.035
translateTargetId0.0140.0020.019
trinarySimilarity0.2830.0010.284