Back to the "Multiple platform build/check report" A [B] C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for bioassayR on oaxaca

This page was generated on 2017-02-15 16:14:04 -0500 (Wed, 15 Feb 2017).

Package 106/1333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioassayR 1.13.1
Tyler Backman
Snapshot Date: 2017-02-14 17:15:56 -0500 (Tue, 14 Feb 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bioassayR
Last Changed Rev: 123182 / Revision: 126756
Last Changed Date: 2016-10-29 12:49:17 -0400 (Sat, 29 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  ERROR  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: bioassayR
Version: 1.13.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioassayR_1.13.1.tar.gz
StartedAt: 2017-02-14 22:50:08 -0800 (Tue, 14 Feb 2017)
EndedAt: 2017-02-14 22:51:34 -0800 (Tue, 14 Feb 2017)
EllapsedTime: 86.1 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_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/bioassayR.Rcheck’
* using R Under development (unstable) (2016-10-26 r71594)
* 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 ‘1.13.1’
* 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-3.5-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
activeAgainst0.0120.0010.014
activeTargets0.0070.0010.007
addBioassayIndex0.0110.0040.016
addDataSource0.0140.0030.018
allCids0.0260.0000.027
allTargets0.0070.0010.009
assaySetTargets0.0510.0010.053
bioactivityFingerprint0.4340.0020.437
bioassay-class0.0060.0020.008
bioassaySet-class0.0020.0000.002
connectBioassayDB0.0110.0020.013
crossReactivityProbability0.1570.0010.158
disconnectBioassayDB0.0090.0020.011
dropBioassay0.0480.0080.058
dropBioassayIndex0.0220.0130.038
getAssay0.0100.0020.011
getAssays0.0280.0030.031
getBioassaySetByCids0.1950.0040.199
inactiveTargets0.0110.0010.012
loadBioassay0.0390.0040.045
loadIdMapping0.0100.0030.013
newBioassayDB0.0100.0020.013
parsePubChemBioassay0.0170.0010.017
perTargetMatrix0.3250.0010.326
queryBioassayDB0.0330.0100.044
samplebioassay0.0030.0010.004
scaleBioassaySet0.0400.0010.041
screenedAtLeast0.0150.0010.015
selectiveAgainst0.0980.0020.100
targetSelectivity0.0250.0010.026
translateTargetId0.0110.0020.014
trinarySimilarity0.2820.0020.284