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BioC 3.3: CHECK report for bioassayR on morelia

This page was generated on 2016-04-21 13:24:38 -0700 (Thu, 21 Apr 2016).

Package 98/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioassayR 1.9.37
Tyler Backman
Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bioassayR
Last Changed Rev: 115854 / Revision: 116626
Last Changed Date: 2016-04-05 18:42:44 -0700 (Tue, 05 Apr 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / 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: 1.9.37
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioassayR_1.9.37.tar.gz
StartedAt: 2016-04-20 23:36:24 -0700 (Wed, 20 Apr 2016)
EndedAt: 2016-04-20 23:37:40 -0700 (Wed, 20 Apr 2016)
EllapsedTime: 75.4 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_1.9.37.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/bioassayR.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.9.37’
* 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 ... [6s/6s] 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 ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [4s/4s]
 [4s/4s] 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

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-class0.0020.0010.002
activeAgainst0.0090.0000.010
activeTargets0.0110.0000.011
addBioassayIndex0.0140.0050.020
addDataSource0.0130.0020.016
allCids0.0080.0000.008
allTargets0.0070.0010.007
assaySetTargets0.0430.0020.045
bioactivityFingerprint0.1950.0020.197
bioassay-class0.0190.0040.023
bioassaySet-class0.0010.0000.001
connectBioassayDB0.0070.0030.011
disconnectBioassayDB0.0110.0030.015
dropBioassay0.0500.0100.061
dropBioassayIndex0.0260.0070.035
getAssay0.010.000.01
getAssays0.0210.0000.022
getBioassaySetByCids0.2700.0010.273
inactiveTargets0.0070.0010.008
loadBioassay0.0410.0040.046
loadIdMapping0.0070.0020.010
newBioassayDB0.0080.0020.010
parsePubChemBioassay0.0210.0010.022
perTargetMatrix0.0390.0010.041
queryBioassayDB0.0330.0120.044
samplebioassay0.0030.0010.004
scaleBioassaySet0.0330.0010.034
screenedAtLeast0.0110.0000.012
selectiveAgainst0.1540.0030.156
targetSelectivity0.0170.0010.018
translateTargetId0.0100.0020.015