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BioC 3.2: CHECK report for bioassayR on linux1.bioconductor.org

This page was generated on 2015-10-27 17:26:08 -0400 (Tue, 27 Oct 2015).

Package 92/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioassayR 1.8.0
Tyler Backman
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/bioassayR
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bioassayR
Version: 1.8.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings bioassayR_1.8.0.tar.gz
StartedAt: 2015-10-27 01:21:55 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 01:22:50 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 55.0 seconds
RetCode: 0
Status:  OK 
CheckDir: bioassayR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings bioassayR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/bioassayR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.0’
* 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 ‘bioassayR’ can be installed ... [5s/5s] 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 ... 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 ... [3s/3s] 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
** 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-class0.0010.0010.001
activeAgainst0.0080.0000.008
activeTargets0.0070.0000.007
addBioassayIndex0.0090.0000.009
addDataSource0.010.000.01
allCids0.0040.0000.004
allTargets0.0000.0030.004
assaySetTargets0.0300.0010.031
bioassay-class0.0150.0000.015
bioassaySet-class0.0010.0000.000
connectBioassayDB0.0070.0000.008
disconnectBioassayDB0.0070.0000.008
dropBioassay0.0320.0000.032
dropBioassayIndex0.0140.0000.014
getAssay0.0060.0000.006
getAssays0.0150.0000.015
getBioassaySetByCids0.3510.0000.352
inactiveTargets0.0070.0000.007
loadBioassay0.0220.0000.023
loadIdMapping0.0060.0030.007
newBioassayDB0.0040.0010.006
parsePubChemBioassay0.0080.0000.007
perTargetMatrix0.0290.0000.028
queryBioassayDB0.0250.0070.032
samplebioassay0.0010.0000.002
screenedAtLeast0.0100.0000.009
selectiveAgainst0.0870.0000.087
targetSelectivity0.0140.0010.018
translateTargetId0.0070.0000.008