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BioC 3.2: CHECK report for bioassayR on zin1

This page was generated on 2016-04-23 10:13:24 -0700 (Sat, 23 Apr 2016).

Package 92/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioassayR 1.8.37
Tyler Backman
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/bioassayR
Last Changed Rev: 115855 / Revision: 116712
Last Changed Date: 2016-04-05 18:47:34 -0700 (Tue, 05 Apr 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  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: 1.8.37
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings bioassayR_1.8.37.tar.gz
StartedAt: 2016-04-22 22:27:34 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:28:42 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 67.5 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_1.8.37.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/bioassayR.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.8.37’
* 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 ... [5s/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-class0.0010.0000.001
activeAgainst0.010.000.01
activeTargets0.0090.0000.010
addBioassayIndex0.0070.0040.010
addDataSource0.0090.0000.012
allCids0.0060.0000.005
allTargets0.0050.0000.005
assaySetTargets0.0410.0040.042
bioactivityFingerprint0.2080.0000.210
bioassay-class0.0170.0000.018
bioassaySet-class0.0010.0000.001
connectBioassayDB0.0080.0000.008
disconnectBioassayDB0.0080.0000.007
dropBioassay0.0280.0080.036
dropBioassayIndex0.0160.0000.016
getAssay0.0060.0000.007
getAssays0.020.000.02
getBioassaySetByCids0.190.000.19
inactiveTargets0.0070.0000.007
loadBioassay0.0270.0000.028
loadIdMapping0.0070.0000.008
newBioassayDB0.0060.0000.006
parsePubChemBioassay0.0120.0000.012
perTargetMatrix0.0290.0000.029
queryBioassayDB0.0140.0080.022
samplebioassay0.0000.0040.003
scaleBioassaySet0.0310.0000.031
screenedAtLeast0.0090.0000.009
selectiveAgainst0.0980.0040.102
targetSelectivity0.0180.0000.018
translateTargetId0.0090.0000.013