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BioC 3.1: CHECK report for bioassayR on petty

This page was generated on 2015-10-09 09:36:01 -0700 (Fri, 09 Oct 2015).

Package 88/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioassayR 1.6.1
Tyler Backman
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/bioassayR
Last Changed Rev: 104802 / Revision: 109384
Last Changed Date: 2015-06-10 12:53:00 -0700 (Wed, 10 Jun 2015)
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  ERROR  skipped  skipped 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioassayR_1.6.1.tar.gz
StartedAt: 2015-10-08 21:40:09 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 21:42:06 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 117.0 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_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/bioassayR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.6.1’
* 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 ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/7s] 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-3.1-bioc/meat/bioassayR.Rcheck/00check.log’
for details.


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-class0.0010.0000.002
activeAgainst0.0130.0010.014
activeTargets0.0150.0000.016
addBioassayIndex0.0180.0060.032
addDataSource0.0230.0060.190
bioassay-class0.0370.0050.043
bioassaySet-class0.0030.0000.003
connectBioassayDB0.0170.0040.037
disconnectBioassayDB0.0180.0040.023
dropBioassay0.0640.0110.088
dropBioassayIndex0.0340.0140.241
getAssay0.0160.0010.017
getAssays0.0700.0010.072
getBioassaySetByCids0.9770.0030.982
inactiveTargets0.0190.0010.021
loadBioassay0.0470.0070.068
loadIdMapping0.0170.0050.033
newBioassayDB0.0140.0040.182
parsePubChemBioassay0.0160.0010.017
perTargetMatrix0.0780.0020.080
queryBioassayDB0.1030.0360.140
samplebioassay0.0050.0000.006
screenedAtLeast0.0190.0010.020
selectiveAgainst0.2910.0040.300
targetSelectivity0.0420.0010.043
translateTargetId0.0140.0050.027