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BioC 3.0: CHECK report for inSilicoDb on perceval

This page was generated on 2015-04-10 09:55:58 -0700 (Fri, 10 Apr 2015).

Package 456/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
inSilicoDb 2.2.1
InSilico DB
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/inSilicoDb
Last Changed Rev: 99533 / Revision: 102249
Last Changed Date: 2015-02-17 01:04:51 -0800 (Tue, 17 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: inSilicoDb
Version: 2.2.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch inSilicoDb_2.2.1.tar.gz
StartedAt: 2015-04-10 02:53:33 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:55:47 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 134.2 seconds
RetCode: 0
Status:  OK 
CheckDir: inSilicoDb.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch inSilicoDb_2.2.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/inSilicoDb.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘inSilicoDb/DESCRIPTION’ ... OK
* this is package ‘inSilicoDb’ version ‘2.2.1’
* 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 ‘inSilicoDb’ can be installed ... [4s/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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘RCurl’ ‘rjson’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
checkBinary: no visible global function definition for ‘fromJSON’
getInSilicoBinary: no visible global function definition for
  ‘basicHeaderGatherer’
getInSilicoBinary: no visible global function definition for
  ‘getCurlHandle’
getInSilicoBinary: no visible global function definition for
  ‘getBinaryURL’
getInSilicoJSON: no visible global function definition for
  ‘basicHeaderGatherer’
getInSilicoJSON: no visible global function definition for
  ‘getCurlHandle’
getInSilicoJSON: no visible global function definition for ‘postForm’
getInSilicoJSON: no visible global function definition for ‘fromJSON’
writeInSilicoCache: no visible binding for global variable ‘cache’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/92s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getDatasets            2.796  0.958  30.979
getDataset             0.817  0.051  14.727
getDatasetPlatformList 0.672  0.023  12.381
getDatasetList         0.594  0.014  11.136
getDatasetInfo         0.443  0.007   7.960
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/inSilicoDb.Rcheck/00check.log’
for details.

inSilicoDb.Rcheck/00install.out:

* installing *source* package ‘inSilicoDb’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (inSilicoDb)

inSilicoDb.Rcheck/inSilicoDb-Ex.timings:

nameusersystemelapsed
getAnnotations0.1730.0051.865
getCurationInfo0.1300.0021.560
getDataset 0.817 0.05114.727
getDatasetInfo0.4430.0077.960
getDatasetList 0.594 0.01411.136
getDatasetPlatformList 0.672 0.02312.381
getDatasets 2.796 0.95830.979
getDefaultCuration0.1110.0231.551
getPlatformList0.3760.0064.673
getPlatforms0.1970.0043.103