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CHECK report for RImmPort on veracruz1

This page was generated on 2018-04-12 13:42:20 -0400 (Thu, 12 Apr 2018).

Package 1179/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RImmPort 1.7.2
Zicheng Hu , Ravi Shankar
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/RImmPort
Branch: RELEASE_3_6
Last Commit: f8beded
Last Changed Date: 2018-03-30 16:36:48 -0400 (Fri, 30 Mar 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RImmPort
Version: 1.7.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RImmPort_1.7.2.tar.gz
StartedAt: 2018-04-12 08:46:16 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 08:47:14 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 58.4 seconds
RetCode: 0
Status:  OK 
CheckDir: RImmPort.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 RImmPort_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/RImmPort.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RImmPort/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RImmPort’ version ‘1.7.2’
* 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 ‘RImmPort’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
* 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 ... NOTE
buildNewSqliteDb: no visible global function definition for
  ‘dbListTables’
Undefined global functions or variables:
  dbListTables
* 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 ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/RImmPort.Rcheck/00check.log’
for details.



Installation output

RImmPort.Rcheck/00install.out

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

Tests output


Example timings

RImmPort.Rcheck/RImmPort-Ex.timings

nameusersystemelapsed
Events-class0.9130.1471.037
Findings-class1.6800.1691.660
Interventions-class0.2790.0480.219
SpecialPurpose-class0.3220.0650.214
Study-class0.2480.0310.239
TrialDesign-class0.4420.0790.324
buildNewSqliteDb0.0020.0010.002
getAssayDataOfStudies0.0760.0080.088
getDomainCode0.0000.0000.001
getDomainDataOfStudies0.0470.0040.052
getListOfAssayTypes0.0000.0000.001
getListOfDomains000
getListOfStudies0.0340.0040.037
getStudiesWithSpecificAssayData0.0340.0030.037
getStudiesWithSpecificDomainData0.0340.0040.039
getStudy0.2730.0470.209
loadSerializedStudyData0.0110.0030.007
mergeDomainAndSupplemental0.3080.0590.205
serialzeStudyData0.8930.1500.658
setImmPortDataSource0.0980.0190.061