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CHECK report for RImmPort on celaya2

This page was generated on 2020-01-16 13:44:25 -0500 (Thu, 16 Jan 2020).

Package 1432/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RImmPort 1.15.0
Zicheng Hu , Ravi Shankar
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/RImmPort
Branch: master
Last Commit: 3f789f0
Last Changed Date: 2019-10-29 13:40:28 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RImmPort
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RImmPort.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RImmPort_1.15.0.tar.gz
StartedAt: 2020-01-16 08:13:14 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 08:14:36 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 81.7 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 --install=check:RImmPort.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RImmPort_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/RImmPort.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.15.0’
* 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 ‘RImmPort’ can be installed ... 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 ... 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 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/RImmPort.Rcheck/00check.log’
for details.



Installation output

RImmPort.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RImmPort
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘RImmPort’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RImmPort)

Tests output


Example timings

RImmPort.Rcheck/RImmPort-Ex.timings

nameusersystemelapsed
Events-class1.1260.7550.924
Findings-class1.1940.8710.667
Interventions-class0.9630.7160.445
SpecialPurpose-class2.0610.6630.414
Study-class1.7060.8180.405
TrialDesign-class1.2181.0160.385
buildNewSqliteDb0.0060.0060.002
getAssayDataOfStudies0.6120.4760.201
getDomainCode0.0020.0020.001
getDomainDataOfStudies0.3210.2340.106
getListOfAssayTypes0.0010.0010.001
getListOfDomains0.0010.0010.000
getListOfStudies0.1160.0340.109
getStudiesWithSpecificAssayData0.0980.0180.115
getStudiesWithSpecificDomainData0.1020.0170.118
getStudy0.7570.5090.426
loadSerializedStudyData0.0430.0410.015
mergeDomainAndSupplemental1.4980.2050.238
serialzeStudyData2.2921.7300.797
setImmPortDataSource0.3740.2980.112