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CHECK report for RImmPort on malbec1

This page was generated on 2019-04-16 11:51:52 -0400 (Tue, 16 Apr 2019).

Package 1312/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RImmPort 1.10.0
Zicheng Hu , Ravi Shankar
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/RImmPort
Branch: RELEASE_3_8
Last Commit: abbe516
Last Changed Date: 2018-10-30 11:42:00 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RImmPort
Version: 1.10.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RImmPort.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RImmPort_1.10.0.tar.gz
StartedAt: 2019-04-16 02:37:59 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:38:50 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 50.9 seconds
RetCode: 0
Status:  OK 
CheckDir: RImmPort.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RImmPort.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RImmPort_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/RImmPort.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.10.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
serialzeStudyData 7.156  0.032   3.375
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/RImmPort.Rcheck/00check.log’
for details.



Installation output

RImmPort.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL RImmPort
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘RImmPort’ ...
** 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
* DONE (RImmPort)

Tests output


Example timings

RImmPort.Rcheck/RImmPort-Ex.timings

nameusersystemelapsed
Events-class2.4560.0321.416
Findings-class2.0960.0240.761
Interventions-class1.5800.0040.477
SpecialPurpose-class1.8760.0200.540
Study-class2.0480.0200.824
TrialDesign-class2.1280.0120.861
buildNewSqliteDb0.0000.0000.001
getAssayDataOfStudies0.2560.0040.283
getDomainCode000
getDomainDataOfStudies0.0520.0160.167
getListOfAssayTypes000
getListOfDomains000
getListOfStudies0.0520.0040.069
getStudiesWithSpecificAssayData0.0560.0040.059
getStudiesWithSpecificDomainData0.0480.0080.059
getStudy2.0960.0160.870
loadSerializedStudyData0.0040.0000.006
mergeDomainAndSupplemental1.6240.0040.618
serialzeStudyData7.1560.0323.375
setImmPortDataSource0.0600.0000.116