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CHECK report for TxRegInfra on merida2

This page was generated on 2019-04-09 13:36:59 -0400 (Tue, 09 Apr 2019).

Package 1658/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TxRegInfra 1.3.6
VJ Carey
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/TxRegInfra
Branch: master
Last Commit: 783cf8c
Last Changed Date: 2019-03-31 22:03:03 -0400 (Sun, 31 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: TxRegInfra
Version: 1.3.6
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TxRegInfra.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TxRegInfra_1.3.6.tar.gz
StartedAt: 2019-04-09 04:17:16 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:20:39 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 202.9 seconds
RetCode: 0
Status:  OK 
CheckDir: TxRegInfra.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TxRegInfra.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TxRegInfra_1.3.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TxRegInfra.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TxRegInfra/DESCRIPTION’ ... OK
* this is package ‘TxRegInfra’ version ‘1.3.6’
* package encoding: UTF-8
* 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 ‘TxRegInfra’ 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 ... NOTE
'library' or 'require' call to 'shiny' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dnmetaApp: no visible global function definition for ‘fluidPage’
dnmetaApp: no visible global function definition for ‘sidebarLayout’
dnmetaApp: no visible global function definition for ‘sidebarPanel’
dnmetaApp: no visible global function definition for ‘helpText’
dnmetaApp: no visible global function definition for ‘radioButtons’
dnmetaApp: no visible global function definition for
  ‘checkboxGroupInput’
dnmetaApp: no visible global function definition for ‘uiOutput’
dnmetaApp: no visible global function definition for ‘mainPanel’
dnmetaApp: no visible global function definition for ‘dataTableOutput’
dnmetaApp : server: no visible global function definition for
  ‘renderUI’
dnmetaApp : server: no visible global function definition for
  ‘selectInput’
dnmetaApp : server: no visible global function definition for
  ‘renderDataTable’
dnmetaApp: no visible global function definition for ‘runApp’
Undefined global functions or variables:
  checkboxGroupInput dataTableOutput fluidPage helpText mainPanel
  radioButtons renderDataTable renderUI runApp selectInput
  sidebarLayout sidebarPanel uiOutput
* 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 ... NOTE
  Note: found 14 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
txmodels 19.427  2.221  23.875
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/TxRegInfra.Rcheck/00check.log’
for details.



Installation output

TxRegInfra.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TxRegInfra
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘TxRegInfra’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (TxRegInfra)

Tests output


Example timings

TxRegInfra.Rcheck/TxRegInfra-Ex.timings

nameusersystemelapsed
URL_txregInAWS000
basicColData0.0730.0030.141
basicFormatter0.0160.0000.015
dgf_meta0.0050.0010.006
dnmeta0.0540.0060.060
dnmetaApp0.0010.0000.001
getDocumentFields0.0010.0010.001
getFieldNames0.0940.0101.713
grConverter0.0260.0000.027
importBedToMongo0.0070.0030.010
listAllCollections0.0010.0010.003
makeAggregator0.0070.0040.008
makeColData0.0020.0030.007
oldbasicColData0.0070.0020.008
ragged41FP0.1880.0050.226
sbov0.0050.0040.008
txmodels19.427 2.22123.875
txregCollections0.0040.0030.007
verifyHasMongoCmd0.0010.0000.001
verifyRunningMongodb0.0000.0010.000