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CHECK report for RSVSim on celaya2

This page was generated on 2019-10-16 12:50:55 -0400 (Wed, 16 Oct 2019).

Package 1426/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RSVSim 1.24.0
Christoph Bartenhagen
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/RSVSim
Branch: RELEASE_3_9
Last Commit: 77efbac
Last Changed Date: 2019-05-02 11:53:40 -0400 (Thu, 02 May 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

Summary

Package: RSVSim
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RSVSim.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RSVSim_1.24.0.tar.gz
StartedAt: 2019-10-16 06:27:11 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:31:53 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 282.0 seconds
RetCode: 0
Status:  OK 
CheckDir: RSVSim.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RSVSim.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RSVSim_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RSVSim.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RSVSim/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RSVSim’ version ‘1.24.0’
* 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 ‘RSVSim’ 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' calls in package code:
  ‘BSgenome.Hsapiens.UCSC.hg19’ ‘BSgenome.Hsapiens.UCSC.hg19.masked’
  ‘MASS’ ‘rtracklayer’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.drawPos: no visible global function definition for ‘seqlevels’
.drawPos: no visible global function definition for ‘queryHits’
.getHG19: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
.getHG19: no visible binding for global variable ‘Hsapiens’
.getHG19: no visible global function definition for ‘as’
.getSVSizes: no visible global function definition for ‘rbeta’
.loadFromBSGenome_TandemRepeats: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
.loadFromBSGenome_TandemRepeats: no visible global function definition
  for ‘seqlevels<-’
.loadFromBSGenome_TandemRepeats: no visible global function definition
  for ‘as’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘browserSession’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘genome<-’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘ucscTableQuery’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘txtProgressBar’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘range<-’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘getTable’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘setTxtProgressBar’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘data’
.loadFromUCSC_SegDups: no visible global function definition for
  ‘browserSession’
.loadFromUCSC_SegDups: no visible global function definition for
  ‘genome<-’
.loadFromUCSC_SegDups: no visible global function definition for
  ‘getTable’
.loadFromUCSC_SegDups: no visible global function definition for
  ‘ucscTableQuery’
.readRepeatMaskerOutput: no visible global function definition for
  ‘read.table’
.readRepeatMaskerOutput: no visible global function definition for
  ‘data’
.simInsertionPositions: no visible global function definition for
  ‘txtProgressBar’
.simInsertionPositions: no visible global function definition for
  ‘seqlevels’
.simInsertionPositions: no visible global function definition for
  ‘setTxtProgressBar’
.simPositions: no visible global function definition for
  ‘txtProgressBar’
.simPositions: no visible global function definition for
  ‘setTxtProgressBar’
.simTranslocationPositions: no visible global function definition for
  ‘txtProgressBar’
.simTranslocationPositions: no visible global function definition for
  ‘seqlevels’
.simTranslocationPositions: no visible global function definition for
  ‘setTxtProgressBar’
.subtractIntervals: no visible global function definition for
  ‘seqlevels<-’
.testSVSim: no visible global function definition for ‘metadata’
compareSV,character-character: no visible global function definition
  for ‘read.table’
compareSV,character-data.frame: no visible global function definition
  for ‘read.table’
estimateSVSizes,numeric-numeric-ANY-ANY-missing: no visible global
  function definition for ‘fitdistr’
simulateSV,ANY: no visible global function definition for ‘data’
simulateSV,ANY: no visible global function definition for
  ‘txtProgressBar’
simulateSV,ANY: no visible global function definition for
  ‘setTxtProgressBar’
simulateSV,ANY: no visible global function definition for ‘write.table’
simulateSV,ANY: no visible global function definition for ‘metadata<-’
Undefined global functions or variables:
  BSgenome.Hsapiens.UCSC.hg19.masked Hsapiens as browserSession data
  fitdistr genome<- getTable metadata metadata<- queryHits range<-
  rbeta read.table seqlevels seqlevels<- setTxtProgressBar
  txtProgressBar ucscTableQuery write.table
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbeta")
  importFrom("utils", "data", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
simulateSV 10.370  0.175  10.548
compareSVs  5.359  0.417   5.778
* 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-3.9-bioc/meat/RSVSim.Rcheck/00check.log’
for details.



Installation output

RSVSim.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RSVSim
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘RSVSim’ ...
** using staged installation
** R
** data
** 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 (RSVSim)

Tests output


Example timings

RSVSim.Rcheck/RSVSim-Ex.timings

nameusersystemelapsed
compareSVs5.3590.4175.778
estimateSVSizes0.3870.0430.430
segmentalDuplications0.1160.0080.123
simulateSV10.370 0.17510.548
weightsMechanisms0.0060.0040.010
weightsRepeats0.0060.0050.010