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BioC 3.4: CHECK report for RSVSim on moscato1

This page was generated on 2016-09-21 03:44:32 -0700 (Wed, 21 Sep 2016).

Package 1058/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RSVSim 1.13.0
Christoph Bartenhagen
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RSVSim
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RSVSim
Version: 1.13.0
Command: rm -rf RSVSim.buildbin-libdir RSVSim.Rcheck && mkdir RSVSim.buildbin-libdir RSVSim.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RSVSim.buildbin-libdir RSVSim_1.13.0.tar.gz >RSVSim.Rcheck\00install.out 2>&1 && cp RSVSim.Rcheck\00install.out RSVSim-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RSVSim.buildbin-libdir --install="check:RSVSim-install.out" --force-multiarch --no-vignettes --timings RSVSim_1.13.0.tar.gz
StartedAt: 2016-09-20 15:53:39 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 15:58:00 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 260.3 seconds
RetCode: 0
Status:  OK  
CheckDir: RSVSim.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RSVSim.buildbin-libdir RSVSim.Rcheck && mkdir RSVSim.buildbin-libdir RSVSim.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RSVSim.buildbin-libdir RSVSim_1.13.0.tar.gz >RSVSim.Rcheck\00install.out 2>&1 && cp RSVSim.Rcheck\00install.out RSVSim-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RSVSim.buildbin-libdir --install="check:RSVSim-install.out" --force-multiarch --no-vignettes --timings RSVSim_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/RSVSim.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RSVSim/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RSVSim' version '1.13.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
simulateSV 6.04   0.02    6.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
simulateSV 6.61   0.04    6.64
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/RSVSim.Rcheck/00check.log'
for details.


RSVSim.Rcheck/00install.out:


install for i386

* installing *source* package 'RSVSim' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'RSVSim' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RSVSim' as RSVSim_1.13.0.zip
* DONE (RSVSim)

RSVSim.Rcheck/examples_i386/RSVSim-Ex.timings:

nameusersystemelapsed
compareSVs2.390.002.39
estimateSVSizes0.120.000.13
segmentalDuplications0.170.000.17
simulateSV6.040.026.05
weightsMechanisms000
weightsRepeats0.020.000.02

RSVSim.Rcheck/examples_x64/RSVSim-Ex.timings:

nameusersystemelapsed
compareSVs2.870.002.87
estimateSVSizes0.090.020.11
segmentalDuplications0.110.010.13
simulateSV6.610.046.64
weightsMechanisms000
weightsRepeats0.020.000.02