Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

CHECK report for RSVSim on tokay2

This page was generated on 2020-10-17 11:57:42 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RSVSim PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1544/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RSVSim 1.28.0
Christoph Bartenhagen
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/RSVSim
Branch: RELEASE_3_11
Last Commit: 355d478
Last Changed Date: 2020-04-27 14:32:32 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RSVSim
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RSVSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RSVSim_1.28.0.tar.gz
StartedAt: 2020-10-17 07:48:42 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:53:33 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 291.6 seconds
RetCode: 0
Status:  OK  
CheckDir: RSVSim.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RSVSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RSVSim_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/RSVSim.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.28.0'
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
simulateSV 7.34   0.44    7.78
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
simulateSV 7.84      0    7.86
* 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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/RSVSim.Rcheck/00check.log'
for details.



Installation output

RSVSim.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/RSVSim_1.28.0.tar.gz && rm -rf RSVSim.buildbin-libdir && mkdir RSVSim.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RSVSim.buildbin-libdir RSVSim_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL RSVSim_1.28.0.zip && rm RSVSim_1.28.0.tar.gz RSVSim_1.28.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  351k  100  351k    0     0  5231k      0 --:--:-- --:--:-- --:--:-- 5859k

install for i386

* installing *source* package 'RSVSim' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RSVSim'
    finding HTML links ... done
    compareSVs                              html  
    estimateSVSizes                         html  
    segmentalDuplications                   html  
    simulateSV                              html  
    weightsMechanisms                       html  
    weightsRepeats                          html  
** 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

install for x64

* installing *source* package 'RSVSim' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RSVSim' as RSVSim_1.28.0.zip
* DONE (RSVSim)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'RSVSim' successfully unpacked and MD5 sums checked

Tests output


Example timings

RSVSim.Rcheck/examples_i386/RSVSim-Ex.timings

nameusersystemelapsed
compareSVs4.250.064.31
estimateSVSizes0.920.040.97
segmentalDuplications0.130.000.13
simulateSV7.340.447.78
weightsMechanisms000
weightsRepeats000

RSVSim.Rcheck/examples_x64/RSVSim-Ex.timings

nameusersystemelapsed
compareSVs3.350.093.46
estimateSVSizes0.430.020.43
segmentalDuplications0.740.010.78
simulateSV7.840.007.86
weightsMechanisms000
weightsRepeats000