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CHECK report for sarks on tokay2

This page was generated on 2020-10-17 11:57:44 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE sarks PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1575/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sarks 1.0.0
Dennis Wylie
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/sarks
Branch: RELEASE_3_11
Last Commit: 8e91544
Last Changed Date: 2020-04-27 15:34:35 -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 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sarks
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sarks.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings sarks_1.0.0.tar.gz
StartedAt: 2020-10-17 07:56:40 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:59:01 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 141.3 seconds
RetCode: 0
Status:  OK  
CheckDir: sarks.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sarks.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings sarks_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/sarks.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 'sarks/DESCRIPTION' ... OK
* this is package 'sarks' version '1.0.0'
* 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 whether package 'sarks' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* 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: OK


Installation output

sarks.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/sarks_1.0.0.tar.gz && rm -rf sarks.buildbin-libdir && mkdir sarks.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sarks.buildbin-libdir sarks_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL sarks_1.0.0.zip && rm sarks_1.0.0.tar.gz sarks_1.0.0.zip
###
##############################################################################
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  % 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 2045k  100 2045k    0     0  11.7M      0 --:--:-- --:--:-- --:--:-- 12.2M

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'sarks' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sarks'
    finding HTML links ... done
    Sarks                                   html  
    blockInfo                               html  
    blockScores                             html  
    clusterCounts                           html  
    clusterKmers                            html  
    estimateFalsePositiveRate               html  
    extendKmers                             html  
    kmerCounts                              html  
    kmerPeaks                               html  
    locateClusters                          html  
    locateKmers                             html  
    mergedKmerSubPeaks                      html  
    permutationDistribution                 html  
    permutationThresholds                   html  
    pruneIntervals                          html  
    regexCounts                             html  
    regexLocate                             html  
    sarksFilters                            html  
    simulatedScores                         html  
    simulatedSeqs                           html  
    sourceBlock                             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

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'sarks' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sarks' as sarks_1.0.0.zip
* DONE (sarks)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'sarks' successfully unpacked and MD5 sums checked

Tests output

sarks.Rcheck/tests_i386/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage('sarks')


RUNIT TEST PROTOCOL -- Sat Oct 17 07:58:46 2020 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sarks RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   6.59    0.23    6.71 

sarks.Rcheck/tests_x64/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage('sarks')


RUNIT TEST PROTOCOL -- Sat Oct 17 07:58:52 2020 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sarks RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   6.71    0.26    6.32 

Example timings

sarks.Rcheck/examples_i386/sarks-Ex.timings

nameusersystemelapsed
Sarks0.110.000.30
blockInfo0.230.050.25
blockScores0.000.030.03
clusterCounts0.000.020.01
clusterKmers2.780.012.80
estimateFalsePositiveRate0.140.000.13
extendKmers0.170.020.17
kmerCounts0.020.000.01
kmerPeaks0.100.020.13
locateClusters0.020.000.01
locateKmers0.020.000.02
mergedKmerSubPeaks0.110.030.14
permutationDistribution0.070.010.09
permutationThresholds0.10.00.1
pruneIntervals0.060.020.08
regexCounts0.000.010.01
regexLocate000
sarksFilters0.060.020.08
sourceBlock0.020.000.02

sarks.Rcheck/examples_x64/sarks-Ex.timings

nameusersystemelapsed
Sarks0.170.020.09
blockInfo0.610.000.27
blockScores0.050.000.03
clusterCounts000
clusterKmers3.310.013.22
estimateFalsePositiveRate0.200.050.16
extendKmers0.420.030.19
kmerCounts0.020.000.01
kmerPeaks0.170.000.13
locateClusters000
locateKmers0.030.010.01
mergedKmerSubPeaks0.280.000.17
permutationDistribution0.190.000.10
permutationThresholds0.310.000.09
pruneIntervals0.270.000.13
regexCounts000
regexLocate0.000.020.01
sarksFilters0.080.000.08
sourceBlock0.000.020.02