Multiple platform build/check report for BioC 3.13 - CHECK results for sojourner on tokay2

Package: sojourner

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sojourner.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings sojourner_1.6.0.tar.gz

StartedAt: 2021-10-15 05:57:40 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 06:12:36 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 895.8 seconds

RetCode: 0

Status: WARNINGS

CheckDir: sojourner.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sojourner.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings sojourner_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/sojourner.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sojourner/DESCRIPTION' ... OK
* this is package 'sojourner' version '1.6.0'
* 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 'sojourner' can be installed ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for 'area'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/sojourner.Rcheck/00install.out' for details.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
plotLocalizations_Density-methods 32.17   0.31   32.49
fitNormDistr-methods              29.72   0.08   29.79
plotTrackOverlay_Dcoef-methods    22.64   0.01   22.65
maskTracks-methods                11.21   0.31   11.56
plotIndividual_Tracks-methods      8.15   0.11    8.26
Dcoef-methods                      7.94   0.14    8.08
compare_RT_CDF-methods             3.30   0.03   87.08
combineTrackll-methods             3.00   0.06   90.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
plotLocalizations_Density-methods 32.28   0.05   32.33
fitNormDistr-methods              25.74   0.05   25.79
plotTrackOverlay_Dcoef-methods    22.08   0.02   22.09
maskTracks-methods                 9.76   0.14    9.91
Dcoef-methods                      9.15   0.08    9.24
plotIndividual_Tracks-methods      6.50   0.03    6.53
compare_RT_CDF-methods             3.39   0.03   98.82
combineTrackll-methods             3.19   0.04   95.11
* 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/sojourner.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/sojourner_1.6.0.tar.gz && rm -rf sojourner.buildbin-libdir && mkdir sojourner.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sojourner.buildbin-libdir sojourner_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL sojourner_1.6.0.zip && rm sojourner_1.6.0.tar.gz sojourner_1.6.0.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
  0 12.8M    0 44574    0     0   281k      0  0:00:46 --:--:--  0:00:46  282k
 21 12.8M   21 2814k    0     0  2478k      0  0:00:05  0:00:01  0:00:04 2477k
 49 12.8M   49 6573k    0     0  3084k      0  0:00:04  0:00:02  0:00:02 3084k
 87 12.8M   87 11.2M    0     0  3676k      0  0:00:03  0:00:03 --:--:-- 3676k
 95 12.8M   95 12.2M    0     0  3043k      0  0:00:04  0:00:04 --:--:-- 3043k
 95 12.8M   95 12.3M    0     0  2454k      0  0:00:05  0:00:05 --:--:-- 2521k
 96 12.8M   96 12.4M    0     0  2074k      0  0:00:06  0:00:06 --:--:-- 1982k
100 12.8M  100 12.8M    0     0  2131k      0  0:00:06  0:00:06 --:--:-- 1631k

install for i386

* installing *source* package 'sojourner' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: multiple methods tables found for 'area'
** help
*** installing help indices
  converting help for package 'sojourner'
    finding HTML links ... done
    Dcoef-methods                           html  
    combineTrackll-methods                  html  
    compareFolder-methods                   html  
    compare_RT_CDF-methods                  html  
    createTrackll-methods                   html  
    dispVariance-methods                    html  
    displacementCDF-methods                 html  
    dwellTime-methods                       html  
    exportTrackll-methods                   html  
    filterTrack-methods                     html  
    fitNormDistr-methods                    html  
    fitRT-methods                           html  
    linkSkippedFrames-methods               html  
    maskTracks-methods                      html  
    mergeTracks-methods                     html  
    msd-methods                             html  
    plotIndividual_Tracks-methods           html  
    plotLocalizations_Density-methods       html  
    plotTrack-methods                       html  
    plotTrackOverlay_Dcoef-methods          html  
    sojourner                               html  
    sojournerGUI-methods                    html  
    squareDisp-methods                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: multiple methods tables found for 'area'
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for 'area'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'sojourner' ...
** testing if installed package can be loaded
Warning: multiple methods tables found for 'area'
* MD5 sums
packaged installation of 'sojourner' as sojourner_1.6.0.zip
* DONE (sojourner)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'sojourner' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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("sojourner")

Reading ParticleTracker file:  SWR1_WT_140mW_image6.csv ...

 mage6 read and processed.

Process complete.

Reading ParticleTracker file:  SWR1_WT_140mW_image6.csv ...

 mage6 read and processed.

Process complete.
applying filter, min 5   max Inf 

Reading ParticleTracker file:  SWR1_WT_140mW_image6.csv ...

 mage6 read and processed.

Process complete.
applying filter, min 5   max Inf 
applying filter, min 7   max Inf 

 45 	tracks length > & =	 1
 45 	tracks length > & =	 2
 45 	tracks length > & =	 3
 45 	tracks length > & =	 4
 45 	tracks length > & =	 5
 45 	tracks length > & =	 6

...

Reading ParticleTracker file:  SWR1_WT_140mW_image6.csv ...

 mage6 read and processed.

Process complete.
applying trimmer, min 1   max 20 


RUNIT TEST PROTOCOL -- Fri Oct 15 06:12:04 2021 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sojourner RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
Warning message:
multiple methods tables found for 'area' 
> 
> proc.time()
   user  system elapsed 
   8.37    0.56    8.92


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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("sojourner")

Reading ParticleTracker file:  SWR1_WT_140mW_image6.csv ...

 mage6 read and processed.

Process complete.

Reading ParticleTracker file:  SWR1_WT_140mW_image6.csv ...

 mage6 read and processed.

Process complete.
applying filter, min 5   max Inf 

Reading ParticleTracker file:  SWR1_WT_140mW_image6.csv ...

 mage6 read and processed.

Process complete.
applying filter, min 5   max Inf 
applying filter, min 7   max Inf 

 45 	tracks length > & =	 1
 45 	tracks length > & =	 2
 45 	tracks length > & =	 3
 45 	tracks length > & =	 4
 45 	tracks length > & =	 5
 45 	tracks length > & =	 6

...

Reading ParticleTracker file:  SWR1_WT_140mW_image6.csv ...

 mage6 read and processed.

Process complete.
applying trimmer, min 1   max 20 


RUNIT TEST PROTOCOL -- Fri Oct 15 06:12:16 2021 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sojourner RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
Warning message:
multiple methods tables found for 'area' 
> 
> proc.time()
   user  system elapsed 
  11.81    0.48   12.28

name	user	system	elapsed
Dcoef-methods	7.94	0.14	8.08
combineTrackll-methods	3.00	0.06	90.37
compareFolder-methods	0.11	0.00	0.11
compare_RT_CDF-methods	3.30	0.03	87.08
createTrackll-methods	0.06	0.00	0.06
dispVariance-methods	1.13	0.00	1.12
displacementCDF-methods	1.79	0.02	1.82
dwellTime-methods	0.35	0.00	0.34
exportTrackll-methods	0.06	0.01	0.08
filterTrack-methods	0.08	0.00	0.08
fitNormDistr-methods	29.72	0.08	29.79
fitRT-methods	3.93	0.02	3.96
linkSkippedFrames-methods	0.11	0.00	0.11
maskTracks-methods	11.21	0.31	11.56
mergeTracks-methods	0.03	0.00	0.03
msd-methods	2.72	0.30	3.02
plotIndividual_Tracks-methods	8.15	0.11	8.26
plotLocalizations_Density-methods	32.17	0.31	32.49
plotTrack-methods	4.13	0.05	4.17
plotTrackOverlay_Dcoef-methods	22.64	0.01	22.65
sojournerGUI-methods	0	0	0
squareDisp-methods	0.14	0.00	0.14

name	user	system	elapsed
Dcoef-methods	9.15	0.08	9.24
combineTrackll-methods	3.19	0.04	95.11
compareFolder-methods	0.11	0.00	0.11
compare_RT_CDF-methods	3.39	0.03	98.82
createTrackll-methods	0.03	0.00	0.03
dispVariance-methods	0.98	0.02	1.00
displacementCDF-methods	1.78	0.06	1.84
dwellTime-methods	0.35	0.00	0.34
exportTrackll-methods	0.06	0.00	0.07
filterTrack-methods	0.06	0.02	0.07
fitNormDistr-methods	25.74	0.05	25.79
fitRT-methods	3.68	0.01	3.70
linkSkippedFrames-methods	0.10	0.00	0.09
maskTracks-methods	9.76	0.14	9.91
mergeTracks-methods	0.03	0.00	0.03
msd-methods	2.94	0.00	2.94
plotIndividual_Tracks-methods	6.50	0.03	6.53
plotLocalizations_Density-methods	32.28	0.05	32.33
plotTrack-methods	3.77	0.06	3.86
plotTrackOverlay_Dcoef-methods	22.08	0.02	22.09
sojournerGUI-methods	0	0	0
squareDisp-methods	0.12	0.00	0.13

CHECK results for sojourner on tokay2

Summary

Command output

Installation output

Tests output

Example timings