Multiple platform build/check report for BioC 3.12 - CHECK report for sojourner on tokay1

Package: sojourner

Version: 1.4.2

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sojourner.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings sojourner_1.4.2.tar.gz

StartedAt: 2021-05-06 07:08:04 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 07:26:45 -0400 (Thu, 06 May 2021)

EllapsedTime: 1121.1 seconds

RetCode: 0

Status: OK

CheckDir: sojourner.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sojourner.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings sojourner_1.4.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/sojourner.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.4.2'
* 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 ... 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 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 47.90   0.18   48.09
fitNormDistr-methods              42.64   0.09   43.36
plotTrackOverlay_Dcoef-methods    30.06   0.05   30.11
maskTracks-methods                15.30   0.27   15.67
plotIndividual_Tracks-methods     12.69   0.03   12.72
Dcoef-methods                      9.91   0.01    9.92
plotTrack-methods                  6.64   0.08    6.74
fitRT-methods                      5.67   0.27    5.93
combineTrackll-methods             3.95   0.07  107.21
compare_RT_CDF-methods             3.88   0.00  103.00
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
plotLocalizations_Density-methods 41.59   0.02   41.63
fitNormDistr-methods              31.55   0.00   31.55
plotTrackOverlay_Dcoef-methods    29.04   0.02   29.05
Dcoef-methods                     11.22   0.00   11.22
maskTracks-methods                10.22   0.25   10.47
plotIndividual_Tracks-methods      8.34   0.00    8.34
plotTrack-methods                  4.89   0.06    5.15
combineTrackll-methods             4.24   0.03  102.66
compare_RT_CDF-methods             4.06   0.06  107.52
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/sojourner_1.4.2.tar.gz && rm -rf sojourner.buildbin-libdir && mkdir sojourner.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sojourner.buildbin-libdir sojourner_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL sojourner_1.4.2.zip && rm sojourner_1.4.2.tar.gz sojourner_1.4.2.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 12.8M  100 12.8M    0     0  77.5M      0 --:--:-- --:--:-- --:--:-- 78.0M

install for i386

* installing *source* package 'sojourner' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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
** 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 'sojourner' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sojourner' as sojourner_1.4.2.zip
* DONE (sojourner)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'sojourner' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 -- Thu May 06 07:26:24 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 
> 
> proc.time()
   user  system elapsed 
  12.96    0.82   13.78


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 -- Thu May 06 07:26:35 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 
> 
> proc.time()
   user  system elapsed 
  10.64    0.32   10.96

name	user	system	elapsed
Dcoef-methods	9.91	0.01	9.92
combineTrackll-methods	3.95	0.07	107.21
compareFolder-methods	0.2	0.0	0.2
compare_RT_CDF-methods	3.88	0.00	103.00
createTrackll-methods	0.03	0.00	0.04
dispVariance-methods	1.15	0.00	1.15
displacementCDF-methods	2.71	0.10	2.81
dwellTime-methods	0.36	0.00	0.36
exportTrackll-methods	0.09	0.02	0.13
filterTrack-methods	0.11	0.00	0.11
fitNormDistr-methods	42.64	0.09	43.36
fitRT-methods	5.67	0.27	5.93
linkSkippedFrames-methods	0.17	0.00	0.18
maskTracks-methods	15.30	0.27	15.67
mergeTracks-methods	0.06	0.00	0.06
msd-methods	4.85	0.00	4.86
plotIndividual_Tracks-methods	12.69	0.03	12.72
plotLocalizations_Density-methods	47.90	0.18	48.09
plotTrack-methods	6.64	0.08	6.74
plotTrackOverlay_Dcoef-methods	30.06	0.05	30.11
sojournerGUI-methods	0	0	0
squareDisp-methods	0.16	0.00	0.14

name	user	system	elapsed
Dcoef-methods	11.22	0.00	11.22
combineTrackll-methods	4.24	0.03	102.66
compareFolder-methods	0.11	0.01	0.12
compare_RT_CDF-methods	4.06	0.06	107.52
createTrackll-methods	0.07	0.00	0.06
dispVariance-methods	1.11	0.02	1.13
displacementCDF-methods	2.73	0.03	2.76
dwellTime-methods	0.56	0.00	0.56
exportTrackll-methods	0.14	0.02	0.16
filterTrack-methods	0.14	0.00	0.14
fitNormDistr-methods	31.55	0.00	31.55
fitRT-methods	3.58	0.01	3.59
linkSkippedFrames-methods	0.08	0.00	0.08
maskTracks-methods	10.22	0.25	10.47
mergeTracks-methods	0.03	0.00	0.03
msd-methods	3.11	0.00	3.11
plotIndividual_Tracks-methods	8.34	0.00	8.34
plotLocalizations_Density-methods	41.59	0.02	41.63
plotTrack-methods	4.89	0.06	5.15
plotTrackOverlay_Dcoef-methods	29.04	0.02	29.05
sojournerGUI-methods	0	0	0
squareDisp-methods	0.10	0.00	0.11

CHECK report for sojourner on tokay1

Summary

Command output

Installation output

Tests output

Example timings