Multiple platform build/check report for BioC 3.14 - CHECK results for sojourner on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: sojourner

Version: 1.8.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sojourner.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sojourner_1.8.0.tar.gz

StartedAt: 2022-04-13 03:14:58 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 03:30:25 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 926.8 seconds

RetCode: 0

Status: OK

CheckDir: sojourner.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sojourner.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sojourner_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/sojourner.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.8.0'
* 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 ... 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 42.72   0.75   43.48
fitNormDistr-methods              28.88   0.19   29.07
plotTrackOverlay_Dcoef-methods    24.82   0.01   25.12
maskTracks-methods                10.39   0.26   10.83
Dcoef-methods                      9.85   0.12   10.05
plotIndividual_Tracks-methods      7.08   0.11    7.19
plotTrack-methods                  5.18   0.08    6.94
combineTrackll-methods             3.18   0.14   85.53
compare_RT_CDF-methods             3.12   0.08   94.06
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
plotLocalizations_Density-methods 43.62   0.66   44.31
fitNormDistr-methods              29.51   0.03   29.55
plotTrackOverlay_Dcoef-methods    25.49   0.04   25.52
Dcoef-methods                     10.30   0.02   10.31
maskTracks-methods                 9.67   0.13    9.80
plotIndividual_Tracks-methods      7.47   0.09    7.57
combineTrackll-methods             3.26   0.01   94.85
compare_RT_CDF-methods             3.04   0.03   92.06
* 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://155.52.207.166/BBS/3.14/bioc/src/contrib/sojourner_1.8.0.tar.gz && rm -rf sojourner.buildbin-libdir && mkdir sojourner.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sojourner.buildbin-libdir sojourner_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL sojourner_1.8.0.zip && rm sojourner_1.8.0.tar.gz sojourner_1.8.0.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
  7 12.8M    7  984k    0     0  1371k      0  0:00:09 --:--:--  0:00:09 1371k
 25 12.8M   25 3377k    0     0  1966k      0  0:00:06  0:00:01  0:00:05 1965k
 45 12.8M   45 5936k    0     0  2184k      0  0:00:06  0:00:02  0:00:04 2184k
 62 12.8M   62 8240k    0     0  2225k      0  0:00:05  0:00:03  0:00:02 2225k
 88 12.8M   88 11.3M    0     0  2467k      0  0:00:05  0:00:04  0:00:01 2466k
100 12.8M  100 12.8M    0     0  2595k      0  0:00:05  0:00:05 --:--:-- 2796k

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_1.8.0.zip
* DONE (sojourner)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'sojourner' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 -- Wed Apr 13 03:30:04 2022 
*********************************************** 
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 
   9.95    0.67   10.62


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 -- Wed Apr 13 03:30:16 2022 
*********************************************** 
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 
  10.71    0.45   11.15

name	user	system	elapsed
Dcoef-methods	9.85	0.12	10.05
combineTrackll-methods	3.18	0.14	85.53
compareFolder-methods	0.13	0.00	0.12
compare_RT_CDF-methods	3.12	0.08	94.06
createTrackll-methods	0.05	0.00	0.05
dispVariance-methods	1.14	0.00	1.14
displacementCDF-methods	1.75	0.05	1.80
dwellTime-methods	0.34	0.00	0.34
exportTrackll-methods	0.07	0.00	0.06
filterTrack-methods	0.06	0.00	0.07
fitNormDistr-methods	28.88	0.19	29.07
fitRT-methods	3.59	0.03	3.62
linkSkippedFrames-methods	0.08	0.00	0.08
maskTracks-methods	10.39	0.26	10.83
mergeTracks-methods	0.03	0.00	0.03
msd-methods	2.77	0.27	3.03
plotIndividual_Tracks-methods	7.08	0.11	7.19
plotLocalizations_Density-methods	42.72	0.75	43.48
plotTrack-methods	5.18	0.08	6.94
plotTrackOverlay_Dcoef-methods	24.82	0.01	25.12
sojournerGUI-methods	0	0	0
squareDisp-methods	0.12	0.00	0.13

name	user	system	elapsed
Dcoef-methods	10.30	0.02	10.31
combineTrackll-methods	3.26	0.01	94.85
compareFolder-methods	0.12	0.00	0.13
compare_RT_CDF-methods	3.04	0.03	92.06
createTrackll-methods	0.03	0.00	0.03
dispVariance-methods	1.03	0.00	1.03
displacementCDF-methods	1.89	0.02	1.91
dwellTime-methods	0.36	0.00	0.36
exportTrackll-methods	0.11	0.00	2.27
filterTrack-methods	0.13	0.00	0.12
fitNormDistr-methods	29.51	0.03	29.55
fitRT-methods	4.07	0.05	4.11
linkSkippedFrames-methods	0.09	0.00	0.09
maskTracks-methods	9.67	0.13	9.80
mergeTracks-methods	0.03	0.00	0.03
msd-methods	3.13	0.00	3.12
plotIndividual_Tracks-methods	7.47	0.09	7.57
plotLocalizations_Density-methods	43.62	0.66	44.31
plotTrack-methods	4.03	0.04	4.09
plotTrackOverlay_Dcoef-methods	25.49	0.04	25.52
sojournerGUI-methods	0	0	0
squareDisp-methods	0.12	0.00	0.12

CHECK results for sojourner on tokay2

Summary

Command output

Installation output

Tests output

Example timings