Sojourner Developer
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/sojourner |
| Branch: RELEASE_3_11 |
| Last Commit: f0a6b71 |
| Last Changed Date: 2020-05-29 20:21:02 -0400 (Fri, 29 May 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:50 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE sojourner PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1697/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sojourner 1.2.1 Sojourner Developer
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: sojourner |
| Version: 1.2.1 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sojourner.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings sojourner_1.2.1.tar.gz |
| StartedAt: 2020-10-17 08:28:31 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 08:42:18 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 826.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: sojourner.Rcheck |
| Warnings: NA |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sojourner.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings sojourner_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/sojourner.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 'sojourner/DESCRIPTION' ... OK
* this is package 'sojourner' version '1.2.1'
* 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' ... ERROR
Running examples in 'sojourner-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: maskTracks
> ### Title: maskTracks
> ### Aliases: maskTracks maskPoint filterOnCell sampleTracks
>
> ### ** Examples
>
> #Basic masking with folder path with image masks
> folder = system.file('extdata','ImageJ',package='sojourner')
> trackll = createTrackll(folder=folder, input=3)
Reading ParticleTracker file: epl11AA_HTZ1Halo_No_RAP_fr10ms_120mW_1.tif.csv ...
0mW_1 read and processed.
Reading ParticleTracker file: epl11AA_HTZ1Halo_No_RAP_fr10ms_120mW_2.tif.csv ...
0mW_2 read and processed.
Process complete.
> trackll.masked <- maskTracks(folder = folder, trackll = trackll)
Reading mask file epl11AA_HTZ1Halo_No_RAP_fr10ms_120mW_1_MASK.tif
Reading mask file epl11AA_HTZ1Halo_No_RAP_fr10ms_120mW_2_MASK.tif
All files masked.
>
> #Compare the masking effect
> plotTrackOverlay(trackll)
Processing epl11AA_HTZ1Halo_No_RAP_fr10ms_120mW_1.tif.csv
Processing epl11AA_HTZ1Halo_No_RAP_fr10ms_120mW_2.tif.csv
Output combined plot...
Done!> plotTrackOverlay(trackll.masked)
Processing epl11AA_HTZ1Halo_No_RAP_fr10ms_120mW_1.tif.csv
Processing epl11AA_HTZ1Halo_No_RAP_fr10ms_120mW_2.tif.csv
Output combined plot...
Done!>
> #Plot mask
> mask.list=list.files(path=folder,pattern='_MASK.tif',full.names=TRUE)
> plotMask(folder)
Reading mask file epl11AA_HTZ1Halo_No_RAP_fr10ms_120mW_1_MASK.tif
Reading mask file epl11AA_HTZ1Halo_No_RAP_fr10ms_120mW_2_MASK.tif
Done!>
> #If Nuclear image is available
> plotNucTrackOverlay(folder=folder,trackll=trackll)
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotLocalizations_Density-methods 40.25 0.03 40.28
fitNormDistr-methods 34.08 0.04 34.13
plotTrackOverlay_Dcoef-methods 30.25 0.00 30.26
maskTracks-methods 14.50 0.21 16.29
Dcoef-methods 10.33 0.11 10.44
plotIndividual_Tracks-methods 10.17 0.02 10.22
plotTrack-methods 8.39 0.01 9.02
compare_RT_CDF-methods 4.60 0.08 106.95
combineTrackll-methods 4.28 0.03 94.57
* 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 ERROR
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/sojourner.Rcheck/00check.log'
for details.
sojourner.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/sojourner_1.2.1.tar.gz && rm -rf sojourner.buildbin-libdir && mkdir sojourner.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sojourner.buildbin-libdir sojourner_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL sojourner_1.2.1.zip && rm sojourner_1.2.1.tar.gz sojourner_1.2.1.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 34.5M 0 --:--:-- --:--:-- --:--:-- 35.1M
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_1.2.1.zip
* DONE (sojourner)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'sojourner' successfully unpacked and MD5 sums checked
|
sojourner.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("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 -- Sat Oct 17 08:41:48 2020
***********************************************
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
8.46 0.64 9.09
|
sojourner.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("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 -- Sat Oct 17 08:41:57 2020
***********************************************
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
8.35 0.29 8.64
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sojourner.Rcheck/examples_i386/sojourner-Ex.timings
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sojourner.Rcheck/examples_x64/sojourner-Ex.timings
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