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This page was generated on 2022-07-01 12:08:07 -0400 (Fri, 01 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for imageHTS on merida1


To the developers/maintainers of the imageHTS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/imageHTS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 946/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
imageHTS 1.46.0  (landing page)
Joseph Barry
Snapshot Date: 2022-06-30 13:55:04 -0400 (Thu, 30 Jun 2022)
git_url: https://git.bioconductor.org/packages/imageHTS
git_branch: RELEASE_3_15
git_last_commit: 9c5ea7c
git_last_commit_date: 2022-04-26 11:05:32 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: imageHTS
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:imageHTS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings imageHTS_1.46.0.tar.gz
StartedAt: 2022-07-01 03:31:14 -0400 (Fri, 01 Jul 2022)
EndedAt: 2022-07-01 03:37:03 -0400 (Fri, 01 Jul 2022)
EllapsedTime: 349.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: imageHTS.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:imageHTS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings imageHTS_1.46.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/imageHTS.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘imageHTS/DESCRIPTION’ ... OK
* this is package ‘imageHTS’ version ‘1.46.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘imageHTS’ 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘imageHTS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: segmentYeastBF
> ### Title: Segmentation of yeast cells and ring-shaped objects.
> ### Aliases: segmentYeastBF segmentRing
> 
> ### ** Examples
> 
> filename = system.file('yeast.jpeg', package='imageHTS')
> a = readImage(filename)
> if (interactive()) display(a)
> p = list(edge.threshold=0.05, max.membrane.thickness=5, crown.thickness=8,
+     crown.steps=c(31, 61, 4), locmin.threshold.width=9, locmin.threshold.offset=0.15, 
+     locmin.erode.size=3, cell.max.overlap=2, nucleus.radius.offset=10,
+     cell.radius.offset=4)
> seg = segmentRing(a, p)
Error in if (nrow(cs) > 0) { : argument is of length zero
Calls: segmentRing -> extractCells
Execution halted
* 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
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/imageHTS.Rcheck/00check.log’
for details.


Installation output

imageHTS.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL imageHTS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘imageHTS’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (imageHTS)

Tests output


Example timings

imageHTS.Rcheck/imageHTS-Ex.timings

nameusersystemelapsed
collectCellFeatures000
countObjects10.011 0.53710.562
extractFeatures19.462 0.73820.222
fileHTS3.5910.0273.620
getImageConf1.8420.0061.852
getUnames4.6090.0144.630
getWellFeatures5.4130.0155.435
highlightSegmentation000
installCellPicker2.7240.0272.756
makeCellHTS0.0000.0010.000
parseDCF0.0020.0000.003
parseImageConf1.7670.0041.774
popCellPicker1.7850.0061.794
prw2uname0.0040.0000.004
readLearnTS000
segmentATH000
segmentWells6.7510.2326.999