Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-13 15:04:57 -0400 (Wed, 13 Oct 2021).

CHECK results for cytomapper on nebbiolo1

To the developers/maintainers of the cytomapper package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cytomapper.git to
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raw results

Package 434/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cytomapper 1.4.1  (landing page)
Nils Eling
Snapshot Date: 2021-10-12 04:50:13 -0400 (Tue, 12 Oct 2021)
git_url: https://git.bioconductor.org/packages/cytomapper
git_branch: RELEASE_3_13
git_last_commit: edd9a70
git_last_commit_date: 2021-05-21 05:14:02 -0400 (Fri, 21 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cytomapper
Version: 1.4.1
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cytomapper.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cytomapper_1.4.1.tar.gz
StartedAt: 2021-10-12 09:36:45 -0400 (Tue, 12 Oct 2021)
EndedAt: 2021-10-12 09:51:03 -0400 (Tue, 12 Oct 2021)
EllapsedTime: 857.2 seconds
RetCode: 0
Status:   OK  
CheckDir: cytomapper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cytomapper.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cytomapper_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/cytomapper.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cytomapper/DESCRIPTION’ ... OK
* this is package ‘cytomapper’ version ‘1.4.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cytomapper’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plotting-param 4.952  0.064   5.016
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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


Installation output

cytomapper.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL cytomapper
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘cytomapper’ ...
** using staged installation
** R
** data
** 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 (cytomapper)

Tests output

cytomapper.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> library(testthat)
> library(cytomapper)
Loading required package: EBImage
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following objects are masked from 'package:EBImage':

    resize, tile

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

The following object is masked from 'package:EBImage':

    channel


Attaching package: 'cytomapper'

The following objects are masked from 'package:Biobase':

    channelNames, channelNames<-

> 
> test_check("cytomapper")
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can 
  be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can 
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This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can 
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This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can 
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can 
  be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can 
  be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can 
  be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can 
  be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can 
  be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can 
  be deactivated with `verify_fa = FALSE`
This Font Awesome icon ('') does not exist:
* if providing a custom `html_dependency` these `name` checks can 
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
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This Font Awesome icon ('') does not exist:
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══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (5)
• empty test (5)

[ FAIL 0 | WARN 0 | SKIP 10 | PASS 2914 ]
> 
> proc.time()
   user  system elapsed 
561.749  15.117 575.334 

Example timings

cytomapper.Rcheck/cytomapper-Ex.timings

nameusersystemelapsed
CytoImageList-manipulation1.8960.0351.933
CytoImageList-naming0.0500.0040.054
CytoImageList-subsetting1.9450.0251.970
CytoImageList0.1420.0200.162
cytomapperShiny0.0010.0000.001
loadImages1.0170.1441.081
measureObjects3.9180.1423.997
plotCells4.7500.1204.871
plotPixels1.9420.0521.994
plotting-param4.9520.0645.016