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This page was generated on 2023-06-06 11:00:42 -0000 (Tue, 06 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4366
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CHECK results for SpatialOmicsOverlay on kunpeng2


To the developers/maintainers of the SpatialOmicsOverlay package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialOmicsOverlay.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1949/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpatialOmicsOverlay 1.1.0  (landing page)
Maddy Griswold
Snapshot Date: 2023-06-05 06:35:06 -0000 (Mon, 05 Jun 2023)
git_url: https://git.bioconductor.org/packages/SpatialOmicsOverlay
git_branch: devel
git_last_commit: 4a868db
git_last_commit_date: 2023-04-25 15:44:04 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

Summary

Package: SpatialOmicsOverlay
Version: 1.1.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:SpatialOmicsOverlay.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings SpatialOmicsOverlay_1.1.0.tar.gz
StartedAt: 2023-06-06 07:28:58 -0000 (Tue, 06 Jun 2023)
EndedAt: 2023-06-06 07:53:31 -0000 (Tue, 06 Jun 2023)
EllapsedTime: 1473.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SpatialOmicsOverlay.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:SpatialOmicsOverlay.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings SpatialOmicsOverlay_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SpatialOmicsOverlay.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK
* this is package ‘SpatialOmicsOverlay’ version ‘1.1.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SpatialOmicsOverlay’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 loading without being on the library search path ... 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 ... NOTE
plotSpatialOverlay: no visible binding for global variable ‘xcoor’
plotSpatialOverlay: no visible binding for global variable ‘ycoor’
plotSpatialOverlay: no visible binding for global variable ‘sampleID’
plotSpatialOverlay: no visible binding for global variable ‘Target’
scaleBarPrinting: no visible binding for global variable ‘X’
scaleBarPrinting: no visible binding for global variable ‘Y’
Undefined global functions or variables:
  Target X Y sampleID xcoor ycoor
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
add4ChannelImage        27.378  1.495  23.925
readSpatialOverlay      23.561  0.781  23.605
cropSamples             21.830  1.216  21.537
changeColoringIntensity 21.814  1.012  20.801
addImageOmeTiff         21.555  1.186  21.092
changeImageColoring     20.564  0.722  19.537
recolor                 20.644  0.635  20.449
cropTissue              20.126  0.747  20.031
flipY                   19.893  0.700  19.537
flipX                   19.930  0.583  19.767
createMask               9.911  0.118  10.051
parseOverlayAttrs        6.345  0.238   5.891
xmlExtraction            5.731  0.309   5.735
parseScanMetadata        5.797  0.206   5.573
checkValidRes            5.055  0.244   4.704
createCoordFile          5.110  0.144   5.265
* 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 ...
  ‘SpatialOmicsOverlay.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/SpatialOmicsOverlay.Rcheck/00check.log’
for details.



Installation output

SpatialOmicsOverlay.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL SpatialOmicsOverlay
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘SpatialOmicsOverlay’ ...
** 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 (SpatialOmicsOverlay)

Tests output

SpatialOmicsOverlay.Rcheck/tests/testthat.Rout


R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(vdiffr)
> 
> options( java.parameters = "-Xmx4g" )
> library( "RBioFormats" )
BioFormats library version 6.12.0
> 
> library(SpatialOmicsOverlay)
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0 
> 
> # #run tests
> test_check("SpatialOmicsOverlay")
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, aperm, 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

Welcome to Bioconductor

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

Loading required package: NanoStringNCTools
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: ggplot2
Extracting XML
Parsing XML - scan metadata
Parsing XML - overlay data
Generating Coordinates
Extracting XML
Parsing XML - scan metadata
Parsing XML - overlay data
Generating Coordinates
Calculating and scaling coordinates
Calculating and scaling coordinates
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 422 ]
Deleting unused snapshots:
• all/4-channel-no-scalebar.svg
• all/add-ometiff-res-8.svg
• all/cropsamples-all-rois.svg
• all/cropsamples-sampsonly.svg
• all/croptissue.svg
• all/flipx.svg
• all/flipy.svg
• all/fluorlegend-2-row.svg
• all/image-scalebar.svg
• all/imagecoloring.svg
• all/lowres-fluorlegend.svg
• all/no-image-scalebar.svg
• all/recolor.svg
• all/scale-bar-check-1.svg
• all/scale-bar-check-2.svg
• all/scale-bar-check-3.svg
> 
> 
> 
> proc.time()
   user  system elapsed 
270.450   7.186 267.465 

Example timings

SpatialOmicsOverlay.Rcheck/SpatialOmicsOverlay-Ex.timings

nameusersystemelapsed
add4ChannelImage27.378 1.49523.925
addImageOmeTiff21.555 1.18621.092
addPlottingFactor0.4850.0120.501
bookendStr0.0010.0000.001
changeColoringIntensity21.814 1.01220.801
changeImageColoring20.564 0.72219.537
checkValidRes5.0550.2444.704
createCoordFile5.1100.1445.265
createMask 9.911 0.11810.051
cropSamples21.830 1.21621.537
cropTissue20.126 0.74720.031
downloadMouseBrainImage0.1910.0040.194
flipX19.930 0.58319.767
flipY19.893 0.70019.537
fluorLegend2.4140.0162.433
moveCoords0.1680.0040.172
parseOverlayAttrs6.3450.2385.891
parseScanMetadata5.7970.2065.573
plotSpatialOverlay2.5000.0712.575
readLabWorksheet0.0050.0000.005
readSpatialOverlay23.561 0.78123.605
recolor20.644 0.63520.449
removeSample0.2440.0040.249
xmlExtraction5.7310.3095.735