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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 2037/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpatialOmicsOverlay 1.4.0  (landing page)
Maddy Griswold
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/SpatialOmicsOverlay
git_branch: RELEASE_3_19
git_last_commit: b94e6f9
git_last_commit_date: 2024-04-30 11:48:37 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SpatialOmicsOverlay on nebbiolo1

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.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SpatialOmicsOverlay
Version: 1.4.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SpatialOmicsOverlay.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SpatialOmicsOverlay_1.4.0.tar.gz
StartedAt: 2024-06-13 03:52:44 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 04:08:50 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 965.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SpatialOmicsOverlay.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SpatialOmicsOverlay.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SpatialOmicsOverlay_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialOmicsOverlay.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK
* this is package ‘SpatialOmicsOverlay’ version ‘1.4.0’
* 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 code 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
recolor                 25.377  1.256  14.063
flipX                   24.155  0.821  13.013
add4ChannelImage        22.295  2.002  17.154
changeColoringIntensity 22.420  1.067  13.887
addImageOmeTiff         22.060  1.297  13.999
flipY                   22.341  0.819  13.731
readSpatialOverlay      21.459  0.698  15.283
cropSamples             19.497  1.007  14.817
changeImageColoring     16.461  0.870  13.474
cropTissue              16.067  0.804  13.034
parseOverlayAttrs        8.559  0.517   4.313
parseScanMetadata        8.623  0.432   3.995
xmlExtraction            7.759  0.433   4.021
createMask               7.585  0.366   7.946
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialOmicsOverlay.Rcheck/00check.log’
for details.


Installation output

SpatialOmicsOverlay.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SpatialOmicsOverlay
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 7.3.0
> 
> library(SpatialOmicsOverlay)
> 
> # #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, 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 3 | SKIP 0 | PASS 422 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 422 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
183.059   9.187 159.080 

Example timings

SpatialOmicsOverlay.Rcheck/SpatialOmicsOverlay-Ex.timings

nameusersystemelapsed
add4ChannelImage22.295 2.00217.154
addImageOmeTiff22.060 1.29713.999
addPlottingFactor0.4320.0050.436
bookendStr0.0000.0020.001
changeColoringIntensity22.420 1.06713.887
changeImageColoring16.461 0.87013.474
checkValidRes3.4960.1513.123
createCoordFile3.2810.0053.283
createMask7.5850.3667.946
cropSamples19.497 1.00714.817
cropTissue16.067 0.80413.034
downloadMouseBrainImage0.1460.0080.153
flipX24.155 0.82113.013
flipY22.341 0.81913.731
fluorLegend1.4760.0321.508
moveCoords0.1600.0040.164
parseOverlayAttrs8.5590.5174.313
parseScanMetadata8.6230.4323.995
plotSpatialOverlay1.7920.1041.895
readLabWorksheet0.0030.0000.003
readSpatialOverlay21.459 0.69815.283
recolor25.377 1.25614.063
removeSample0.2160.0040.220
xmlExtraction7.7590.4334.021