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This page was generated on 2024-05-20 11:37:55 -0400 (Mon, 20 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4666
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4401
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4428
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 2019/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Statial 1.7.0  (landing page)
Farhan Ameen
Snapshot Date: 2024-05-17 14:05:07 -0400 (Fri, 17 May 2024)
git_url: https://git.bioconductor.org/packages/Statial
git_branch: devel
git_last_commit: a8188d2
git_last_commit_date: 2024-04-30 11:46:00 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for Statial on merida1


To the developers/maintainers of the Statial package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Statial.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: Statial
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Statial.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Statial_1.7.0.tar.gz
StartedAt: 2024-05-18 11:35:16 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 11:53:18 -0400 (Sat, 18 May 2024)
EllapsedTime: 1082.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Statial.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Statial.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Statial_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Statial.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Statial/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Statial’ version ‘1.7.0’
* 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 ‘Statial’ 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 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘data.table’ ‘spatstat.explore’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.generateBPParam’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Kontextual: no visible binding for global variable ‘test’
Kontextual: no visible binding for global variable ‘parent_name’
calcContamination: no visible global function definition for ‘predict’
calcContamination: no visible binding for global variable ‘.’
calcContamination: no visible binding for global variable ‘cellID’
calcKontextual: no visible binding for global variable ‘d’
calcKontextual: no visible binding for global variable ‘i’
calcKontextual: no visible binding for global variable ‘cellTypeI’
calcKontextual: no visible binding for global variable ‘cellTypeJ’
calcKontextual: no visible binding for global variable ‘Kontext’
calcStateChanges: no visible binding for global variable ‘cellID’
calcStateChanges: no visible binding for global variable
  ‘rfMaxCellProb’
calcStateChanges: no visible binding for global variable
  ‘rfSecondLargestCellProb’
calcStateChanges: no visible binding for global variable
  ‘rfMainCellProb’
calcStateChanges: no visible binding for global variable
  ‘primaryCellType’
calcStateChanges: no visible binding for global variable
  ‘otherCellType’
calcStateChanges: no visible binding for global variable ‘coef’
calcStateChanges: no visible binding for global variable ‘tval’
calcStateChanges: no visible binding for global variable ‘pval’
calcStateChanges: no visible binding for global variable ‘fdr’
calculateChangesMarker : <anonymous>: no visible global function
  definition for ‘pt’
distanceCalculator: no visible binding for global variable ‘cellType’
distanceCalculator: no visible binding for global variable ‘d’
getMarkerMeans: no visible binding for global variable ‘value’
kontextCurve: no visible binding for global variable ‘type’
kontextCurve: no visible binding for global variable ‘r’
kontextCurve: no visible binding for global variable ‘original’
kontextCurve: no visible binding for global variable ‘kontextual’
kontextPlot: no visible binding for global variable ‘r’
kontextPlot: no visible binding for global variable ‘kontextualSd’
kontextPlot: no visible binding for global variable ‘originalSd’
kontextPlot: no visible binding for global variable ‘value’
kontextPlot: no visible binding for global variable ‘name’
kontextPlot: no visible binding for global variable ‘lower’
kontextPlot: no visible binding for global variable ‘upper’
parentCombinations: no visible binding for global variable ‘from’
parentCombinations: no visible binding for global variable ‘to’
plotStateChanges: no visible global function definition for ‘lm’
plotStateChanges: no visible global function definition for ‘formula’
plotStateChanges: no visible global function definition for ‘predict’
plotStateChanges: no visible binding for global variable ‘x’
plotStateChanges: no visible binding for global variable ‘y’
plotStateChanges: no visible binding for global variable ‘density’
plotStateChanges: no visible binding for global variable ‘lm’
prepMatrix: no visible binding for global variable ‘imageID’
prepMatrix: no visible binding for global variable ‘kontextual’
prepMatrix: no visible binding for global variable ‘primaryCellType’
prepMatrix: no visible binding for global variable ‘otherCellType’
prepMatrix: no visible binding for global variable ‘marker’
prepMatrix: no visible binding for global variable ‘type’
relabel: no visible binding for global variable ‘cellType’
Undefined global functions or variables:
  . Kontext cellID cellType cellTypeI cellTypeJ coef d density fdr
  formula from i imageID kontextual kontextualSd lm lower marker name
  original originalSd otherCellType parent_name predict primaryCellType
  pt pval r rfMainCellProb rfMaxCellProb rfSecondLargestCellProb test
  to tval type upper value x y
Consider adding
  importFrom("stats", "coef", "density", "formula", "lm", "predict",
             "pt")
to your NAMESPACE file.
* 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
kontextCurve      303.021 30.879 303.659
kontextPlot       242.130 14.558  10.223
calcContamination 171.072  2.234  41.736
plotStateChanges  152.680 19.699 189.070
relabelKontextual  59.659  9.894  33.692
getMarkerMeans     18.845  0.528  20.880
getAbundances       9.543  0.714  11.379
getDistances        8.931  0.461  10.198
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/Statial.Rcheck/00check.log’
for details.


Installation output

Statial.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘Statial’ ...
** using staged installation
** R
** data
** 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 (Statial)

Tests output

Statial.Rcheck/tests/testthat.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(Statial)
> 
> test_check("Statial")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 20.389   1.235  23.733 

Example timings

Statial.Rcheck/Statial-Ex.timings

nameusersystemelapsed
Kontextual4.0880.1444.699
calcContamination171.072 2.234 41.736
calcStateChanges3.5870.2004.311
getAbundances 9.543 0.71411.379
getDistances 8.931 0.46110.198
getMarkerMeans18.845 0.52820.880
isKontextual0.0000.0000.001
kontextCurve303.021 30.879303.659
kontextPlot242.130 14.558 10.223
makeWindow0.0050.0020.007
parentCombinations0.0250.0060.034
plotStateChanges152.680 19.699189.070
prepMatrix2.9540.0753.299
relabelKontextual59.659 9.89433.692