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This page was generated on 2023-10-20 09:38:13 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 2027/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stJoincount 1.2.0  (landing page)
Jiarong Song
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/stJoincount
git_branch: RELEASE_3_17
git_last_commit: 61cc1fd
git_last_commit_date: 2023-04-25 11:41:07 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for stJoincount on kjohnson2


To the developers/maintainers of the stJoincount package:
- 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: stJoincount
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:stJoincount.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings stJoincount_1.2.0.tar.gz
StartedAt: 2023-10-19 05:00:34 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 05:15:00 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 866.2 seconds
RetCode: 0
Status:   OK  
CheckDir: stJoincount.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:stJoincount.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings stJoincount_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/stJoincount.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘stJoincount/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘stJoincount’ version ‘1.2.0’
* 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 ‘stJoincount’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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

stJoincount.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘stJoincount’ ...
** 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 (stJoincount)

Tests output

stJoincount.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.

> # 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(stJoincount)
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)
> 
> test_check("stJoincount")
No optimal number found, using n = 110 instead.
In this case, there may be minor deviations in the subsequent calculation process.
        The results are for reference only
No optimal number found, using n = 110 instead.
In this case, there may be minor deviations in the subsequent calculation process.
        The results are for reference only
No optimal number found, using n = 110 instead.
In this case, there may be minor deviations in the subsequent calculation process.
        The results are for reference only
No optimal number found, using n = 110 instead.
In this case, there may be minor deviations in the subsequent calculation process.
        The results are for reference only
No optimal number found, using n = 110 instead.
In this case, there may be minor deviations in the subsequent calculation process.
        The results are for reference only
No optimal number found, using n = 110 instead.
In this case, there may be minor deviations in the subsequent calculation process.
        The results are for reference only
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
 32.692   1.469  60.766 

Example timings

stJoincount.Rcheck/stJoincount-Ex.timings

nameusersystemelapsed
customDict0.0020.0010.005
dataPrepFromSeurat0.1080.0060.195
dataPrepFromSpE0.2920.0100.516
extentBuffer1.5340.1423.002
joincountAnalysis1.7440.0633.242
mosaicIntPlot2.1650.0403.951
rasterPrep0.0280.0010.057
rasterizeEachCluster1.6390.0142.959
resolutionCalc0.0260.0010.043
zscoreMatrix1.6410.0152.916
zscorePlot1.8220.0203.332