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This page was generated on 2025-08-11 12:12 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4532
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 1894/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scHOT 1.21.0  (landing page)
Shila Ghazanfar
Snapshot Date: 2025-08-10 13:45 -0400 (Sun, 10 Aug 2025)
git_url: https://git.bioconductor.org/packages/scHOT
git_branch: devel
git_last_commit: 092e074
git_last_commit_date: 2025-04-15 11:57:03 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for scHOT on kjohnson3

To the developers/maintainers of the scHOT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scHOT.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: scHOT
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scHOT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scHOT_1.21.0.tar.gz
StartedAt: 2025-08-10 21:31:15 -0400 (Sun, 10 Aug 2025)
EndedAt: 2025-08-10 21:32:46 -0400 (Sun, 10 Aug 2025)
EllapsedTime: 91.0 seconds
RetCode: 0
Status:   OK  
CheckDir: scHOT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scHOT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scHOT_1.21.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scHOT.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scHOT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scHOT’ version ‘1.21.0’
* 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 ‘scHOT’ 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 ... 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 LazyData ... 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
scHOT                        6.361  0.211   6.579
scHOT_performPermutationTest 6.201  0.272   6.485
scHOT_estimatePvalues        5.979  0.308   6.300
* 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: OK


Installation output

scHOT.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘scHOT’ ...
** this is package ‘scHOT’ version ‘1.21.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (scHOT)

Tests output


Example timings

scHOT.Rcheck/scHOT-Ex.timings

nameusersystemelapsed
params-set0.0590.0010.060
plotColouredExpression0.2700.0130.283
plotHigherOrderSequence0.7130.0060.720
positionColData-set0.0240.0010.026
positionType-set0.0230.0010.025
scHOT6.3610.2116.579
scHOT_addTestingScaffold0.0300.0010.031
scHOT_buildFromMatrix0.0230.0020.025
scHOT_buildFromSCE0.0980.0110.109
scHOT_calculateGlobalHigherOrderFunction0.0550.0030.058
scHOT_calculateHigherOrderTestStatistics0.1080.0030.111
scHOT_estimatePvalues5.9790.3086.300
scHOT_output-set0.0260.0010.026
scHOT_performPermutationTest6.2010.2726.485
scHOT_setPermutationScaffold0.0430.0010.044
scHOT_setWeightMatrix0.0390.0040.043
scHOT_stripOutput0.0260.0030.029
spatialWeightMatrix0.0010.0000.001
testingScaffold-set0.0330.0040.037
thin0.0040.0000.003
trajectoryWeightMatrix0.0010.0000.000
weightMatrix-set0.0700.0060.075
weightedPearson000
weightedSpearman000
weightedVariance0.0000.0000.001
weightedZIKendall0.0010.0000.000
weightedZISpearman000