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This page was generated on 2024-06-11 14:44 -0400 (Tue, 11 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
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1896/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scHOT 1.16.0  (landing page)
Shila Ghazanfar
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/scHOT
git_branch: RELEASE_3_19
git_last_commit: 5e0fcbf
git_last_commit_date: 2024-04-30 11:22:50 -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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2024-06-11 04:35:15 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 04:43:07 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 471.5 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/scHOT.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scHOT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scHOT’ version ‘1.16.0’
* 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                        23.911  0.254  36.722
scHOT_performPermutationTest 22.755  0.256  33.412
scHOT_estimatePvalues        22.570  0.226  34.748
* 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/4.4-arm64/Resources/library’
* installing *source* package ‘scHOT’ ...
** 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-set0.3590.0260.591
plotColouredExpression1.2530.0601.985
plotHigherOrderSequence2.7110.0654.311
positionColData-set0.1730.0050.262
positionType-set0.1650.0090.257
scHOT23.911 0.25436.722
scHOT_addTestingScaffold0.1890.0050.301
scHOT_buildFromMatrix0.1670.0030.234
scHOT_buildFromSCE0.6130.0270.951
scHOT_calculateGlobalHigherOrderFunction0.2450.0060.366
scHOT_calculateHigherOrderTestStatistics0.4900.0090.726
scHOT_estimatePvalues22.570 0.22634.748
scHOT_output-set0.1620.0040.224
scHOT_performPermutationTest22.755 0.25633.412
scHOT_setPermutationScaffold0.2460.0060.379
scHOT_setWeightMatrix0.2170.0060.348
scHOT_stripOutput0.1850.0060.302
spatialWeightMatrix0.0030.0000.004
testingScaffold-set0.2070.0060.334
thin0.0110.0020.018
trajectoryWeightMatrix0.0030.0000.006
weightMatrix-set0.4280.0240.673
weightedPearson0.0000.0010.000
weightedSpearman0.0000.0000.001
weightedVariance000
weightedZIKendall0.0010.0000.002
weightedZISpearman0.0010.0000.001