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This page was generated on 2023-10-20 09:38:11 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1841/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scHOT 1.12.0  (landing page)
Shila Ghazanfar
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/scHOT
git_branch: RELEASE_3_17
git_last_commit: b93eca3
git_last_commit_date: 2023-04-25 11:17:07 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for scHOT on kjohnson2


To the developers/maintainers of the scHOT 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: scHOT
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2023-10-18 22:28:59 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 22:42:48 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 829.1 seconds
RetCode: 0
Status:   OK  
CheckDir: scHOT.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/scHOT.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 ‘scHOT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scHOT’ version ‘1.12.0’
* 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 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 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_estimatePvalues        86.299  0.770 155.130
scHOT                        86.149  0.858 152.594
scHOT_performPermutationTest 85.740  0.788 152.937
* 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

scHOT.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scHOT
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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-set0.4000.0390.773
plotColouredExpression1.1110.0882.185
plotHigherOrderSequence2.8350.0624.819
positionColData-set0.2040.0040.325
positionType-set0.2000.0040.323
scHOT 86.149 0.858152.594
scHOT_addTestingScaffold0.2160.0040.372
scHOT_buildFromMatrix0.1850.0040.315
scHOT_buildFromSCE0.6160.0301.108
scHOT_calculateGlobalHigherOrderFunction0.2660.0050.474
scHOT_calculateHigherOrderTestStatistics1.1470.0161.990
scHOT_estimatePvalues 86.299 0.770155.130
scHOT_output-set0.1830.0030.335
scHOT_performPermutationTest 85.740 0.788152.937
scHOT_setPermutationScaffold0.2780.0050.509
scHOT_setWeightMatrix0.2450.0050.442
scHOT_stripOutput0.2010.0040.374
spatialWeightMatrix0.0040.0000.009
testingScaffold-set0.2020.0070.374
thin0.0100.0010.020
trajectoryWeightMatrix0.0020.0000.007
weightMatrix-set0.4830.0190.875
weightedPearson0.0010.0000.000
weightedSpearman0.0010.0000.000
weightedVariance0.0000.0000.001
weightedZIKendall0.0010.0000.005
weightedZISpearman0.0000.0000.001