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This page was generated on 2024-03-04 11:37:50 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 1877/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scHOT 1.14.0  (landing page)
Shila Ghazanfar
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/scHOT
git_branch: RELEASE_3_18
git_last_commit: 7445339
git_last_commit_date: 2023-10-24 11:21:09 -0500 (Tue, 24 Oct 2023)
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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for scHOT on lconway


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: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2024-03-03 23:17:36 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 23:22:42 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 306.6 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_1.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/scHOT.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scHOT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scHOT’ version ‘1.14.0’
* 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                        27.961  0.357  28.497
scHOT_performPermutationTest 26.115  0.274  26.556
scHOT_estimatePvalues        25.458  0.313  25.985
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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-set0.4050.0220.431
plotColouredExpression1.2780.0491.334
plotHigherOrderSequence2.5750.0472.636
positionColData-set0.1960.0060.205
positionType-set0.1990.0200.220
scHOT27.961 0.35728.497
scHOT_addTestingScaffold0.2050.0060.213
scHOT_buildFromMatrix0.1720.0060.179
scHOT_buildFromSCE0.5460.0310.581
scHOT_calculateGlobalHigherOrderFunction0.2520.0040.257
scHOT_calculateHigherOrderTestStatistics0.5100.0070.519
scHOT_estimatePvalues25.458 0.31325.985
scHOT_output-set0.1780.0040.184
scHOT_performPermutationTest26.115 0.27426.556
scHOT_setPermutationScaffold0.2770.0070.285
scHOT_setWeightMatrix0.2370.0050.243
scHOT_stripOutput0.1770.0030.181
spatialWeightMatrix0.0030.0000.003
testingScaffold-set0.2210.0100.233
thin0.0110.0000.011
trajectoryWeightMatrix0.0030.0010.003
weightMatrix-set0.3950.0210.419
weightedPearson000
weightedSpearman0.0000.0000.001
weightedVariance0.0000.0010.000
weightedZIKendall0.0010.0000.002
weightedZISpearman0.0010.0000.001