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This page was generated on 2022-08-18 11:08:19 -0400 (Thu, 18 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4379
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4161
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4169
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

CHECK results for muscat on lconway


To the developers/maintainers of the muscat package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/muscat.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1286/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
muscat 1.11.2  (landing page)
Helena L. Crowell
Snapshot Date: 2022-08-17 14:00:04 -0400 (Wed, 17 Aug 2022)
git_url: https://git.bioconductor.org/packages/muscat
git_branch: master
git_last_commit: fd893e8
git_last_commit_date: 2022-06-17 01:39:15 -0400 (Fri, 17 Jun 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: muscat
Version: 1.11.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:muscat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings muscat_1.11.2.tar.gz
StartedAt: 2022-08-17 21:21:58 -0400 (Wed, 17 Aug 2022)
EndedAt: 2022-08-17 21:28:37 -0400 (Wed, 17 Aug 2022)
EllapsedTime: 398.5 seconds
RetCode: 0
Status:   OK  
CheckDir: muscat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:muscat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings muscat_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/muscat.Rcheck’
* using R version 4.2.1 Patched (2022-07-09 r82577)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘muscat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘muscat’ version ‘1.11.2’
* 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 ‘muscat’ 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 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
mmDS      8.311  0.204   8.564
simData   7.497  0.282   7.805
pbHeatmap 6.003  0.101   6.152
* 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

muscat.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘muscat’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.0
Current TMB version is 1.9.1
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.0
Current TMB version is 1.9.1
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** testing if installed package can be loaded from final location
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.0
Current TMB version is 1.9.1
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** testing if installed package keeps a record of temporary installation path
* DONE (muscat)

Tests output

muscat.Rcheck/tests/testthat.Rout


R version 4.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> library(testthat)
> library(muscat)
Warning message:
In checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.0
Current TMB version is 1.9.1
Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
> 
> test_check("muscat")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 551 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 551 ]
> 
> proc.time()
   user  system elapsed 
 99.465   2.075 101.881 

Example timings

muscat.Rcheck/muscat-Ex.timings

nameusersystemelapsed
aggregateData3.0100.0943.114
calcExprFreqs0.5870.0340.629
data000
mmDS8.3110.2048.564
pbDS1.4960.0251.530
pbFlatten0.9310.0280.963
pbHeatmap6.0030.1016.152
pbMDS0.7420.0170.761
prepSCE0.6380.0160.656
prepSim4.7150.2294.985
resDS2.4860.0542.548
simData7.4970.2827.805