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This page was generated on 2024-06-17 12:23 -0400 (Mon, 17 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4685
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4400
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 1234/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microSTASIS 1.5.0  (landing page)
Pedro Sánchez-Sánchez
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/microSTASIS
git_branch: devel
git_last_commit: 00fe97a
git_last_commit_date: 2024-04-30 11:46:12 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  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


CHECK results for microSTASIS on nebbiolo2

To the developers/maintainers of the microSTASIS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/microSTASIS.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: microSTASIS
Version: 1.5.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:microSTASIS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings microSTASIS_1.5.0.tar.gz
StartedAt: 2024-06-17 00:56:01 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 01:01:18 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 316.5 seconds
RetCode: 0
Status:   OK  
CheckDir: microSTASIS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:microSTASIS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings microSTASIS_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/microSTASIS.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘microSTASIS/DESCRIPTION’ ... OK
* this is package ‘microSTASIS’ version ‘1.5.0’
* 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 ‘microSTASIS’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘TreeSummarizedExperiment’
  All declared Imports should be used.
* 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 ... NOTE
Rd files without \alias:
  ‘microSTASIS.Rd’
* 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
plotmSlinesCV         20.552  0.971  11.628
mSerrorCV             20.524  0.890  11.602
iterativeClusteringCV 19.888  0.776  11.024
plotmSdynamics         9.336  0.442   6.807
plotmSscatter          9.203  0.560   6.831
plotmSheatmap          9.186  0.496   6.678
iterativeClustering    9.209  0.417   6.819
mSmetadataGroups       8.976  0.576   6.353
mSpreviz               8.712  0.397   6.284
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/microSTASIS.Rcheck/00check.log’
for details.


Installation output

microSTASIS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL microSTASIS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘microSTASIS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘pairedTimes’ with signature ‘"TreeSummarizedExperiment"’: no definition for class “TreeSummarizedExperiment”
** help
*** installing help indices
*** copying figures
** 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 (microSTASIS)

Tests output

microSTASIS.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(microSTASIS)
> 
> test_check("microSTASIS")
[ FAIL 0 | WARN 21 | SKIP 0 | PASS 20 ]

[ FAIL 0 | WARN 21 | SKIP 0 | PASS 20 ]
> 
> proc.time()
   user  system elapsed 
345.726   9.266 155.117 

Example timings

microSTASIS.Rcheck/microSTASIS-Ex.timings

nameusersystemelapsed
iterativeClustering9.2090.4176.819
iterativeClusteringCV19.888 0.77611.024
mSerrorCV20.524 0.89011.602
mSinternalPairedTimes0.0220.0000.021
mSmetadataGroups8.9760.5766.353
mSpreviz8.7120.3976.284
pairedTimes-methods0.0220.0000.022
plotmSdynamics9.3360.4426.807
plotmSheatmap9.1860.4966.678
plotmSlinesCV20.552 0.97111.628
plotmSscatter9.2030.5606.831