Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:10 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 mistyR on nebbiolo2


To the developers/maintainers of the mistyR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mistyR.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 1227/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mistyR 1.6.1  (landing page)
Jovan Tanevski
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/mistyR
git_branch: RELEASE_3_16
git_last_commit: 23b3fdf
git_last_commit_date: 2023-02-20 03:54:27 -0400 (Mon, 20 Feb 2023)
nebbiolo2Linux (Ubuntu 20.04.5 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 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: mistyR
Version: 1.6.1
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:mistyR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings mistyR_1.6.1.tar.gz
StartedAt: 2023-04-10 22:03:08 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 22:16:47 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 819.7 seconds
RetCode: 0
Status:   OK  
CheckDir: mistyR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:mistyR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings mistyR_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/mistyR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘mistyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mistyR’ version ‘1.6.1’
* 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 ‘mistyR’ 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 loading without being on the library search path ... 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 ... NOTE
aggregate_results: no visible binding for global variable ‘.data’
aggregate_results_subset: no visible binding for global variable
  ‘.data’
bagged_mars_model: no visible binding for global variable ‘.data’
collect_results : <anonymous>: no visible binding for global variable
  ‘.data’
collect_results: no visible binding for global variable ‘.data’
collect_results : <anonymous> : <anonymous>: no visible binding for
  global variable ‘.data’
extract_signature: no visible binding for global variable ‘.data’
extract_signature : <anonymous>: no visible binding for global variable
  ‘.data’
gradient_boosting_model: no visible binding for global variable ‘.data’
linear_model: no visible binding for global variable ‘.data’
mars_model: no visible binding for global variable ‘.data’
mlp_model: no visible binding for global variable ‘.data’
plot_contrast_heatmap: no visible binding for global variable ‘.data’
plot_contrast_results: no visible binding for global variable ‘.data’
plot_contrast_results : <anonymous>: no visible binding for global
  variable ‘.data’
plot_improvement_stats: no visible binding for global variable ‘.data’
plot_interaction_communities: no visible binding for global variable
  ‘.data’
plot_interaction_heatmap: no visible binding for global variable
  ‘.data’
plot_view_contributions: no visible binding for global variable ‘.data’
run_misty : <anonymous>: no visible binding for global variable ‘.data’
svm_model: no visible binding for global variable ‘.data’
Undefined global functions or variables:
  .data
* 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
collect_results        136.559  6.082 142.042
reexports               46.291  1.876  48.000
run_misty               46.001  2.032  47.872
remove_views            25.937  0.210  26.147
add_paraview            22.674  0.148  22.822
add_juxtaview            6.286  0.128   6.414
create_view              5.564  0.016   5.580
plot_improvement_stats   4.992  0.443   5.192
* 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 ...
  ‘mistyR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/mistyR.Rcheck/00check.log’
for details.



Installation output

mistyR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL mistyR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘mistyR’ ...
** using staged installation
** R
** data
** inst
** 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 (mistyR)

Tests output

mistyR.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(mistyR)
mistyR is able to run computationally intensive functions
  in parallel. Please consider specifying a future::plan(). For example by running
  future::plan(future::multisession) before calling mistyR functions.
> 
> test_check("mistyR")

Generating paraview

Attaching package: 'purrr'

The following object is masked from 'package:testthat':

    is_null


Training models

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Generating paraview

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Computing triangulation

Generating juxtaview

Generating paraview

Generating paraview using 20 nearest neighbors per unit

Approximating RBF matrix using the Nystrom method

Computing triangulation

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[ FAIL 0 | WARN 74 | SKIP 0 | PASS 173 ]

[ FAIL 0 | WARN 74 | SKIP 0 | PASS 173 ]
> 
> proc.time()
   user  system elapsed 
337.996   3.683 342.718 

Example timings

mistyR.Rcheck/mistyR-Ex.timings

nameusersystemelapsed
add_juxtaview6.2860.1286.414
add_paraview22.674 0.14822.822
add_views0.0110.0000.011
clear_cache0.0030.0000.003
collect_results136.559 6.082142.042
create_initial_view0.3630.0080.371
create_view5.5640.0165.580
extract_signature2.3350.2562.484
filter_views1.2210.0001.222
plot_contrast_heatmap2.9550.2563.098
plot_contrast_results3.4650.2763.662
plot_improvement_stats4.9920.4435.192
plot_interaction_communities2.4970.2242.595
plot_interaction_heatmap2.8370.2362.957
plot_view_contributions2.5800.2152.672
reexports46.291 1.87648.000
remove_views25.937 0.21026.147
rename_view0.0130.0000.013
run_misty46.001 2.03247.872
select_markers0.3140.0040.317