Multiple platform build/check report for BioC 3.20 - CHECK results for SimBu on palomino6

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4677
palomino6	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4416
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4444
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4393
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4373
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 SimBu on palomino6

To the developers/maintainers of the SimBu package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SimBu.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: SimBu

Version: 1.7.0

Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SimBu.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SimBu_1.7.0.tar.gz

StartedAt: 2024-07-16 04:16:45 -0400 (Tue, 16 Jul 2024)

EndedAt: 2024-07-16 04:23:36 -0400 (Tue, 16 Jul 2024)

EllapsedTime: 411.1 seconds

RetCode: 0

Status: OK

CheckDir: SimBu.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SimBu.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SimBu_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/SimBu.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SimBu/DESCRIPTION' ... OK
* this is package 'SimBu' version '1.7.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  .pre-commit-config.yaml
  .prettierignore
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'SimBu' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/SimBu.Rcheck/00install.out' for details.
* 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 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 line endings in shell scripts ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
setup_sfaira       9.46  24.49  146.86
simulate_bulk     25.29   2.62   27.16
dataset           10.48   0.28   10.73
merge_simulations  9.44   0.15    9.80
dataset_seurat     4.31   0.64    5.60
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/SimBu.Rcheck/00check.log'
for details.

Installation output

SimBu.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL SimBu
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'SimBu' ...
** using non-staged installation via StagedInstall field
** R
** 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
* DONE (SimBu)

Tests output

SimBu.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(SimBu)
> 
> test_check("SimBu")
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

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

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Filtering genes...
Created dataset.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'spam'
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
Finished simulation.
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`

...
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Using EPIC scaling factors.
Finished simulation.
Using EPIC scaling factors.
Finished simulation.
Using ABIS scaling factors.
Finished simulation.
Using quanTIseq scaling factors.
Finished simulation.
Using quanTIseq scaling factors.
Finished simulation.
Using custom scaling factors.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
Finished simulation.
[ FAIL 0 | WARN 41 | SKIP 0 | PASS 31 ]

[ FAIL 0 | WARN 41 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
 123.82    4.28  132.51

Example timings

SimBu.Rcheck/SimBu-Ex.timings

name	user	system	elapsed
census	1.36	0.13	1.50
dataset	10.48	0.28	10.73
dataset_h5ad	0	0	0
dataset_merge	2.42	0.05	2.85
dataset_seurat	4.31	0.64	5.60
dataset_sfaira	0	0	0
dataset_sfaira_multiple	0	0	0
merge_simulations	9.44	0.15	9.80
plot_simulation	2.87	0.11	3.17
save_simulation	3.82	0.14	3.68
setup_sfaira	9.46	24.49	146.86
sfaira_overview	0	0	0
simulate_bulk	25.29	2.62	27.16