Alexander Dietrich
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/SimBu |
| git_branch: RELEASE_3_18 |
| git_last_commit: 0c37a0d |
| git_last_commit_date: 2023-11-21 10:41:33 -0400 (Tue, 21 Nov 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:38:15 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 1959/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SimBu 1.4.3 (landing page) Alexander Dietrich
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: SimBu |
| Version: 1.4.3 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SimBu.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SimBu_1.4.3.tar.gz |
| StartedAt: 2024-03-28 08:59:58 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 09:05:58 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 359.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SimBu.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SimBu.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SimBu_1.4.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/SimBu.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
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 ‘SimBu/DESCRIPTION’ ... OK
* this is package ‘SimBu’ version ‘1.4.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SimBu’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.18-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 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 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
simulate_bulk 22.475 1.125 25.664
setup_sfaira 11.426 3.211 58.974
dataset 11.099 0.446 12.242
dataset_seurat 9.144 0.700 10.459
merge_simulations 5.929 0.126 6.527
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc/meat/SimBu.Rcheck/00check.log’
for details.
SimBu.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SimBu ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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)
SimBu.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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(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, sort, 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
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 0 | SKIP 0 | PASS 31 ]
>
> proc.time()
user system elapsed
152.454 3.579 165.063
SimBu.Rcheck/SimBu-Ex.timings
| name | user | system | elapsed | |
| census | 3.166 | 0.216 | 3.567 | |
| dataset | 11.099 | 0.446 | 12.242 | |
| dataset_h5ad | 0.000 | 0.000 | 0.001 | |
| dataset_merge | 1.791 | 0.115 | 2.013 | |
| dataset_seurat | 9.144 | 0.700 | 10.459 | |
| dataset_sfaira | 0.000 | 0.001 | 0.023 | |
| dataset_sfaira_multiple | 0.000 | 0.000 | 0.001 | |
| merge_simulations | 5.929 | 0.126 | 6.527 | |
| plot_simulation | 3.432 | 0.102 | 3.850 | |
| save_simulation | 2.884 | 0.072 | 3.185 | |
| setup_sfaira | 11.426 | 3.211 | 58.974 | |
| sfaira_overview | 0.000 | 0.001 | 0.000 | |
| simulate_bulk | 22.475 | 1.125 | 25.664 | |