Multiple platform build/check report for BioC 3.21 - CHECK results for scQTLtools on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4831
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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 scQTLtools on kjohnson3

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

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scQTLtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scQTLtools_1.0.0.tar.gz

StartedAt: 2025-04-17 21:34:29 -0400 (Thu, 17 Apr 2025)

EndedAt: 2025-04-17 21:38:28 -0400 (Thu, 17 Apr 2025)

EllapsedTime: 238.8 seconds

RetCode: 0

Status: OK

CheckDir: scQTLtools.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scQTLtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scQTLtools_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scQTLtools.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scQTLtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scQTLtools’ version ‘1.0.0’
* 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 ‘scQTLtools’ 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 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
zinbModel     17.727  1.299  19.053
callQTL        1.582  0.103  30.034
createGeneLoc  0.726  0.061  13.981
* 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: OK

Installation output

scQTLtools.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘scQTLtools’ ...
** this is package ‘scQTLtools’ version ‘1.0.0’
** 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 (scQTLtools)

Tests output

scQTLtools.Rcheck/tests/testthat.Rout


R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(scQTLtools)

> 
> test_check("scQTLtools")
Normalization completed using method: logNormalize

Dimensions of normalized data:84 2705

Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Loading required package: SummarizedExperiment
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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

No Normalized counts found named 'normcounts',
                you can achieve data normalization with `normalizeGene()`,
                or check if it is has been renamed.
Normalization completed using method: logNormalize

Dimensions of normalized data:84 2705


Attaching package: 'limma'

The following object is masked from 'package:DESeq2':

    plotMA

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

    plotMA

Normalization completed using method: logNormalize

Dimensions of normalized data:84 2705

Normalization completed using method: CPM

Dimensions of normalized data:84 2705

Normalization completed using method: TPM

Dimensions of normalized data:84 2705

converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Normalization completed using method: DESeq

Dimensions of normalized data:84 2705

Normalization completed using method: limma

Dimensions of normalized data:84 2705

Normalization completed using method: logNormalize

Dimensions of normalized data:84 2705

Normalization completed using method: logNormalize

Dimensions of normalized data:84 2705

Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Normalization completed using method: logNormalize

Dimensions of normalized data:74 500

Start the sc-eQTLs calling.
CMP:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
GMP:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 54 ]
> 
> proc.time()
   user  system elapsed 
 42.073   4.292  49.555

Example timings

scQTLtools.Rcheck/scQTLtools-Ex.timings

name	user	system	elapsed
CPM_normalize	0.383	0.244	0.630
DESeq_normalize	3.295	0.269	3.576
TPM_normalize	0.394	0.234	0.635
adjust_pvalues	0	0	0
buildZINB	0.104	0.026	0.129
callQTL	1.582	0.103	30.034
checkSNPList	0.048	0.001	0.053
createGeneLoc	0.726	0.061	13.981
createQTLObject	0.592	0.021	0.656
createSNPsLoc	0.587	0.054	1.736
draw_QTLplot	0.136	0.005	0.140
draw_boxplot	0.055	0.001	0.056
draw_histplot	0.082	0.001	0.083
draw_violinplot	0.048	0.001	0.049
filterGeneSNP	0.777	0.055	0.832
filter_by_abs_b	0.001	0.000	0.001
get_cell_groups	0.491	0.021	0.513
get_counts	0.014	0.001	0.015
get_filter_data	0.037	0.116	0.155
get_model_info	0.016	0.002	0.018
get_raw_data	0.128	0.450	0.588
get_result_info	0.015	0.002	0.018
initialize_progress_bar	0.005	0.001	2.199
limma_normalize	0.191	0.222	0.415
linearModel	0.731	0.034	0.769
load_biclassify_info	0.016	0.002	0.018
load_group_info	0.016	0.004	0.020
load_species_info	0.015	0.003	0.018
log_normalize	0.367	0.264	0.649
normalizeGene	0.017	0.002	0.019
plots_theme_opts	0.036	0.000	0.037
poissonModel	1.192	0.073	1.275
process_matrix	0	0	0
remove_outliers	0.001	0.000	0.000
set_filter_data-eQTLObject-method	0.015	0.002	0.018
set_filter_data	0.015	0.002	0.016
set_model_info-eQTLObject-method	0.014	0.001	0.016
set_model_info	0.015	0.001	0.016
set_raw_data-eQTLObject-method	0.015	0.002	0.016
set_raw_data	0.014	0.001	0.016
set_result_info-eQTLObject-method	0.014	0.001	0.016
set_result_info	0.015	0.002	0.017
show-eQTLObject-method	0.015	0.002	0.017
testEQTL	0.029	0.003	0.032
testGene	0.012	0.001	0.014
testSNP	0.044	0.005	0.048
testSNP2	0.002	0.000	0.003
testSeurat	0.095	0.003	0.097
visualizeQTL	0.881	0.011	0.897
zinbModel	17.727	1.299	19.053