Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-03-14 11:40 -0400 (Fri, 14 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4781
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4537
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4567
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4519
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4451
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 586/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dittoSeq 1.19.0  (landing page)
Daniel Bunis
Snapshot Date: 2025-03-13 13:40 -0400 (Thu, 13 Mar 2025)
git_url: https://git.bioconductor.org/packages/dittoSeq
git_branch: devel
git_last_commit: 849ef42
git_last_commit_date: 2024-10-29 10:43:55 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for dittoSeq on nebbiolo1

To the developers/maintainers of the dittoSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dittoSeq.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: dittoSeq
Version: 1.19.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:dittoSeq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings dittoSeq_1.19.0.tar.gz
StartedAt: 2025-03-13 21:38:16 -0400 (Thu, 13 Mar 2025)
EndedAt: 2025-03-13 21:46:24 -0400 (Thu, 13 Mar 2025)
EllapsedTime: 488.6 seconds
RetCode: 0
Status:   OK  
CheckDir: dittoSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:dittoSeq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings dittoSeq_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/dittoSeq.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘dittoSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dittoSeq’ version ‘1.19.0’
* 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 ‘dittoSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... 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 ... NOTE
checkRd: (-1) Darken.Rd:10: Lost braces
    10 | \item{colors}{the color(s) input. Can be a list of colors, for example, /code{dittoColors()}.}
       |                                                                              ^
checkRd: (-1) Lighten.Rd:10: Lost braces
    10 | \item{colors}{the color(s) input. Can be a list of colors, for example, /code{dittoColors()}.}
       |                                                                              ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addDimReduction.Rd: SingleCellExperiment-class
  addPrcomp.Rd: SingleCellExperiment-class
  dittoDimPlot.Rd: ggrepel, SingleCellExperiment
  dittoFreqPlot.Rd: geom_violin
  dittoHeatmap.Rd: pheatmap
  dittoHex.Rd: ggrepel
  dittoPlot.Rd: geom_violin
  dittoPlotVarsAcrossGroups.Rd: geom_violin
  dittoScatterPlot.Rd: ggrepel
  importDittoBulk.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class
  setBulk.Rd: SingleCellExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 LazyData ... 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
dittoPlot                   7.630  0.024   7.655
dittoHex                    7.504  0.091   7.600
multi_dittoDimPlotVaryCells 5.575  0.064   5.640
dittoDimPlot                5.230  0.096   5.326
multi_dittoPlot             5.113  0.210   5.324
dittoFreqPlot               5.166  0.086   5.253
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/dittoSeq.Rcheck/00check.log’
for details.


Installation output

dittoSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL dittoSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘dittoSeq’ ...
** this is package ‘dittoSeq’ version ‘1.19.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (dittoSeq)

Tests output

dittoSeq.Rcheck/tests/testthat.Rout

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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.

> library(testthat)
> test_check("dittoSeq")
Loading required package: dittoSeq
Loading required package: ggplot2
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

[ FAIL 0 | WARN 82 | SKIP 0 | PASS 846 ]

[ FAIL 0 | WARN 82 | SKIP 0 | PASS 846 ]
> 
> proc.time()
   user  system elapsed 
139.648   2.098 141.713 

Example timings

dittoSeq.Rcheck/dittoSeq-Ex.timings

nameusersystemelapsed
Darken0.0080.0000.008
Lighten0.0020.0010.003
Simulate1.4870.0751.562
addDimReduction0.7040.0060.711
addPrcomp0.6140.0370.652
demux.SNP.summary1.5490.0681.618
demux.calls.summary1.4070.0381.447
dittoBarPlot2.0120.0322.043
dittoColors0.0110.0630.074
dittoDimPlot5.2300.0965.326
dittoDotPlot4.7150.0694.786
dittoFreqPlot5.1660.0865.253
dittoHeatmap2.6250.0452.670
dittoHex7.5040.0917.600
dittoPlot7.6300.0247.655
dittoPlotVarsAcrossGroups2.3500.0122.345
dittoScatterPlot4.6100.0104.621
gene2.8270.0522.879
getGenes0.5140.0220.536
getMetas0.4440.0070.452
getReductions0.5270.0110.538
importDemux1.3800.0381.418
importDittoBulk0.4110.0120.423
isBulk0.4520.0070.459
isGene0.5570.0030.560
isMeta0.4190.0090.428
meta0.4610.0070.468
metaLevels0.4150.0060.422
multi_dittoDimPlot2.2870.0312.318
multi_dittoDimPlotVaryCells5.5750.0645.640
multi_dittoPlot5.1130.2105.324
setBulk0.6150.0890.704