António Sousa
| Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/Coralysis |
| git_branch: devel |
| git_last_commit: 652e7cc |
| git_last_commit_date: 2025-05-07 08:24:08 -0400 (Wed, 07 May 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-19 12:02 -0400 (Thu, 19 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4810 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4528 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4493 |
| 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 438/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Coralysis 0.99.6 (landing page) António Sousa
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the Coralysis package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Coralysis.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: Coralysis |
| Version: 0.99.6 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Coralysis.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Coralysis_0.99.6.tar.gz |
| StartedAt: 2025-06-18 22:01:03 -0400 (Wed, 18 Jun 2025) |
| EndedAt: 2025-06-18 22:18:40 -0400 (Wed, 18 Jun 2025) |
| EllapsedTime: 1056.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Coralysis.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Coralysis.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Coralysis_0.99.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Coralysis.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘Coralysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Coralysis’ version ‘0.99.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘Coralysis’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘utils’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PlotDimRed: no visible global function definition for ‘tail’
PlotExpression: no visible global function definition for ‘tail’
PlotDimRed,SingleCellExperiment: no visible global function definition
for ‘tail’
PlotExpression,SingleCellExperiment: no visible global function
definition for ‘tail’
Undefined global functions or variables:
tail
Consider adding
importFrom("utils", "tail")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AggregateDataByBatch 21.568 0.392 30.280
RunUMAP 6.002 3.434 6.407
PlotClusterTree 5.934 2.908 5.312
CellClusterProbabilityDistribution 5.472 3.126 4.908
GetFeatureCoefficients 5.103 3.314 4.597
PCAElbowPlot 4.697 3.668 5.529
SummariseCellClusterProbability 4.682 3.372 4.946
RunParallelDivisiveICP 4.401 3.038 4.607
RunPCA 4.227 2.955 4.393
ReferenceMapping 4.535 2.298 4.850
GetCellClusterProbability 3.373 2.907 3.605
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/Coralysis.Rcheck/00check.log’
for details.
Coralysis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Coralysis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘Coralysis’ ... ** this is package ‘Coralysis’ version ‘0.99.6’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (Coralysis)
Coralysis.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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.
> # 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(Coralysis)
>
> test_check("Coralysis")
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
WARNING: Setting 'divisive.method' to 'cluster' as 'batch.label=NULL'.
If 'batch.label=NULL', 'divisive.method' can be one of: 'cluster', 'random'.
Initializing divisive ICP clustering...
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Divisive ICP clustering completed successfully.
Predicting cell cluster probabilities using ICP models...
Prediction of cell cluster probabilities completed successfully.
Multi-level integration completed successfully.
Divisive ICP: selecting ICP tables multiple of 1
WARNING: Setting 'divisive.method' to 'cluster' as 'batch.label=NULL'.
If 'batch.label=NULL', 'divisive.method' can be one of: 'cluster', 'random'.
Initializing divisive ICP clustering...
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Divisive ICP clustering completed successfully.
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Divisive ICP: selecting ICP tables multiple of 1
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Divisive ICP clustering completed successfully.
Predicting cell cluster probabilities using ICP models...
Prediction of cell cluster probabilities completed successfully.
Multi-level integration completed successfully.
Parallelism disabled, because threads = 1
Initializing divisive ICP clustering...
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Divisive ICP clustering completed successfully.
Predicting cell cluster probabilities using ICP models...
Prediction of cell cluster probabilities completed successfully.
Multi-level integration completed successfully.
Initializing divisive ICP clustering...
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Divisive ICP clustering completed successfully.
Predicting cell cluster probabilities using ICP models...
Prediction of cell cluster probabilities completed successfully.
Multi-level integration completed successfully.
WARNING: Setting 'divisive.method' to 'cluster' as 'batch.label=NULL'.
If 'batch.label=NULL', 'divisive.method' can be one of: 'cluster', 'random'.
Initializing divisive ICP clustering...
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Divisive ICP clustering completed successfully.
Predicting cell cluster probabilities using ICP models...
Prediction of cell cluster probabilities completed successfully.
Multi-level integration completed successfully.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
>
> proc.time()
user system elapsed
36.448 12.599 32.984
Coralysis.Rcheck/Coralysis-Ex.timings
| name | user | system | elapsed | |
| AggregateDataByBatch | 21.568 | 0.392 | 30.280 | |
| BinCellClusterProbability | 0.000 | 0.000 | 0.001 | |
| CellBinsFeatureCorrelation | 0.000 | 0.000 | 0.001 | |
| CellClusterProbabilityDistribution | 5.472 | 3.126 | 4.908 | |
| FindAllClusterMarkers | 0.237 | 0.023 | 0.260 | |
| FindClusterMarkers | 0.228 | 0.018 | 0.246 | |
| GetCellClusterProbability | 3.373 | 2.907 | 3.605 | |
| GetFeatureCoefficients | 5.103 | 3.314 | 4.597 | |
| HeatmapFeatures | 0.452 | 0.060 | 0.512 | |
| MajorityVotingFeatures | 0 | 0 | 0 | |
| PCAElbowPlot | 4.697 | 3.668 | 5.529 | |
| PlotClusterTree | 5.934 | 2.908 | 5.312 | |
| PlotDimRed | 1.589 | 0.147 | 1.736 | |
| PlotExpression | 1.341 | 0.048 | 1.389 | |
| PrepareData | 0.299 | 0.004 | 0.303 | |
| ReferenceMapping | 4.535 | 2.298 | 4.850 | |
| RunPCA | 4.227 | 2.955 | 4.393 | |
| RunParallelDivisiveICP | 4.401 | 3.038 | 4.607 | |
| RunTSNE | 1.588 | 0.108 | 1.696 | |
| RunUMAP | 6.002 | 3.434 | 6.407 | |
| SummariseCellClusterProbability | 4.682 | 3.372 | 4.946 | |
| TabulateCellBinsByGroup | 0 | 0 | 0 | |
| VlnPlot | 1.092 | 0.090 | 1.181 | |