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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1034/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ILoReg 1.18.0  (landing page)
Johannes Smolander
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/ILoReg
git_branch: RELEASE_3_21
git_last_commit: 9ed83b0
git_last_commit_date: 2025-04-15 12:05:33 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for ILoReg on kjohnson1

To the developers/maintainers of the ILoReg package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ILoReg.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: ILoReg
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ILoReg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ILoReg_1.18.0.tar.gz
StartedAt: 2025-10-15 00:52:10 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 00:58:33 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 383.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ILoReg.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ILoReg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ILoReg_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ILoReg.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ILoReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ILoReg’ version ‘1.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 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 ‘ILoReg’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘Matrix::det’ by ‘SparseM::det’ when loading ‘ILoReg’
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/ILoReg.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 ... WARNING
Codoc mismatches from Rd file 'FindAllGeneMarkers.Rd':
FindAllGeneMarkers.SingleCellExperiment
  Code: function(object, clustering.type, test, log2fc.threshold,
                 min.pct, min.diff.pct, min.cells.group,
                 max.cells.per.cluster, return.thresh, only.pos)
  Docs: function(object, clustering.type, test, log2fc.threshold,
                 min.pct, min.diff.pct, min.cells.group,
                 max.cells.per.cluster, pseudocount.use, return.thresh,
                 only.pos)
  Argument names in docs not in code:
    pseudocount.use
  Mismatches in argument names:
    Position: 9 Code: return.thresh Docs: pseudocount.use
    Position: 10 Code: only.pos Docs: return.thresh
\S4method{FindAllGeneMarkers}{SingleCellExperiment}
  Code: function(object, clustering.type = "manual", test = "wilcox",
                 log2fc.threshold = 0.25, min.pct = 0.1, min.diff.pct =
                 NULL, min.cells.group = 3, max.cells.per.cluster =
                 NULL, return.thresh = 0.01, only.pos = FALSE)
  Docs: function(object, clustering.type = "manual", test = "wilcox",
                 log2fc.threshold = 0.25, min.pct = 0.1, min.diff.pct =
                 NULL, min.cells.group = 3, max.cells.per.cluster =
                 NULL, pseudocount.use = 1, return.thresh = 0.01,
                 only.pos = FALSE)
  Argument names in docs not in code:
    pseudocount.use
  Mismatches in argument names:
    Position: 9 Code: return.thresh Docs: pseudocount.use
    Position: 10 Code: only.pos Docs: return.thresh

Codoc mismatches from Rd file 'FindGeneMarkers.Rd':
FindGeneMarkers.SingleCellExperiment
  Code: function(object, clusters.1, clusters.2, clustering.type, test,
                 logfc.threshold, min.pct, min.diff.pct,
                 min.cells.group, max.cells.per.cluster, return.thresh,
                 only.pos)
  Docs: function(object, clusters.1, clusters.2, clustering.type, test,
                 logfc.threshold, min.pct, min.diff.pct,
                 min.cells.group, max.cells.per.cluster,
                 pseudocount.use, return.thresh, only.pos)
  Argument names in docs not in code:
    pseudocount.use
  Mismatches in argument names:
    Position: 11 Code: return.thresh Docs: pseudocount.use
    Position: 12 Code: only.pos Docs: return.thresh
\S4method{FindGeneMarkers}{SingleCellExperiment}
  Code: function(object, clusters.1 = NULL, clusters.2 = NULL,
                 clustering.type = "", test = "wilcox", logfc.threshold
                 = 0.25, min.pct = 0.1, min.diff.pct = NULL,
                 min.cells.group = 3, max.cells.per.cluster = NULL,
                 return.thresh = 0.01, only.pos = FALSE)
  Docs: function(object, clusters.1 = NULL, clusters.2 = NULL,
                 clustering.type = "", test = "wilcox", logfc.threshold
                 = 0.25, min.pct = 0.1, min.diff.pct = NULL,
                 min.cells.group = 3, max.cells.per.cluster = NULL,
                 pseudocount.use = 1, return.thresh = 0.01, only.pos =
                 FALSE)
  Argument names in docs not in code:
    pseudocount.use
  Mismatches in argument names:
    Position: 11 Code: return.thresh Docs: pseudocount.use
    Position: 12 Code: only.pos Docs: return.thresh

Codoc mismatches from Rd file 'RunICP.Rd':
RunICP
  Code: function(normalized.data = NULL, k = 15, d = 0.3, r = 5, C = 5,
                 reg.type = "L1", max.iter = 200, icp.batch.size = Inf)
  Docs: function(normalized.data = NULL, k = 15, d = 0.3, r = 5, C = 5,
                 reg.type = "L1", max.iter = 200)
  Argument names in code not in docs:
    icp.batch.size

Codoc mismatches from Rd file 'RunParallelICP.Rd':
RunParallelICP.SingleCellExperiment
  Code: function(object, k, d, L, r, C, reg.type, max.iter, threads,
                 icp.batch.size)
  Docs: function(object, k, d, L, r, C, reg.type, max.iter, threads)
  Argument names in code not in docs:
    icp.batch.size
\S4method{RunParallelICP}{SingleCellExperiment}
  Code: function(object, k = 15, d = 0.3, L = 200, r = 5, C = 0.3,
                 reg.type = "L1", max.iter = 200, threads = 0,
                 icp.batch.size = Inf)
  Docs: function(object, k = 15, d = 0.3, L = 200, r = 5, C = 0.3,
                 reg.type = "L1", max.iter = 200, threads = 0)
  Argument names in code not in docs:
    icp.batch.size

* 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
FindAllGeneMarkers    14.600  1.289  15.950
SelectTopGenes        14.118  1.417  15.556
ClusteringScatterPlot 11.749  1.055  12.904
AnnotationScatterPlot 10.438  0.992  11.510
GeneHeatmap            9.542  1.193  10.776
GeneScatterPlot        8.571  1.082   9.744
RunUMAP                6.528  0.897   7.456
FindGeneMarkers        6.540  0.788   7.358
CalcSilhInfo           6.097  0.968   7.148
RunTSNE                5.620  0.674   6.402
SilhouetteCurve        5.300  0.929   6.257
VlnPlot                5.090  1.093   6.204
RenameAllClusters      4.757  0.917   5.716
MergeClusters          4.783  0.813   5.621
SelectKClusters        4.000  1.507   5.555
RunParallelICP         4.665  0.686   5.370
RenameCluster          3.625  1.568   5.241
PCAElbowPlot           4.030  0.865   5.036
* 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 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/ILoReg.Rcheck/00check.log’
for details.


Installation output

ILoReg.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘ILoReg’ ...
** this is package ‘ILoReg’ version ‘1.18.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Matrix::det’ by ‘SparseM::det’ when loading ‘ILoReg’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Matrix::det’ by ‘SparseM::det’ when loading ‘ILoReg’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Matrix::det’ by ‘SparseM::det’ when loading ‘ILoReg’
** testing if installed package keeps a record of temporary installation path
* DONE (ILoReg)

Tests output


Example timings

ILoReg.Rcheck/ILoReg-Ex.timings

nameusersystemelapsed
AnnotationScatterPlot10.438 0.99211.510
CalcSilhInfo6.0970.9687.148
ClusteringScatterPlot11.749 1.05512.904
FindAllGeneMarkers14.600 1.28915.950
FindGeneMarkers6.5400.7887.358
GeneHeatmap 9.542 1.19310.776
GeneScatterPlot8.5711.0829.744
HierarchicalClustering3.9820.7224.728
MergeClusters4.7830.8135.621
PCAElbowPlot4.0300.8655.036
PrepareILoReg0.2420.0130.260
RenameAllClusters4.7570.9175.716
RenameCluster3.6251.5685.241
RunPCA3.7760.5994.378
RunParallelICP4.6650.6865.370
RunTSNE5.6200.6746.402
RunUMAP6.5280.8977.456
SelectKClusters4.0001.5075.555
SelectTopGenes14.118 1.41715.556
SilhouetteCurve5.3000.9296.257
VlnPlot5.0901.0936.204
pbmc3k_5000.0020.0010.003