Johannes Smolander
| Snapshot Date: 2025-11-17 13:45 -0500 (Mon, 17 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/ILoReg |
| git_branch: RELEASE_3_22 |
| git_last_commit: 50b509c |
| git_last_commit_date: 2025-10-29 11:00:58 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-20 12:05 -0500 (Thu, 20 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4615 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4610 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4598 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 1045/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ILoReg 1.20.0 (landing page) Johannes Smolander
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. |
| Package: ILoReg |
| Version: 1.20.0 |
| 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_1.20.0.tar.gz |
| StartedAt: 2025-11-18 09:05:12 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 09:16:08 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 656.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ILoReg.Rcheck |
| Warnings: 2 |
##############################################################################
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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_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ILoReg.Rcheck’
* using R version 4.5.2 Patched (2025-11-05 r88990)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ILoReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ILoReg’ version ‘1.20.0’
* 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-3.22-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 26.111 1.418 31.254
SelectTopGenes 22.746 1.153 25.742
ClusteringScatterPlot 18.206 1.104 19.992
GeneHeatmap 14.898 1.060 17.345
GeneScatterPlot 14.786 0.803 16.805
AnnotationScatterPlot 13.505 1.098 14.915
RunUMAP 11.531 0.894 13.914
FindGeneMarkers 11.058 0.933 13.175
VlnPlot 8.978 0.807 10.470
CalcSilhInfo 8.850 0.842 10.478
SilhouetteCurve 8.038 0.936 9.747
RunTSNE 8.192 0.749 9.844
RenameAllClusters 6.894 0.704 8.224
RunPCA 6.718 0.797 8.486
MergeClusters 6.823 0.684 8.245
PCAElbowPlot 6.463 0.654 7.800
SelectKClusters 6.194 0.705 7.362
HierarchicalClustering 6.072 0.664 7.298
RenameCluster 6.024 0.710 7.554
RunParallelICP 5.991 0.704 7.533
* 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-3.22-bioc/meat/ILoReg.Rcheck/00check.log’
for details.
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-x86_64/Resources/library’ * installing *source* package ‘ILoReg’ ... ** this is package ‘ILoReg’ version ‘1.20.0’ ** 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)
ILoReg.Rcheck/ILoReg-Ex.timings
| name | user | system | elapsed | |
| AnnotationScatterPlot | 13.505 | 1.098 | 14.915 | |
| CalcSilhInfo | 8.850 | 0.842 | 10.478 | |
| ClusteringScatterPlot | 18.206 | 1.104 | 19.992 | |
| FindAllGeneMarkers | 26.111 | 1.418 | 31.254 | |
| FindGeneMarkers | 11.058 | 0.933 | 13.175 | |
| GeneHeatmap | 14.898 | 1.060 | 17.345 | |
| GeneScatterPlot | 14.786 | 0.803 | 16.805 | |
| HierarchicalClustering | 6.072 | 0.664 | 7.298 | |
| MergeClusters | 6.823 | 0.684 | 8.245 | |
| PCAElbowPlot | 6.463 | 0.654 | 7.800 | |
| PrepareILoReg | 0.590 | 0.021 | 0.631 | |
| RenameAllClusters | 6.894 | 0.704 | 8.224 | |
| RenameCluster | 6.024 | 0.710 | 7.554 | |
| RunPCA | 6.718 | 0.797 | 8.486 | |
| RunParallelICP | 5.991 | 0.704 | 7.533 | |
| RunTSNE | 8.192 | 0.749 | 9.844 | |
| RunUMAP | 11.531 | 0.894 | 13.914 | |
| SelectKClusters | 6.194 | 0.705 | 7.362 | |
| SelectTopGenes | 22.746 | 1.153 | 25.742 | |
| SilhouetteCurve | 8.038 | 0.936 | 9.747 | |
| VlnPlot | 8.978 | 0.807 | 10.470 | |
| pbmc3k_500 | 0.003 | 0.002 | 0.006 | |