Johannes Smolander
| Snapshot Date: 2025-11-04 13:40 -0500 (Tue, 04 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/ILoReg |
| git_branch: devel |
| git_last_commit: 676b5a1 |
| git_last_commit_date: 2025-10-29 11:00:58 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-05 11:32 -0500 (Wed, 05 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4818 |
| 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 1030/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ILoReg 1.21.0 (landing page) Johannes Smolander
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
|
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: 1.21.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ILoReg.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ILoReg_1.21.0.tar.gz |
| StartedAt: 2025-11-05 00:22:30 -0500 (Wed, 05 Nov 2025) |
| EndedAt: 2025-11-05 00:29:43 -0500 (Wed, 05 Nov 2025) |
| EllapsedTime: 433.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ILoReg.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ILoReg.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ILoReg_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ILoReg.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ILoReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ILoReg’ version ‘1.21.0’
* 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 ‘/home/biocbuild/bbs-3.23-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 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 ... 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 13.548 0.408 13.958
SelectTopGenes 12.287 0.276 12.564
ClusteringScatterPlot 9.747 0.094 9.842
AnnotationScatterPlot 8.592 0.166 8.758
GeneHeatmap 7.185 0.242 7.428
GeneScatterPlot 7.295 0.019 7.315
CalcSilhInfo 6.498 0.118 6.616
FindGeneMarkers 5.738 0.284 6.021
RunTSNE 5.345 0.052 5.397
RunUMAP 5.203 0.038 5.241
* 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 WARNINGs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/ILoReg.Rcheck/00check.log’
for details.
ILoReg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ILoReg ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘ILoReg’ ... ** this is package ‘ILoReg’ version ‘1.21.0’ ** 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 | 8.592 | 0.166 | 8.758 | |
| CalcSilhInfo | 6.498 | 0.118 | 6.616 | |
| ClusteringScatterPlot | 9.747 | 0.094 | 9.842 | |
| FindAllGeneMarkers | 13.548 | 0.408 | 13.958 | |
| FindGeneMarkers | 5.738 | 0.284 | 6.021 | |
| GeneHeatmap | 7.185 | 0.242 | 7.428 | |
| GeneScatterPlot | 7.295 | 0.019 | 7.315 | |
| HierarchicalClustering | 4.079 | 0.034 | 4.115 | |
| MergeClusters | 3.280 | 0.013 | 3.292 | |
| PCAElbowPlot | 3.480 | 0.007 | 3.488 | |
| PrepareILoReg | 0.271 | 0.005 | 0.277 | |
| RenameAllClusters | 3.431 | 0.033 | 3.465 | |
| RenameCluster | 3.928 | 0.094 | 4.022 | |
| RunPCA | 3.402 | 0.035 | 3.439 | |
| RunParallelICP | 3.291 | 0.052 | 3.343 | |
| RunTSNE | 5.345 | 0.052 | 5.397 | |
| RunUMAP | 5.203 | 0.038 | 5.241 | |
| SelectKClusters | 3.366 | 0.037 | 3.404 | |
| SelectTopGenes | 12.287 | 0.276 | 12.564 | |
| SilhouetteCurve | 4.822 | 0.099 | 4.940 | |
| VlnPlot | 4.590 | 0.006 | 4.596 | |
| pbmc3k_500 | 0.002 | 0.000 | 0.001 | |