Johannes Smolander
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/ILoReg |
| git_branch: RELEASE_3_20 |
| git_last_commit: 0694b79 |
| git_last_commit_date: 2024-10-29 10:48:50 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 1016/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ILoReg 1.16.0 (landing page) Johannes Smolander
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.16.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ILoReg.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ILoReg_1.16.0.tar.gz |
| StartedAt: 2024-11-20 04:34:40 -0500 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 04:39:46 -0500 (Wed, 20 Nov 2024) |
| EllapsedTime: 306.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ILoReg.Rcheck |
| Warnings: 2 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ILoReg.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ILoReg_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ILoReg.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ILoReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ILoReg’ version ‘1.16.0’
* 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 ‘ILoReg’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘Matrix::det’ by ‘SparseM::det’ when loading ‘ILoReg’
See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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 10.434 0.412 10.846
SelectTopGenes 9.925 0.249 10.176
GeneHeatmap 6.623 0.272 6.896
AnnotationScatterPlot 5.364 0.117 5.482
GeneScatterPlot 5.259 0.051 5.312
* 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
‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ILoReg.Rcheck/00check.log’
for details.
ILoReg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ILoReg ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘ILoReg’ ... ** 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 | 5.364 | 0.117 | 5.482 | |
| CalcSilhInfo | 3.399 | 0.073 | 3.472 | |
| ClusteringScatterPlot | 4.792 | 0.115 | 4.907 | |
| FindAllGeneMarkers | 10.434 | 0.412 | 10.846 | |
| FindGeneMarkers | 3.910 | 0.141 | 4.050 | |
| GeneHeatmap | 6.623 | 0.272 | 6.896 | |
| GeneScatterPlot | 5.259 | 0.051 | 5.312 | |
| HierarchicalClustering | 2.043 | 0.023 | 2.075 | |
| MergeClusters | 2.723 | 0.006 | 2.732 | |
| PCAElbowPlot | 2.113 | 0.007 | 2.121 | |
| PrepareILoReg | 0.161 | 0.009 | 0.170 | |
| RenameAllClusters | 2.666 | 0.005 | 2.671 | |
| RenameCluster | 2.007 | 0.005 | 2.012 | |
| RunPCA | 2.632 | 0.005 | 2.637 | |
| RunParallelICP | 1.990 | 0.001 | 1.992 | |
| RunTSNE | 3.771 | 0.004 | 3.774 | |
| RunUMAP | 3.355 | 0.004 | 3.359 | |
| SelectKClusters | 2.709 | 0.016 | 2.725 | |
| SelectTopGenes | 9.925 | 0.249 | 10.176 | |
| SilhouetteCurve | 2.967 | 0.034 | 3.002 | |
| VlnPlot | 2.505 | 0.009 | 2.516 | |
| pbmc3k_500 | 0.000 | 0.002 | 0.002 | |