Johannes Smolander
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/ILoReg |
| git_branch: master |
| git_last_commit: 18ebc7d |
| git_last_commit_date: 2022-03-08 08:42:53 -0400 (Tue, 08 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:48 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the ILoReg package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 923/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ILoReg 1.5.1 (landing page) Johannes Smolander
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: ILoReg |
| Version: 1.5.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ILoReg.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ILoReg_1.5.1.tar.gz |
| StartedAt: 2022-03-17 19:21:59 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:27:50 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 351.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ILoReg.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ILoReg.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ILoReg_1.5.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ILoReg.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ILoReg/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ILoReg' version '1.5.1'
* 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 whether package 'ILoReg' 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 R 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 documentation object 'FindAllGeneMarkers':
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 documentation object 'FindGeneMarkers':
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 documentation object 'RunICP':
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 documentation object 'RunParallelICP':
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 16.47 2.77 19.23
SelectTopGenes 15.43 2.30 17.74
GeneHeatmap 10.69 2.36 13.05
ClusteringScatterPlot 10.71 1.80 12.52
GeneScatterPlot 10.30 1.80 12.09
AnnotationScatterPlot 10.31 1.28 11.60
CalcSilhInfo 8.09 2.03 10.13
RunUMAP 8.02 1.59 9.61
FindGeneMarkers 7.75 1.76 9.52
RunTSNE 7.91 1.49 9.40
VlnPlot 7.31 1.54 8.86
RenameCluster 7.25 1.52 8.84
SilhouetteCurve 6.77 1.83 8.59
RunPCA 6.61 1.64 8.25
PCAElbowPlot 6.41 1.61 8.02
RenameAllClusters 6.14 1.59 8.10
SelectKClusters 6.14 1.53 7.67
HierarchicalClustering 6.17 1.47 7.64
RunParallelICP 5.73 1.53 7.27
MergeClusters 5.33 1.56 6.89
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
'D:/biocbuild/bbs-3.15-bioc/meat/ILoReg.Rcheck/00check.log'
for details.
ILoReg.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ILoReg
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ILoReg' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ILoReg'
finding HTML links ... done
AnnotationScatterPlot html
CalcSilhInfo html
ClusteringScatterPlot html
DownOverSampling html
FindAllGeneMarkers html
FindGeneMarkers html
GeneHeatmap html
GeneScatterPlot html
HierarchicalClustering html
LogisticRegression html
MergeClusters html
PCAElbowPlot html
PrepareILoReg html
RenameAllClusters html
RenameCluster html
RunICP html
RunPCA html
RunParallelICP html
RunTSNE html
RunUMAP html
SelectKClusters html
SelectTopGenes html
SilhouetteCurve html
VlnPlot html
pbmc3k_500 html
** 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 (ILoReg)
Making 'packages.html' ... done
ILoReg.Rcheck/ILoReg-Ex.timings
| name | user | system | elapsed | |
| AnnotationScatterPlot | 10.31 | 1.28 | 11.60 | |
| CalcSilhInfo | 8.09 | 2.03 | 10.13 | |
| ClusteringScatterPlot | 10.71 | 1.80 | 12.52 | |
| FindAllGeneMarkers | 16.47 | 2.77 | 19.23 | |
| FindGeneMarkers | 7.75 | 1.76 | 9.52 | |
| GeneHeatmap | 10.69 | 2.36 | 13.05 | |
| GeneScatterPlot | 10.30 | 1.80 | 12.09 | |
| HierarchicalClustering | 6.17 | 1.47 | 7.64 | |
| MergeClusters | 5.33 | 1.56 | 6.89 | |
| PCAElbowPlot | 6.41 | 1.61 | 8.02 | |
| PrepareILoReg | 0.30 | 0.03 | 0.33 | |
| RenameAllClusters | 6.14 | 1.59 | 8.10 | |
| RenameCluster | 7.25 | 1.52 | 8.84 | |
| RunPCA | 6.61 | 1.64 | 8.25 | |
| RunParallelICP | 5.73 | 1.53 | 7.27 | |
| RunTSNE | 7.91 | 1.49 | 9.40 | |
| RunUMAP | 8.02 | 1.59 | 9.61 | |
| SelectKClusters | 6.14 | 1.53 | 7.67 | |
| SelectTopGenes | 15.43 | 2.30 | 17.74 | |
| SilhouetteCurve | 6.77 | 1.83 | 8.59 | |
| VlnPlot | 7.31 | 1.54 | 8.86 | |
| pbmc3k_500 | 0.02 | 0.00 | 0.02 | |