Back to Build/check report for BioC 3.18:   simplified   long
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2023-06-06 11:00:34 -0000 (Tue, 06 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4366
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

CHECK results for ILoReg on kunpeng2


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 972/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ILoReg 1.11.0  (landing page)
Johannes Smolander
Snapshot Date: 2023-06-05 06:35:06 -0000 (Mon, 05 Jun 2023)
git_url: https://git.bioconductor.org/packages/ILoReg
git_branch: devel
git_last_commit: 2a39997
git_last_commit_date: 2023-04-25 15:20:49 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

Summary

Package: ILoReg
Version: 1.11.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ILoReg.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ILoReg_1.11.0.tar.gz
StartedAt: 2023-06-06 00:21:28 -0000 (Tue, 06 Jun 2023)
EndedAt: 2023-06-06 00:30:25 -0000 (Tue, 06 Jun 2023)
EllapsedTime: 536.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ILoReg.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ILoReg.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ILoReg_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ILoReg.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘ILoReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ILoReg’ version ‘1.11.0’
* 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 ... 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 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 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     30.877  0.415  31.350
SelectTopGenes         24.828  0.159  25.032
ClusteringScatterPlot  20.970  0.100  21.108
AnnotationScatterPlot  20.753  0.287  21.083
CalcSilhInfo           17.632  0.160  17.828
GeneHeatmap            17.349  0.236  17.617
GeneScatterPlot        16.060  0.072  16.159
FindGeneMarkers        14.365  0.259  14.651
RunUMAP                12.912  0.044  12.980
RunTSNE                12.615  0.056  12.696
VlnPlot                11.321  0.076  11.415
SilhouetteCurve        11.001  0.068  11.092
MergeClusters          10.914  0.068  11.001
PCAElbowPlot           10.735  0.195  10.952
RenameAllClusters      10.623  0.076  10.717
HierarchicalClustering 10.571  0.060  10.654
RunPCA                 10.475  0.040  10.539
RunParallelICP         10.384  0.032  10.436
SelectKClusters        10.270  0.024  10.314
RenameCluster          10.009  0.036  10.064
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ILoReg.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘ILoReg.Rmd’ using rmarkdown
Error: processing vignette 'ILoReg.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘ILoReg.Rmd’

SUMMARY: processing the following file failed:
  ‘ILoReg.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ILoReg.Rcheck/00check.log’
for details.

Installation output

ILoReg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL ILoReg
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/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
** help
*** installing help indices
** 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)

Tests output

Example timings

ILoReg.Rcheck/ILoReg-Ex.timings

nameusersystemelapsed
AnnotationScatterPlot20.753 0.28721.083
CalcSilhInfo17.632 0.16017.828
ClusteringScatterPlot20.970 0.10021.108
FindAllGeneMarkers30.877 0.41531.350
FindGeneMarkers14.365 0.25914.651
GeneHeatmap17.349 0.23617.617
GeneScatterPlot16.060 0.07216.159
HierarchicalClustering10.571 0.06010.654
MergeClusters10.914 0.06811.001
PCAElbowPlot10.735 0.19510.952
PrepareILoReg0.5270.0120.540
RenameAllClusters10.623 0.07610.717
RenameCluster10.009 0.03610.064
RunPCA10.475 0.04010.539
RunParallelICP10.384 0.03210.436
RunTSNE12.615 0.05612.696
RunUMAP12.912 0.04412.980
SelectKClusters10.270 0.02410.314
SelectTopGenes24.828 0.15925.032
SilhouetteCurve11.001 0.06811.092
VlnPlot11.321 0.07611.415
pbmc3k_5000.0020.0000.002