Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:06 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 CiteFuse on nebbiolo1


To the developers/maintainers of the CiteFuse package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CiteFuse.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 331/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CiteFuse 1.8.0  (landing page)
Yingxin Lin
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/CiteFuse
git_branch: RELEASE_3_15
git_last_commit: 75bb83a
git_last_commit_date: 2022-04-26 12:04:27 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CiteFuse
Version: 1.8.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CiteFuse.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CiteFuse_1.8.0.tar.gz
StartedAt: 2022-10-18 19:03:13 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:07:21 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 248.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CiteFuse.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CiteFuse.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CiteFuse_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/CiteFuse.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CiteFuse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CiteFuse’ version ‘1.8.0’
* 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 ‘CiteFuse’ 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 'igraphClustering':
igraphClustering
  Code: function(sce, metadata = "SNF_W", method = c("louvain",
                 "leiden", "walktrap", "spinglass", "optimal",
                 "leading_eigen", "label_prop", "fast_greedy",
                 "edge_betweenness"), ...)
  Docs: function(sce, metadata = "SNF_W", method = c("louvain",
                 "walktrap", "spinglass", "optimal", "leading_eigen",
                 "label_prop", "fast_greedy", "edge_betweenness"), ...)
  Mismatches in argument default values:
    Name: 'method'
    Code: c("louvain", "leiden", "walktrap", "spinglass", "optimal", "leading_eigen", 
          "label_prop", "fast_greedy", "edge_betweenness")
    Docs: c("louvain", "walktrap", "spinglass", "optimal", "leading_eigen", 
          "label_prop", "fast_greedy", "edge_betweenness")

* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/CiteFuse.Rcheck/00check.log’
for details.



Installation output

CiteFuse.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL CiteFuse
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘CiteFuse’ ...
** using staged installation
** R
** data
** 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 (CiteFuse)

Tests output


Example timings

CiteFuse.Rcheck/CiteFuse-Ex.timings

nameusersystemelapsed
CiteFuse2.7640.1042.868
DEbubblePlot2.350.062.41
DEcomparisonPlot2.0620.0242.087
DEgenes1.1260.0361.162
DEgenesCross3.8810.0353.917
crossSampleDoublets1.4070.0231.431
geneADTnetwork2.0660.0922.158
igraphClustering0.7030.0090.712
importanceADT1.3370.0271.365
ligandReceptorTest1.9260.0631.990
normaliseExprs0.8180.0250.842
plotHTO3.3210.0433.366
preprocessing0.6530.0080.662
readFrom10X000
reducedDimSNF1.7750.0161.790
selectDEgenes1.0370.0001.037
spectralClustering0.6340.0080.642
visImportance1.9170.0361.953
visLigandReceptor1.3140.0031.318
visualiseDim1.2820.0011.282
visualiseExprs1.6420.0161.658
visualiseExprsList1.1490.0041.153
visualiseKNN0.8590.0000.859
withinSampleDoublets1.2500.0241.274