Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:43 -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 merida1


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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CiteFuse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CiteFuse_1.8.0.tar.gz
StartedAt: 2022-10-19 00:34:56 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 00:42:35 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 458.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CiteFuse.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CiteFuse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CiteFuse_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/CiteFuse.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
DEgenesCross 7.223  0.048   7.279
plotHTO      6.959  0.036   7.004
DEbubblePlot 5.256  0.114   5.392
* 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
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/CiteFuse.Rcheck/00check.log’
for details.



Installation output

CiteFuse.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CiteFuse
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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
CiteFuse2.9310.0753.145
DEbubblePlot5.2560.1145.392
DEcomparisonPlot4.1560.0464.208
DEgenes2.0930.0202.115
DEgenesCross7.2230.0487.279
crossSampleDoublets2.5680.0252.596
geneADTnetwork2.5120.0302.549
igraphClustering1.4760.0421.520
importanceADT2.9170.0322.954
ligandReceptorTest2.6090.0362.647
normaliseExprs1.6990.0141.714
plotHTO6.9590.0367.004
preprocessing1.2680.0181.288
readFrom10X000
reducedDimSNF2.1510.0342.189
selectDEgenes2.1100.0202.131
spectralClustering1.2680.0251.295
visImportance3.4600.0383.504
visLigandReceptor2.8100.0332.847
visualiseDim2.7020.0222.733
visualiseExprs3.4090.0203.443
visualiseExprsList2.3160.0172.337
visualiseKNN1.5010.0131.516
withinSampleDoublets2.5520.0202.576