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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 367/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClusterFoldSimilarity 1.1.0  (landing page)
Oscar Gonzalez-Velasco
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/ClusterFoldSimilarity
git_branch: devel
git_last_commit: 3bef8a1
git_last_commit_date: 2024-07-09 09:50:58 -0400 (Tue, 09 Jul 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


CHECK results for ClusterFoldSimilarity on palomino6

To the developers/maintainers of the ClusterFoldSimilarity package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ClusterFoldSimilarity.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.

raw results


Summary

Package: ClusterFoldSimilarity
Version: 1.1.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ClusterFoldSimilarity.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ClusterFoldSimilarity_1.1.0.tar.gz
StartedAt: 2024-07-15 22:46:28 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 22:50:11 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 222.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ClusterFoldSimilarity.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ClusterFoldSimilarity.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ClusterFoldSimilarity_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/ClusterFoldSimilarity.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ClusterFoldSimilarity/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ClusterFoldSimilarity' version '1.1.0'
* 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 whether package 'ClusterFoldSimilarity' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'SeuratObject'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
clusterFoldSimilarity: no visible global function definition for 'show'
findCommunitiesSimmilarity: no visible global function definition for
  'hcl.colors'
similarityHeatmap : <anonymous>: no visible binding for global variable
  'datasetL'
similarityHeatmap : <anonymous>: no visible binding for global variable
  'datasetR'
similarityHeatmap : <anonymous>: no visible global function definition
  for 'desc'
similarityHeatmap : <anonymous>: no visible binding for global variable
  'clusterL'
similarityHeatmap : <anonymous>: no visible binding for global variable
  'clusterR'
similarityHeatmap : <anonymous>: no visible binding for global variable
  'similarityValue'
Undefined global functions or variables:
  clusterL clusterR datasetL datasetR desc hcl.colors show
  similarityValue
Consider adding
  importFrom("grDevices", "hcl.colors")
  importFrom("methods", "show")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 'findCommunitiesSimmilarity.Rd':
findCommunitiesSimmilarity
  Code: function(similarityTable = NULL, nIterations = 10,
                 leidenResolution = 1)
  Docs: function(similarityTable = NULL)
  Argument names in code not in docs:
    nIterations leidenResolution

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/ClusterFoldSimilarity.Rcheck/00check.log'
for details.


Installation output

ClusterFoldSimilarity.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ClusterFoldSimilarity
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'ClusterFoldSimilarity' ...
** using staged installation
** R
** 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 (ClusterFoldSimilarity)

Tests output


Example timings

ClusterFoldSimilarity.Rcheck/ClusterFoldSimilarity-Ex.timings

nameusersystemelapsed
clusterFoldSimilarity2.800.032.84
findCommunitiesSimmilarity2.550.142.70
plotClustersGraph1.780.111.89
similarityHeatmap2.360.292.64