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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1555/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pipeComp 1.16.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/pipeComp
git_branch: RELEASE_3_20
git_last_commit: 32e4073
git_last_commit_date: 2024-10-29 10:48:04 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for pipeComp on palomino8

To the developers/maintainers of the pipeComp package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pipeComp.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: pipeComp
Version: 1.16.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:pipeComp.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings pipeComp_1.16.0.tar.gz
StartedAt: 2024-12-20 04:38:35 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 04:45:39 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 424.4 seconds
RetCode: 0
Status:   OK  
CheckDir: pipeComp.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:pipeComp.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings pipeComp_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/pipeComp.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'pipeComp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pipeComp' version '1.16.0'
* 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 'pipeComp' 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 ... 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.compileExcludedCells' '.getMM' '.homogenizeDEA' '.runf'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
scrna_describeDatasets: no visible binding for global variable
  'cluster'
scrna_describeDatasets: no visible binding for global variable 'nb'
scrna_describeDatasets : pf: no visible binding for global variable
  '.x'
scrna_describeDatasets : rd: no visible binding for global variable 'y'
scrna_describeDatasets : rd: no visible binding for global variable
  'cluster'
scrna_evalPlot_filtering: no visible binding for global variable
  'max.lost'
scrna_evalPlot_filtering: no visible binding for global variable
  'mean_F1'
scrna_evalPlot_filtering: no visible binding for global variable 'filt'
scrna_evalPlot_filtering: no visible binding for global variable
  'doubletmethod'
scrna_evalPlot_filtering: no visible binding for global variable
  'method'
scrna_evalPlot_overall: no visible binding for global variable
  'true.nbClusts'
scrna_evalPlot_overall: no visible binding for global variable 'n_clus'
Undefined global functions or variables:
  .x cluster doubletmethod filt max.lost mean_F1 method n_clus nb
  true.nbClusts y
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* 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
scrna_evalPlot_overall 4.96   0.09    5.04
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/pipeComp.Rcheck/00check.log'
for details.


Installation output

pipeComp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL pipeComp
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'pipeComp' ...
** 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 (pipeComp)

Tests output


Example timings

pipeComp.Rcheck/pipeComp-Ex.timings

nameusersystemelapsed
PipelineDefinition-methods0.020.000.01
PipelineDefinition000
addPipelineStep000
aggregatePipelineResults1.110.041.17
buildCombMatrix000
checkPipelinePackages2.141.303.44
colCenterScale000
dea_evalPlot_curve0.750.110.86
dea_pipeline000
evalHeatmap2.840.872.65
evaluateClustering0.020.000.02
evaluateDEA0.060.000.06
evaluateDimRed1.880.021.89
evaluateNorm1.730.081.81
farthestPoint000
getQualitativePalette000
match_evaluate_multiple000
mergePipelineResults2.780.082.86
mockPipeline000
parsePipNames0.020.000.02
plotElapsed0.840.010.86
readPipelineResults1.270.051.31
runPipeline1.140.051.19
scrna_evalPlot_filtering0.30.00.3
scrna_evalPlot_overall4.960.095.04
scrna_evalPlot_silh0.980.031.02
scrna_pipeline000