Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-23 14:06:38 -0400 (Sat, 23 Oct 2021).

CHECK results for pipeComp on riesling1

To the developers/maintainers of the pipeComp package:
- Please 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 How and When does the builder pull? When will my changes propagate? here 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 1422/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pipeComp 1.3.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/pipeComp
git_branch: master
git_last_commit: 7c4eb6e
git_last_commit_date: 2021-05-19 12:53:31 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: pipeComp
Version: 1.3.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pipeComp.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings pipeComp_1.3.0.tar.gz
StartedAt: 2021-10-23 07:46:06 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 07:54:32 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 505.6 seconds
RetCode: 0
Status:   OK  
CheckDir: pipeComp.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pipeComp.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings pipeComp_1.3.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/pipeComp.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pipeComp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pipeComp' version '1.3.0'
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/pipeComp.Rcheck/00check.log'
for details.



Installation output

pipeComp.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/pipeComp_1.3.0.tar.gz && rm -rf pipeComp.buildbin-libdir && mkdir pipeComp.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pipeComp.buildbin-libdir pipeComp_1.3.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL pipeComp_1.3.0.zip && rm pipeComp_1.3.0.tar.gz pipeComp_1.3.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  8 1051k    8 94285    0     0   428k      0  0:00:02 --:--:--  0:00:02  428k
100 1051k  100 1051k    0     0  2820k      0 --:--:-- --:--:-- --:--:-- 2820k

install for i386

* installing *source* package 'pipeComp' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pipeComp'
    finding HTML links ... done
    PipelineDefinition-methods              html  
    PipelineDefinition                      html  
    addPipelineStep                         html  
    aggregatePipelineResults                html  
    buildCombMatrix                         html  
    checkPipelinePackages                   html  
    clustMetricsCorr                        html  
    colCenterScale                          html  
    ctrlgenes                               html  
    dea_evalPlot_curve                      html  
    dea_pipeline                            html  
    defaultStepAggregation                  html  
    evalHeatmap                             html  
    evaluateClustering                      html  
    evaluateDEA                             html  
    evaluateDimRed                          html  
    evaluateNorm                            html  
    exampleDEAresults                       html  
    exampleResults                          html  
    farthestPoint                           html  
    getDimensionality                       html  
    getQualitativePalette                   html  
    match_evaluate_multiple                 html  
    mergePipelineResults                    html  
    mockPipeline                            html  
    parsePipNames                           html  
    pipeComp-package                        html  
    plotElapsed                             html  
    readPipelineResults                     html  
    runPipeline                             html  
    scrna_describeDatasets                  html  
    scrna_evalPlot_filtering                html  
    scrna_evalPlot_overall                  html  
    scrna_evalPlot_silh                     html  
    scrna_pipeline                          html  
    stableG                                 html  
** 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

install for x64

* installing *source* package 'pipeComp' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pipeComp' as pipeComp_1.3.0.zip
* DONE (pipeComp)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'pipeComp' successfully unpacked and MD5 sums checked

Tests output


Example timings

pipeComp.Rcheck/examples_i386/pipeComp-Ex.timings

nameusersystemelapsed
PipelineDefinition-methods0.020.000.01
PipelineDefinition000
addPipelineStep0.010.000.02
aggregatePipelineResults0.140.030.17
buildCombMatrix000
checkPipelinePackages1.210.721.92
colCenterScale000
dea_evalPlot_curve0.360.000.36
dea_pipeline000
evalHeatmap1.200.061.26
evaluateClustering0.020.000.02
evaluateDEA0.040.000.04
evaluateDimRed1.380.031.41
evaluateNorm1.920.041.95
farthestPoint000
getQualitativePalette000
match_evaluate_multiple000
mergePipelineResults0.230.060.30
mockPipeline000
parsePipNames000
plotElapsed0.300.010.31
readPipelineResults0.060.050.11
runPipeline0.080.030.11
scrna_evalPlot_filtering0.200.000.21
scrna_evalPlot_overall2.140.002.14
scrna_evalPlot_silh0.460.000.45
scrna_pipeline000

pipeComp.Rcheck/examples_x64/pipeComp-Ex.timings

nameusersystemelapsed
PipelineDefinition-methods000
PipelineDefinition000
addPipelineStep000
aggregatePipelineResults0.120.040.16
buildCombMatrix000
checkPipelinePackages1.110.671.78
colCenterScale000
dea_evalPlot_curve0.910.010.92
dea_pipeline000
evalHeatmap1.140.191.30
evaluateClustering0.010.000.01
evaluateDEA0.020.000.02
evaluateDimRed1.480.001.48
evaluateNorm1.520.021.58
farthestPoint000
getQualitativePalette000
match_evaluate_multiple000
mergePipelineResults0.220.070.29
mockPipeline000
parsePipNames000
plotElapsed0.320.000.32
readPipelineResults0.110.020.12
runPipeline0.070.020.09
scrna_evalPlot_filtering0.240.000.24
scrna_evalPlot_overall2.400.002.41
scrna_evalPlot_silh0.490.000.48
scrna_pipeline000