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CHECK report for CONFESS on tokay2

This page was generated on 2018-10-17 08:42:05 -0400 (Wed, 17 Oct 2018).

Package 297/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CONFESS 1.8.0
Diana LOW
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CONFESS
Branch: RELEASE_3_7
Last Commit: 2fe8958
Last Changed Date: 2018-04-30 10:35:41 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CONFESS
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:CONFESS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CONFESS_1.8.0.tar.gz
StartedAt: 2018-10-17 01:18:24 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:22:39 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 254.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CONFESS.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:CONFESS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CONFESS_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CONFESS.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CONFESS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CONFESS' version '1.8.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'CONFESS' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'stats::BIC' by 'flowMerge::BIC' when loading 'CONFESS'
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CONFESS.Rcheck/00install.out' for details.
* 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 ... 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 or elapsed time > 5s
                 user system elapsed
Fluo_CV_prep    29.21   0.50   29.72
Fluo_adjustment 25.57   0.06   25.64
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/CONFESS.Rcheck/00check.log'
for details.



Installation output

CONFESS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch CONFESS
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
* installing *source* package 'CONFESS' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'stats::BIC' by 'flowMerge::BIC' when loading 'CONFESS'
** help
*** installing help indices
  converting help for package 'CONFESS'
    finding HTML links ... done
    BGcorrectFluo                           html  
    BatchFluo                               html  
    CVsampler                               html  
    DDHFfit                                 html  
    DDHFinput                               html  
    FluoInspection                          html  
    FluoSelection_byRun                     html  
    Fluo_CV_modeling                        html  
    Fluo_CV_prep                            html  
    Fluo_adjustment                         html  
    Fluo_inspection                         html  
    Fluo_modeling                           html  
    Fluo_ordering                           html  
    GAPanalysis                             html  
    GrubbsOutliers                          html  
    LocationMatrix                          html  
    Results                                 html  
    SpotStats                               html  
    SpotbyStrLines                          html  
    addKpredictions                         html  
    adjustFluo                              html  
    aveDiff                                 html  
    boxFluo                                 html  
    boxcoxMatrix                            html  
    boxcoxMatrixEst                         html  
    caseof0s                                html  
    caseof1R0G                              html  
    caseof1R1G                              html  
    caseof1R2G                              html  
    caseof2R1G                              html  
    caseof2R2G                              html  
    caseof2Rs0G                             html  
    clu                                     html  
    cluster2outlier                         html  
    contrastFluo                            html  
    cpPELT                                  html  
    cpoints                                 html  
    createFluo                              html  
    cutpointsEstimator                      html  
    ddhft.np.2                              html  
    defineLocClusters                       html  
    denoisefun                              html  
    denoiser                                html  
    despecklefun                            html  
    diagnoseResiduals                       html  
    distfromcenter                          html  
    doTransform                             html  
    estimate.new.pseudotimes                html  
    estimatePath                            html  
    estimates.2                             html  
    estimates                               html  
    extractBFArea                           html  
    failurecase                             html  
    fclust                                  html  
    files                                   html  
    filled.contour3                         html  
    findPattern                             html  
    fixPath                                 html  
    flowclust_step1                         html  
    flowclust_step2                         html  
    forceBF                                 html  
    function.from.vector                    html  
    getCoordinates_stats                    html  
    getCsFAIL                               html  
    getFluo                                 html  
    getFluo_byRun                           html  
    getSpot                                 html  
    giveWarning                             html  
    grouplines                              html  
    grubbs                                  html  
    highlight.cols                          html  
    invTransform                            html  
    isotone                                 html  
    joinAreas                               html  
    listSorter                              html  
    lmFluo                                  html  
    mean_signal                             html  
    measureB                                html  
    measureF                                html  
    multiplot                               html  
    myt                                     html  
    orderFluo                               html  
    path.initiator                          html  
    pathEstimator                           html  
    pathUpdater                             html  
    plotImages                              html  
    plot_clusgap                            html  
    predict.kmeans                          html  
    processImg                              html  
    project                                 html  
    readChaImg                              html  
    readFiles                               html  
    readOriImg                              html  
    reestimate.pseudos.byCV                 html  
    refineMixes                             html  
    revDDHFinput                            html  
    signal.from.matrix                      html  
    significantSignal                       html  
    simcells                                html  
    sortCentroids                           html  
    spot.simulator                          html  
    spotCenter                              html  
    spotCoords                              html  
    spotEstimator                           html  
    step1                                   html  
    step2.1                                 html  
    step2                                   html  
    step3.1                                 html  
    step3                                   html  
    step4                                   html  
    steps2_4                                html  
    straightColLines                        html  
    straightRowLines                        html  
    subsetAnalysis                          html  
    summarizeAdjFluo                        html  
    transformFluo                           html  
    trigofun                                html  
    unnormalizeC01                          html  
    updateCentroids                         html  
    updateCentroidsPaths                    html  
    which.min.diff                          html  
    zoomInBF                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'stats::BIC' by 'flowMerge::BIC' when loading 'CONFESS'
* DONE (CONFESS)
Making 'packages.html' ... done
In R CMD INSTALL

Tests output


Example timings

CONFESS.Rcheck/CONFESS-Ex.timings

nameusersystemelapsed
FluoSelection_byRun0.030.000.05
Fluo_CV_modeling000
Fluo_CV_prep29.21 0.5029.72
Fluo_adjustment25.57 0.0625.64
Fluo_inspection2.390.082.47
Fluo_modeling4.300.264.56
Fluo_ordering1.450.011.47
LocationMatrix0.020.000.01
cluster2outlier000
createFluo0.020.000.02
defineLocClusters0.060.000.08
files000
getFluo0.030.000.03
getFluo_byRun0.070.000.06
pathEstimator000
readFiles0.030.000.04
simcells4.860.054.90
spotEstimator0.010.000.02