Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:22 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 CONFESS on tokay2


To the developers/maintainers of the CONFESS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CONFESS.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 384/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CONFESS 1.22.0  (landing page)
Diana LOW
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/CONFESS
git_branch: RELEASE_3_14
git_last_commit: f55571a
git_last_commit_date: 2021-10-26 12:26:56 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CONFESS
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CONFESS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CONFESS_1.22.0.tar.gz
StartedAt: 2022-04-12 17:48:27 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 17:56:22 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 474.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CONFESS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CONFESS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CONFESS_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CONFESS.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.22.0'
* 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 '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-3.14-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
* 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 ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
Fluo_CV_prep    37.10   0.20   37.32
Fluo_adjustment 15.69   0.02   15.71
Fluo_modeling   12.06   0.21   12.28
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
Fluo_CV_prep    36.63   0.90   37.57
Fluo_adjustment 17.26   0.11   17.38
Fluo_modeling   14.48   0.81   15.30
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/CONFESS.Rcheck/00check.log'
for details.



Installation output

CONFESS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CONFESS_1.22.0.tar.gz && rm -rf CONFESS.buildbin-libdir && mkdir CONFESS.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CONFESS.buildbin-libdir CONFESS_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CONFESS_1.22.0.zip && rm CONFESS_1.22.0.tar.gz CONFESS_1.22.0.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
 11 1321k   11  151k    0     0   463k      0  0:00:02 --:--:--  0:00:02  463k
100 1321k  100 1321k    0     0  1054k      0  0:00:01  0:00:01 --:--:-- 1054k

install for i386

* installing *source* package 'CONFESS' ...
** using staged installation
** 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 from temporary location
Warning: replacing previous import 'stats::BIC' by 'flowMerge::BIC' when loading 'CONFESS'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'stats::BIC' by 'flowMerge::BIC' when loading 'CONFESS'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CONFESS' ...
** testing if installed package can be loaded
Warning: replacing previous import 'stats::BIC' by 'flowMerge::BIC' when loading 'CONFESS'
* MD5 sums
packaged installation of 'CONFESS' as CONFESS_1.22.0.zip
* DONE (CONFESS)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CONFESS' successfully unpacked and MD5 sums checked

Tests output


Example timings

CONFESS.Rcheck/examples_i386/CONFESS-Ex.timings

nameusersystemelapsed
FluoSelection_byRun0.020.000.02
Fluo_CV_modeling000
Fluo_CV_prep37.10 0.2037.32
Fluo_adjustment15.69 0.0215.71
Fluo_inspection1.730.021.75
Fluo_modeling12.06 0.2112.28
Fluo_ordering0.660.000.65
LocationMatrix0.010.000.02
cluster2outlier000
createFluo0.020.000.02
defineLocClusters0.080.020.12
files0.000.020.02
getFluo0.030.000.03
getFluo_byRun0.060.000.06
pathEstimator000
readFiles0.030.000.03
simcells1.080.011.09
spotEstimator000

CONFESS.Rcheck/examples_x64/CONFESS-Ex.timings

nameusersystemelapsed
FluoSelection_byRun0.010.000.02
Fluo_CV_modeling000
Fluo_CV_prep36.63 0.9037.57
Fluo_adjustment17.26 0.1117.38
Fluo_inspection1.880.051.92
Fluo_modeling14.48 0.8115.30
Fluo_ordering0.800.000.79
LocationMatrix000
cluster2outlier000
createFluo0.010.000.02
defineLocClusters0.050.000.05
files000
getFluo0.030.000.03
getFluo_byRun0.030.000.03
pathEstimator000
readFiles0.020.000.01
simcells1.060.061.13
spotEstimator000