Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-24 15:06:05 -0400 (Fri, 24 Sep 2021).

CHECK results for ChIPSeqSpike on tokay2

To the developers/maintainers of the ChIPSeqSpike package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPSeqSpike.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 299/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPSeqSpike 1.12.0  (landing page)
Nicolas Descostes
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/ChIPSeqSpike
git_branch: RELEASE_3_13
git_last_commit: 8b73542
git_last_commit_date: 2021-05-19 12:33:09 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: ChIPSeqSpike
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPSeqSpike.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChIPSeqSpike_1.12.0.tar.gz
StartedAt: 2021-09-23 20:19:37 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 20:26:19 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 402.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChIPSeqSpike.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPSeqSpike.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChIPSeqSpike_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ChIPSeqSpike.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 'ChIPSeqSpike/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPSeqSpike' version '1.12.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'ChIPSeqSpike' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'ChIPSeqSpike' is deprecated and will be removed from
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ChIPSeqSpike.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
* 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 data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... 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 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/ChIPSeqSpike.Rcheck/00check.log'
for details.



Installation output

ChIPSeqSpike.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ChIPSeqSpike_1.12.0.tar.gz && rm -rf ChIPSeqSpike.buildbin-libdir && mkdir ChIPSeqSpike.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPSeqSpike.buildbin-libdir ChIPSeqSpike_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ChIPSeqSpike_1.12.0.zip && rm ChIPSeqSpike_1.12.0.tar.gz ChIPSeqSpike_1.12.0.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
 13 4081k   13  537k    0     0  1190k      0  0:00:03 --:--:--  0:00:03 1190k
 55 4081k   55 2276k    0     0  1593k      0  0:00:02  0:00:01  0:00:01 1593k
100 4081k  100 4081k    0     0  2304k      0  0:00:01  0:00:01 --:--:-- 2304k

install for i386

* installing *source* package 'ChIPSeqSpike' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ChIPSeqSpike'
    finding HTML links ... done
    ChIPSeqSpikeCore                        html  
    ChIPSeqSpikeDataset-class               html  
    ChIPSeqSpikeDatasetBoost-class          html  
    ChIPSeqSpikeDatasetList-class           html  
    ChIPSeqSpikeDatasetListBoost-class      html  
    Experiment-class                        html  
    ExperimentLoaded-class                  html  
    averageBindingValues                    html  
    bigWigFile                              html  
    boxplotSpike                            html  
    count                                   html  
    datasetList                             html  
    estimateScalingFactors                  html  
    exoCount                                html  
    exogenousScalingFactor                  html  
    experimentList                          html  
    exportBigWigs                           html  
    extractBinding                          html  
    getAverageBindingValues                 html  
    getBam                                  html  
    getBigWigFile                           html  
    getCount                                html  
    getDatasetList                          html  
    getExoCount                             html  
    getExogenousBam                         html  
    getExogenousScalingFactor               html  
    getExpName                              html  
    getExperimentList                       html  
    getExperimentListBigWigs                html  
    getLoadedData                           html  
    getMatBindingValues                     html  
    getRatio                                html  
    getScalingFactor                        html  
    inputSubtraction                        html  
    matBindingValues                        html  
    plotCor                                 html  
    plotHeatmaps                            html  
    plotProfile                             html  
    plotTransform                           html  
    ratio                                   html  
    result_data                             html  
    scaling                                 html  
    scalingFactor                           html  
    spikeDataset                            html  
    spikePipe                               html  
    spikeSummary                            html  
** building package indices
** installing vignettes
   'ChIPSeqSpike.Rmd' using 'UTF-8' 
** testing if installed package can be loaded from temporary location
Warning: Package 'ChIPSeqSpike' is deprecated and will be removed from
  Bioconductor version 3.14
** testing if installed package can be loaded from final location
Warning: Package 'ChIPSeqSpike' is deprecated and will be removed from
  Bioconductor version 3.14
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ChIPSeqSpike' ...
** testing if installed package can be loaded
Warning: Package 'ChIPSeqSpike' is deprecated and will be removed from
  Bioconductor version 3.14
* MD5 sums
packaged installation of 'ChIPSeqSpike' as ChIPSeqSpike_1.12.0.zip
* DONE (ChIPSeqSpike)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ChIPSeqSpike' successfully unpacked and MD5 sums checked

Tests output

ChIPSeqSpike.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> library("ChIPSeqSpike")
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Warning message:
Package 'ChIPSeqSpike' is deprecated and will be removed from
  Bioconductor version 3.14 
> 
> proc.time()
   user  system elapsed 
  12.32    1.15   13.46 

ChIPSeqSpike.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> library("ChIPSeqSpike")
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Warning message:
Package 'ChIPSeqSpike' is deprecated and will be removed from
  Bioconductor version 3.14 
> 
> proc.time()
   user  system elapsed 
  10.65    0.67   11.31 

Example timings

ChIPSeqSpike.Rcheck/examples_i386/ChIPSeqSpike-Ex.timings

nameusersystemelapsed
ChIPSeqSpikeDataset-class0.020.000.01
ChIPSeqSpikeDatasetBoost-class000
ChIPSeqSpikeDatasetList-class0.030.000.03
ChIPSeqSpikeDatasetListBoost-class000
Experiment-class000
ExperimentLoaded-class000
averageBindingValues0.000.012.25
bigWigFile000
boxplotSpike2.330.082.41
count000
datasetList0.330.000.33
estimateScalingFactors0.280.021.15
exoCount0.020.000.02
exogenousScalingFactor000
experimentList000
exportBigWigs0.010.000.01
extractBinding000
getAverageBindingValues0.580.050.63
getBam0.440.020.45
getBigWigFile0.340.090.44
getCount0.300.090.39
getDatasetList0.350.000.35
getExoCount0.580.020.59
getExogenousBam0.400.010.42
getExogenousScalingFactor0.390.020.41
getExpName0.390.050.44
getExperimentList0.350.000.34
getExperimentListBigWigs0.310.030.34
getLoadedData000
getMatBindingValues0.480.040.54
getRatio0.130.000.12
getScalingFactor0.360.020.37
inputSubtraction000
matBindingValues000
plotCor0.530.010.55
plotHeatmaps0.890.000.89
plotProfile0.550.030.58
plotTransform0.750.020.76
scaling0.090.000.10
scalingFactor0.020.000.01
spikeDataset0.010.000.02
spikePipe000
spikeSummary0.020.000.01

ChIPSeqSpike.Rcheck/examples_x64/ChIPSeqSpike-Ex.timings

nameusersystemelapsed
ChIPSeqSpikeDataset-class000
ChIPSeqSpikeDatasetBoost-class000
ChIPSeqSpikeDatasetList-class0.030.000.03
ChIPSeqSpikeDatasetListBoost-class0.020.000.01
Experiment-class000
ExperimentLoaded-class000
averageBindingValues000
bigWigFile0.000.010.02
boxplotSpike2.920.032.95
count000
datasetList0.330.000.33
estimateScalingFactors0.300.030.33
exoCount000
exogenousScalingFactor0.000.020.01
experimentList000
exportBigWigs000
extractBinding000
getAverageBindingValues0.320.020.34
getBam0.290.030.31
getBigWigFile0.310.000.31
getCount0.280.000.29
getDatasetList0.260.000.27
getExoCount0.260.000.27
getExogenousBam0.270.010.28
getExogenousScalingFactor0.390.000.39
getExpName0.370.000.38
getExperimentList0.430.000.42
getExperimentListBigWigs0.430.000.43
getLoadedData000
getMatBindingValues0.580.130.71
getRatio0.160.000.15
getScalingFactor0.280.010.30
inputSubtraction000
matBindingValues0.000.020.02
plotCor0.440.010.45
plotHeatmaps0.820.020.84
plotProfile0.60.00.6
plotTransform0.700.030.76
scaling0.140.020.16
scalingFactor000
spikeDataset0.030.000.03
spikePipe000
spikeSummary0.020.000.02