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This page was generated on 2021-10-15 15:06:25 -0400 (Fri, 15 Oct 2021).

CHECK results for TarSeqQC on tokay2

To the developers/maintainers of the TarSeqQC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TarSeqQC.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 1896/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TarSeqQC 1.22.0  (landing page)
Gabriela Merino
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/TarSeqQC
git_branch: RELEASE_3_13
git_last_commit: 2f87a51
git_last_commit_date: 2021-05-19 12:15:49 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    TIMEOUT    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TarSeqQC
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TarSeqQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TarSeqQC_1.22.0.tar.gz
StartedAt: 2021-10-15 06:27:31 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 07:07:31 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 2400.0 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: TarSeqQC.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TarSeqQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TarSeqQC_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/TarSeqQC.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 'TarSeqQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TarSeqQC' version '1.22.0'
* 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 'TarSeqQC' 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 ... 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 ... NOTE
plotNtdPercentage,TargetExperiment: no visible global function
  definition for 'path'
plotRegion,TargetExperiment: no visible global function definition for
  'path'
readFrequencies,TargetExperiment: no visible global function definition
  for 'path'
Undefined global functions or variables:
  path
* 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
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
TargetExperiment-class             19.25   0.71  472.75
TargetExperiment-plotRegion         2.93   0.20  115.65
TargetExperiment-plotFeature        2.81   0.18  107.39
TargetExperiment-constructor        1.95   0.09   40.67
TargetExperiment-plotNtdPercentage  1.83   0.08   71.42
pileupCounts                        1.84   0.03   74.63
TargetExperiment-readFrequencies    1.12   0.06   15.35
plotInOutFeatures                   1.11   0.06   16.03
TargetExperiment-summarizePanel     0.70   0.00   15.81
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
TargetExperiment-class             21.55   0.61  555.51
TargetExperiment-constructor        3.53   0.09   60.24
TargetExperiment-plotRegion         3.16   0.24  126.78
TargetExperiment-plotFeature        3.03   0.10  127.12
TargetExperiment-plotNtdPercentage  1.94   0.06   75.06
pileupCounts                        1.91   0.09   79.05
plotInOutFeatures                   1.31   0.00   17.87
TargetExperiment-readFrequencies    1.19   0.02   15.28
TargetExperiment-summarizePanel     0.80   0.01   16.23
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'

Installation output

TarSeqQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/TarSeqQC_1.22.0.tar.gz && rm -rf TarSeqQC.buildbin-libdir && mkdir TarSeqQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TarSeqQC.buildbin-libdir TarSeqQC_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TarSeqQC_1.22.0.zip && rm TarSeqQC_1.22.0.tar.gz TarSeqQC_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
 81 1784k   81 1448k    0     0  1763k      0  0:00:01 --:--:--  0:00:01 1762k
100 1784k  100 1784k    0     0  1904k      0 --:--:-- --:--:-- --:--:-- 1904k

install for i386

* installing *source* package 'TarSeqQC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TarSeqQC'
    finding HTML links ... done
    TEList                                  html  
    TarSeqQC-package                        html  
    TargetExperiment-biasExploration        html  
    TargetExperiment-buildFeaturePanel      html  
    TargetExperiment-buildReport            html  
    TargetExperiment-class                  html  
    TargetExperiment-constructor            html  
    TargetExperiment-getters                html  
    TargetExperiment-initialize             html  
    TargetExperiment-plot                   html  
    TargetExperiment-plotAttrExpl           html  
    TargetExperiment-plotAttrPerform        html  
    TargetExperiment-plotFeatPerform        html  
    TargetExperiment-plotFeature            html  
    TargetExperiment-plotGeneAttrPerFeat    html  
    TargetExperiment-plotMetaDataExpl       html  
    TargetExperiment-plotNtdPercentage      html  
    TargetExperiment-plotRegion             html  
    TargetExperiment-print                  html  
    TargetExperiment-readFrequencies        html  
    TargetExperiment-setters                html  
    TargetExperiment-show                   html  
    TargetExperiment-statistics             html  
    TargetExperiment-summarizePanel         html  
    TargetExperimentList-class              html  
    TargetExperimentList-constructor        html  
    TargetExperimentList-initialize         html  
    TargetExperimentList-plotGlobalAttrExpl
                                            html  
    TargetExperimentList-plotPoolPerformance
                                            html  
    ampliPanel                              html  
    ampliPanel2                             html  
    checkBedFasta                           html  
    myCounts                                html  
    object                                  html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/TarSeqQC.buildbin-libdir/00LOCK-TarSeqQC/00new/TarSeqQC/help/object.html
    pileupCounts                            html  
    plotInOutFeatures                       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 'TarSeqQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TarSeqQC' as TarSeqQC_1.22.0.zip
* DONE (TarSeqQC)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'TarSeqQC' successfully unpacked and MD5 sums checked

Tests output

TarSeqQC.Rcheck/tests_i386/runTests.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.

> BiocGenerics:::testPackage("TarSeqQC")

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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows


Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'plyr'

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

    compact

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

    desc

The following object is masked from 'package:S4Vectors':

    rename


Example timings

TarSeqQC.Rcheck/examples_i386/TarSeqQC-Ex.timings

nameusersystemelapsed
TargetExperiment-biasExploration0.080.020.09
TargetExperiment-buildFeaturePanel2.540.052.93
TargetExperiment-buildReport1.810.542.42
TargetExperiment-class 19.25 0.71472.75
TargetExperiment-constructor 1.95 0.0940.67
TargetExperiment-getters0.440.000.44
TargetExperiment-initialize000
TargetExperiment-plot0.370.000.37
TargetExperiment-plotAttrExpl0.140.000.14
TargetExperiment-plotAttrPerform0.080.000.08
TargetExperiment-plotFeatPerform0.710.000.70
TargetExperiment-plotFeature 2.81 0.18107.39
TargetExperiment-plotGeneAttrPerFeat0.50.00.5
TargetExperiment-plotMetaDataExpl0.030.000.03
TargetExperiment-plotNtdPercentage 1.83 0.0871.42
TargetExperiment-plotRegion 2.93 0.20115.65
TargetExperiment-print0.080.030.11
TargetExperiment-readFrequencies 1.12 0.0615.35
TargetExperiment-setters000
TargetExperiment-show0.080.000.08
TargetExperiment-statistics0.100.020.11
TargetExperiment-summarizePanel 0.70 0.0015.81
TargetExperimentList-class0.720.030.75
TargetExperimentList-constructor0.110.000.11
TargetExperimentList-initialize0.110.000.11
TargetExperimentList-plotGlobalAttrExpl0.030.000.03
TargetExperimentList-plotPoolPerformance0.010.000.02
checkBedFasta0.070.000.06
pileupCounts 1.84 0.0374.63
plotInOutFeatures 1.11 0.0616.03

TarSeqQC.Rcheck/examples_x64/TarSeqQC-Ex.timings

nameusersystemelapsed
TargetExperiment-biasExploration0.110.020.13
TargetExperiment-buildFeaturePanel1.500.091.59
TargetExperiment-buildReport1.270.071.36
TargetExperiment-class 21.55 0.61555.51
TargetExperiment-constructor 3.53 0.0960.24
TargetExperiment-getters0.400.010.42
TargetExperiment-initialize000
TargetExperiment-plot0.300.000.29
TargetExperiment-plotAttrExpl0.130.000.13
TargetExperiment-plotAttrPerform0.030.000.03
TargetExperiment-plotFeatPerform0.400.000.41
TargetExperiment-plotFeature 3.03 0.10127.12
TargetExperiment-plotGeneAttrPerFeat0.640.000.64
TargetExperiment-plotMetaDataExpl0.050.000.05
TargetExperiment-plotNtdPercentage 1.94 0.0675.06
TargetExperiment-plotRegion 3.16 0.24126.78
TargetExperiment-print0.090.010.11
TargetExperiment-readFrequencies 1.19 0.0215.28
TargetExperiment-setters0.010.000.02
TargetExperiment-show0.080.000.08
TargetExperiment-statistics0.110.000.11
TargetExperiment-summarizePanel 0.80 0.0116.23
TargetExperimentList-class0.730.000.74
TargetExperimentList-constructor0.110.000.10
TargetExperimentList-initialize0.110.020.13
TargetExperimentList-plotGlobalAttrExpl0.030.000.03
TargetExperimentList-plotPoolPerformance0.020.000.02
checkBedFasta0.060.000.06
pileupCounts 1.91 0.0979.05
plotInOutFeatures 1.31 0.0017.87