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This page was generated on 2021-09-22 15:05:10 -0400 (Wed, 22 Sep 2021).

CHECK results for CAGEfightR on tokay2

To the developers/maintainers of the CAGEfightR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEfightR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 230/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.12.0  (landing page)
Malte Thodberg
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: RELEASE_3_13
git_last_commit: f776ea4
git_last_commit_date: 2021-05-19 12:35:42 -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    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CAGEfightR
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAGEfightR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CAGEfightR_1.12.0.tar.gz
StartedAt: 2021-09-21 20:11:15 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 20:21:17 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 601.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAGEfightR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CAGEfightR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEfightR.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 'CAGEfightR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CAGEfightR' version '1.12.0'
* 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 'CAGEfightR' 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 ... 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
findLinks  5.02   0.06   42.12
trackCTSS  4.33   0.02    5.20
trackLinks 2.12   0.05   21.21
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
findLinks    5.75   0.08   43.73
assignGeneID 5.09   0.12    5.21
trackLinks   2.61   0.06   23.11
* 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: OK


Installation output

CAGEfightR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CAGEfightR_1.12.0.tar.gz && rm -rf CAGEfightR.buildbin-libdir && mkdir CAGEfightR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CAGEfightR.buildbin-libdir CAGEfightR_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CAGEfightR_1.12.0.zip && rm CAGEfightR_1.12.0.tar.gz CAGEfightR_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
 42 2313k   42  987k    0     0  1866k      0  0:00:01 --:--:--  0:00:01 1866k
100 2313k  100 2313k    0     0  2469k      0 --:--:-- --:--:-- --:--:-- 2468k

install for i386

* installing *source* package 'CAGEfightR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CAGEfightR'
    finding HTML links ... done
    assignGeneID                            html  
    assignMissingID                         html  
    assignTxID                              html  
    assignTxType                            html  
    balanceBC                               html  
    balanceD                                html  
    bwCommonGenome                          html  
    bwGenomeCompatibility                   html  
    bwValid                                 html  
    calcBidirectionality                    html  
    calcComposition                         html  
    calcPooled                              html  
    calcShape                               html  
    calcSupport                             html  
    calcTPM                                 html  
    calcTotalTags                           html  
    checkCTSSs                              html  
    checkPeaked                             html  
    checkPooled                             html  
    clusterBidirectionally                  html  
    clusterUnidirectionally                 html  
    combineClusters                         html  
    convertBAM2BigWig                       html  
    convertBED2BigWig                       html  
    convertGRanges2GPos                     html  
    exampleDesign                           html  
    findLinks                               html  
    findStretches                           html  
    quantifyCTSSs                           html  
    quantifyCTSSs2                          html  
    quantifyClusters                        html  
    quantifyGenes                           html  
    quickEnhancers                          html  
    quickGenes                              html  
    quickTSSs                               html  
    shapeEntropy                            html  
    shapeIQR                                html  
    shapeMean                               html  
    shapeMultimodality                      html  
    subsetByBidirectionality                html  
    subsetByComposition                     html  
    subsetBySupport                         html  
    swapRanges                              html  
    swapScores                              html  
    trackBalance                            html  
    trackCTSS                               html  
    trackClusters                           html  
    trackLinks                              html  
    trimToPeak                              html  
    trimToPercentiles                       html  
    tuneTagClustering                       html  
    utilsAggregateRows                      html  
    utilsDeStrand                           html  
    utilsScoreOverlaps                      html  
    utilsSimplifyTxDb                       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 'CAGEfightR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CAGEfightR' as CAGEfightR_1.12.0.zip
* DONE (CAGEfightR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CAGEfightR' successfully unpacked and MD5 sums checked

Tests output


Example timings

CAGEfightR.Rcheck/examples_i386/CAGEfightR-Ex.timings

nameusersystemelapsed
assignGeneID3.750.193.94
assignMissingID1.250.031.28
assignTxID0.940.000.94
assignTxType000
balanceBC000
balanceD000
bwCommonGenome000
bwGenomeCompatibility000
bwValid0.010.000.01
calcBidirectionality0.540.010.55
calcComposition2.420.162.58
calcPooled0.160.000.16
calcShape3.170.783.95
calcSupport0.20.00.2
calcTPM0.220.020.24
calcTotalTags0.130.000.12
checkCTSSs000
checkPeaked0.080.000.08
checkPooled0.060.030.09
clusterBidirectionally000
clusterUnidirectionally1.540.091.63
combineClusters1.120.001.12
convertBAM2BigWig000
convertBED2BigWig000
convertGRanges2GPos0.090.000.09
exampleDesign0.000.030.04
findLinks 5.02 0.0642.12
findStretches0.720.020.74
quantifyCTSSs000
quantifyCTSSs2000
quantifyClusters0.580.030.60
quantifyGenes1.510.061.58
quickEnhancers000
quickGenes000
quickTSSs000
shapeEntropy000
shapeIQR000
shapeMean000
shapeMultimodality000
subsetByBidirectionality0.530.000.53
subsetByComposition1.520.021.54
subsetBySupport0.300.000.31
swapRanges0.470.030.90
swapScores0.290.000.46
trackBalance000
trackCTSS4.330.025.20
trackClusters3.050.013.06
trackLinks 2.12 0.0521.21
trimToPeak1.240.011.25
trimToPercentiles3.390.003.40
tuneTagClustering000
utilsAggregateRows0.500.080.58
utilsDeStrand0.150.000.16
utilsScoreOverlaps0.080.000.07
utilsSimplifyTxDb000

CAGEfightR.Rcheck/examples_x64/CAGEfightR-Ex.timings

nameusersystemelapsed
assignGeneID5.090.125.21
assignMissingID1.580.051.62
assignTxID1.060.011.08
assignTxType000
balanceBC000
balanceD000
bwCommonGenome000
bwGenomeCompatibility000
bwValid0.030.000.03
calcBidirectionality0.660.020.67
calcComposition3.120.063.19
calcPooled0.190.000.19
calcShape3.780.053.82
calcSupport0.280.010.30
calcTPM0.410.000.41
calcTotalTags0.170.020.19
checkCTSSs000
checkPeaked0.140.000.14
checkPooled0.080.000.08
clusterBidirectionally000
clusterUnidirectionally1.810.061.87
combineClusters1.560.001.57
convertBAM2BigWig000
convertBED2BigWig000
convertGRanges2GPos0.120.000.13
exampleDesign0.000.030.03
findLinks 5.75 0.0843.73
findStretches0.720.000.72
quantifyCTSSs000
quantifyCTSSs2000
quantifyClusters0.550.030.58
quantifyGenes2.700.022.72
quickEnhancers000
quickGenes000
quickTSSs000
shapeEntropy000
shapeIQR000
shapeMean000
shapeMultimodality000
subsetByBidirectionality0.50.00.5
subsetByComposition1.370.011.40
subsetBySupport0.140.020.15
swapRanges0.280.020.30
swapScores0.160.000.15
trackBalance000
trackCTSS3.050.003.05
trackClusters2.20.02.2
trackLinks 2.61 0.0623.11
trimToPeak1.660.001.66
trimToPercentiles4.220.004.21
tuneTagClustering000
utilsAggregateRows0.410.140.55
utilsDeStrand0.170.010.19
utilsScoreOverlaps0.110.000.11
utilsSimplifyTxDb000