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This page was generated on 2021-10-20 12:05:00 -0400 (Wed, 20 Oct 2021).

CHECK results for ASpli on riesling1

To the developers/maintainers of the ASpli package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ASpli.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 90/2072HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 2.3.1  (landing page)
Estefania Mancini
Snapshot Date: 2021-10-19 14:50:04 -0400 (Tue, 19 Oct 2021)
git_url: https://git.bioconductor.org/packages/ASpli
git_branch: master
git_last_commit: afabc60
git_last_commit_date: 2021-05-25 21:35:34 -0400 (Tue, 25 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ASpli
Version: 2.3.1
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASpli.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ASpli_2.3.1.tar.gz
StartedAt: 2021-10-20 00:12:51 -0400 (Wed, 20 Oct 2021)
EndedAt: 2021-10-20 00:33:37 -0400 (Wed, 20 Oct 2021)
EllapsedTime: 1246.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ASpli.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASpli.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ASpli_2.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/ASpli.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 'ASpli/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ASpli' version '2.3.1'
* 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 'ASpli' 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 installed files from 'inst/doc' ... 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
ASpli-package           82.17   0.08   82.36
jDUreport               45.45   0.02   45.47
integrateSignals        43.32   0.00   43.33
jCounts-methods         43.19   0.03   43.22
splicingReport          42.99   0.01   43.00
exportIntegratedSignals 42.53   0.13   42.66
exportSplicingReports   42.45   0.09   42.55
gbDUreport-method       36.84   0.02   36.86
gbCounts                36.41   0.01   36.42
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
ASpli-package           94.26   0.09   94.36
exportSplicingReports   51.15   0.14   51.29
splicingReport          50.62   0.05   50.67
jDUreport               49.64   0.00   49.66
exportIntegratedSignals 49.03   0.22   49.35
integrateSignals        48.97   0.01   49.09
jCounts-methods         48.42   0.03   48.45
gbCounts                43.18   0.00   43.17
gbDUreport-method       42.53   0.03   42.57
* 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

ASpli.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ASpli_2.3.1.tar.gz && rm -rf ASpli.buildbin-libdir && mkdir ASpli.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASpli.buildbin-libdir ASpli_2.3.1.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ASpli_2.3.1.zip && rm ASpli_2.3.1.tar.gz ASpli_2.3.1.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
 14 4893k   14  698k    0     0  1446k      0  0:00:03 --:--:--  0:00:03 1446k
 68 4893k   68 3365k    0     0  2283k      0  0:00:02  0:00:01  0:00:01 2281k
100 4893k  100 4893k    0     0  2548k      0  0:00:01  0:00:01 --:--:-- 2547k

install for i386

* installing *source* package 'ASpli' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ASpli'
    finding HTML links ... done
    ASpli-deprecated                        html  
    ASpli-package                           html  
    ASpliAS-class                           html  
    ASpliCounts-class                       html  
    ASpliCounts                             html  
    ASpliDU-class                           html  
    ASpliFeatures-class                     html  
    ASpliIntegratedSignals-class            html  
    ASpliJDU-class                          html  
    ASpliSplicingReport-class               html  
    DUreport                                html  
    finding level-2 HTML links ... done

    DUreport.norm                           html  
    DUreport.offset                         html  
    DUreportBinSplice-method                html  
    acc_AS                                  html  
    acc_DU                                  html  
    acc_JDU                                 html  
    acc_MergedReport                        html  
    acc_counts                              html  
    acc_features                            html  
    acc_is                                  html  
    binGenome-methods                       html  
    binGenome                               html  
    containsJunctions-function              html  
    example_data                            html  
    exportIntegratedSignals                 html  
    exportSplicingReports                   html  
    filterDU-method                         html  
    filterSignals                           html  
    gbCounts                                html  
    gbDUreport-method                       html  
    getConditions-function                  html  
    integrateSignals                        html  
    jCounts-methods                         html  
    jDUreport                               html  
    junctionDUreport                        html  
    loadBAM                                 html  
    mergeBinDUAS-method                     html  
    plotBins                                html  
    plotGenomicRegions                      html  
    rds                                     html  
    show-methods                            html  
    splicingReport                          html  
    subset-methods                          html  
    write-methods                           html  
    write                                   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 'ASpli' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ASpli' as ASpli_2.3.1.zip
* DONE (ASpli)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'ASpli' successfully unpacked and MD5 sums checked

Tests output


Example timings

ASpli.Rcheck/examples_i386/ASpli-Ex.timings

nameusersystemelapsed
ASpli-package82.17 0.0882.36
DUreport000
DUreport.norm000
DUreport.offset000
DUreportBinSplice-method000
acc_AS000
acc_DU000
acc_counts000
acc_features0.150.000.16
binGenome2.460.002.45
containsJunctions-function000
example_data000
exportIntegratedSignals42.53 0.1342.66
exportSplicingReports42.45 0.0942.55
filterDU-method000
filterSignals000
gbCounts36.41 0.0136.42
gbDUreport-method36.84 0.0236.86
getConditions-function000
integrateSignals43.32 0.0043.33
jCounts-methods43.19 0.0343.22
jDUreport45.45 0.0245.47
junctionDUreport000
loadBAM000
mergeBinDUAS-method000
plotBins000
plotGenomicRegions000
rds000
splicingReport42.99 0.0143.00
subset-methods000

ASpli.Rcheck/examples_x64/ASpli-Ex.timings

nameusersystemelapsed
ASpli-package94.26 0.0994.36
DUreport000
DUreport.norm000
DUreport.offset000
DUreportBinSplice-method000
acc_AS000
acc_DU000
acc_counts000
acc_features0.150.000.15
binGenome2.580.022.60
containsJunctions-function000
example_data0.020.000.01
exportIntegratedSignals49.03 0.2249.35
exportSplicingReports51.15 0.1451.29
filterDU-method000
filterSignals000
gbCounts43.18 0.0043.17
gbDUreport-method42.53 0.0342.57
getConditions-function000
integrateSignals48.97 0.0149.09
jCounts-methods48.42 0.0348.45
jDUreport49.64 0.0049.66
junctionDUreport000
loadBAM000
mergeBinDUAS-method000
plotBins000
plotGenomicRegions000
rds000
splicingReport50.62 0.0550.67
subset-methods000