Back to Multiple platform build/check report for BioC 3.12
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for ASpli on tokay1

This page was generated on 2021-05-06 12:29:56 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the ASpli package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 95/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 2.0.0  (landing page)
Estefania Mancini
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ASpli
Branch: RELEASE_3_12
Last Commit: 641dc04
Last Changed Date: 2020-10-27 11:16:38 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: ASpli
Version: 2.0.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASpli.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ASpli_2.0.0.tar.gz
StartedAt: 2021-05-06 00:30:57 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:02:17 -0400 (Thu, 06 May 2021)
EllapsedTime: 1879.7 seconds
RetCode: 0
Status:   OK   
CheckDir: ASpli.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASpli.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ASpli_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ASpli.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '2.0.0'
* 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 '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 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           141.94   1.68  143.72
exportIntegratedSignals  76.15   0.14   78.03
exportSplicingReports    73.14   0.16   73.68
integrateSignals         70.13   0.02   70.50
gbDUreport-method        59.26   0.05   59.33
jCounts-methods          59.29   0.01   59.31
jDUreport                58.63   0.02   59.75
gbCounts                 55.33   0.01   55.36
splicingReport           54.28   0.02   54.29
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
ASpli-package           127.14   0.11  127.39
integrateSignals         73.00   0.00   73.00
splicingReport           70.56   0.02   70.58
jDUreport                67.09   0.04   67.17
jCounts-methods          64.55   0.02   64.57
exportIntegratedSignals  63.53   0.15   67.79
gbCounts                 61.88   0.06   66.89
gbDUreport-method        59.95   0.02   60.25
exportSplicingReports    59.35   0.13   62.94
* 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://172.29.0.3/BBS/3.12/bioc/src/contrib/ASpli_2.0.0.tar.gz && rm -rf ASpli.buildbin-libdir && mkdir ASpli.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASpli.buildbin-libdir ASpli_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ASpli_2.0.0.zip && rm ASpli_2.0.0.tar.gz ASpli_2.0.0.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
100 4047k  100 4047k    0     0  17.8M      0 --:--:-- --:--:-- --:--:-- 17.9M

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_2.0.0.zip
* DONE (ASpli)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ASpli' successfully unpacked and MD5 sums checked

Tests output


Example timings

ASpli.Rcheck/examples_i386/ASpli-Ex.timings

nameusersystemelapsed
ASpli-package141.94 1.68143.72
DUreport000
DUreport.norm000
DUreport.offset0.010.000.01
DUreportBinSplice-method000
acc_AS000
acc_DU000
acc_counts000
acc_features0.430.010.44
binGenome4.750.004.75
containsJunctions-function000
example_data000
exportIntegratedSignals76.15 0.1478.03
exportSplicingReports73.14 0.1673.68
filterDU-method000
filterSignals000
gbCounts55.33 0.0155.36
gbDUreport-method59.26 0.0559.33
getConditions-function000
integrateSignals70.13 0.0270.50
jCounts-methods59.29 0.0159.31
jDUreport58.63 0.0259.75
junctionDUreport000
loadBAM000
mergeBinDUAS-method000
plotBins000
plotGenomicRegions000
rds000
splicingReport54.28 0.0254.29
subset-methods000

ASpli.Rcheck/examples_x64/ASpli-Ex.timings

nameusersystemelapsed
ASpli-package127.14 0.11127.39
DUreport000
DUreport.norm000
DUreport.offset000
DUreportBinSplice-method000
acc_AS000
acc_DU000
acc_counts000
acc_features0.270.000.27
binGenome2.900.022.92
containsJunctions-function000
example_data000
exportIntegratedSignals63.53 0.1567.79
exportSplicingReports59.35 0.1362.94
filterDU-method000
filterSignals000
gbCounts61.88 0.0666.89
gbDUreport-method59.95 0.0260.25
getConditions-function000
integrateSignals73 073
jCounts-methods64.55 0.0264.57
jDUreport67.09 0.0467.17
junctionDUreport000
loadBAM000
mergeBinDUAS-method000
plotBins000
plotGenomicRegions000
rds000
splicingReport70.56 0.0270.58
subset-methods000