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CHECK report for ASpli on tokay1

This page was generated on 2020-04-15 12:27:03 -0400 (Wed, 15 Apr 2020).

Package 91/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 1.12.0
Estefania Mancini
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ASpli
Branch: RELEASE_3_10
Last Commit: 23929ac
Last Changed Date: 2019-10-29 13:09:57 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ASpli
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASpli.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ASpli_1.12.0.tar.gz
StartedAt: 2020-04-15 01:21:43 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:31:24 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 581.6 seconds
RetCode: 0
Status:  OK  
CheckDir: ASpli.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASpli.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ASpli_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ASpli.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '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 '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 or elapsed time > 5s
                     user system elapsed
plotGenomicRegions  12.87   0.11   13.17
plotBins             8.63   0.31    8.94
mergeBinDUAS-method  7.46   0.05    7.52
ASpli-package        6.39   1.03    7.58
subset-methods       5.16   0.01    5.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plotGenomicRegions         20.01   0.11   20.13
ASpli-package              10.69   0.04   10.75
mergeBinDUAS-method        10.55   0.16   10.70
plotBins                   10.09   0.06   10.16
AsDiscover-methods          8.78   0.02    8.80
junctionDUreport            8.75   0.01    8.77
subset-methods              6.99   0.03    7.02
DUreportBinSplice-method    6.75   0.00    6.75
readCounts                  6.59   0.02    6.62
rds                         5.97   0.00    5.97
containsJunctions-function  5.83   0.02    5.85
DUreport                    5.54   0.00    5.53
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/ASpli_1.12.0.tar.gz && rm -rf ASpli.buildbin-libdir && mkdir ASpli.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASpli.buildbin-libdir ASpli_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ASpli_1.12.0.zip && rm ASpli_1.12.0.tar.gz ASpli_1.12.0.zip
###
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  % 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 2227k  100 2227k    0     0  7325k      0 --:--:-- --:--:-- --:--:-- 7425k

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-package                           html  
    ASpliAS-class                           html  
    ASpliCounts-class                       html  
    ASpliCounts                             html  
    ASpliDU-class                           html  
    ASpliFeatures-class                     html  
    AsDiscover-methods                      html  
    DUreport                                html  
    finding level-2 HTML links ... done

    DUreportBinSplice-method                html  
    acc_AS                                  html  
    acc_DU                                  html  
    acc_counts                              html  
    acc_features                            html  
    binGenome-methods                       html  
    binGenome                               html  
    containsJunctions-function              html  
    example_data                            html  
    filterDU-method                         html  
    getConditions-function                  html  
    junctionDUreport                        html  
    loadBAM                                 html  
    mergeBinDUAS-method                     html  
    plotBins                                html  
    plotGenomicRegions                      html  
    rds                                     html  
    readCounts                              html  
    show-methods                            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_1.12.0.zip
* DONE (ASpli)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ASpli' successfully unpacked and MD5 sums checked

Tests output


Example timings

ASpli.Rcheck/examples_i386/ASpli-Ex.timings

nameusersystemelapsed
ASpli-package6.391.037.58
AsDiscover-methods4.820.064.87
DUreport3.960.003.95
DUreportBinSplice-method3.910.033.97
acc_AS0.030.000.30
acc_DU0.020.000.08
acc_counts0.060.000.40
acc_features0.190.000.19
binGenome2.090.022.11
containsJunctions-function4.430.014.44
example_data0.580.030.80
filterDU-method4.370.054.42
getConditions-function0.020.000.02
junctionDUreport4.370.004.37
loadBAM0.150.000.14
mergeBinDUAS-method7.460.057.52
plotBins8.630.318.94
plotGenomicRegions12.87 0.1113.17
rds4.180.004.17
readCounts3.900.053.95
subset-methods5.160.015.17

ASpli.Rcheck/examples_x64/ASpli-Ex.timings

nameusersystemelapsed
ASpli-package10.69 0.0410.75
AsDiscover-methods8.780.028.80
DUreport5.540.005.53
DUreportBinSplice-method6.750.006.75
acc_AS0.030.000.03
acc_DU0.010.000.02
acc_counts0.030.000.03
acc_features0.330.000.32
binGenome3.500.043.55
containsJunctions-function5.830.025.85
example_data0.750.060.81
filterDU-method4.810.024.83
getConditions-function0.020.000.01
junctionDUreport8.750.018.77
loadBAM0.250.000.25
mergeBinDUAS-method10.55 0.1610.70
plotBins10.09 0.0610.16
plotGenomicRegions20.01 0.1120.13
rds5.970.005.97
readCounts6.590.026.62
subset-methods6.990.037.02