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CHECK report for ASpli on malbec1

This page was generated on 2020-08-11 11:22:37 -0400 (Tue, 11 Aug 2020).

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 89/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 1.99.2
Estefania Mancini
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/ASpli
Branch: master
Last Commit: dda9b82
Last Changed Date: 2020-07-21 10:22:53 -0400 (Tue, 21 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ASpli
Version: 1.99.2
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ASpli_1.99.2.tar.gz
StartedAt: 2020-08-11 02:30:51 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 02:48:23 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 1052.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ASpli.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ASpli_1.99.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ASpli.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ASpli/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASpli’ version ‘1.99.2’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
ASpli-package           135.620  0.276 135.213
splicingReport           75.668  0.044  74.649
integrateSignals         74.176  0.028  73.354
exportSplicingReports    72.676  0.324  72.179
jDUreport                72.420  0.016  71.513
exportIntegratedSignals  71.156  0.776  71.040
jCounts-methods          71.480  0.024  70.569
gbDUreport-method        68.672  0.080  67.886
gbCounts                 60.992  0.080  60.069
* 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:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ASpli
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ASpli’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (ASpli)

Tests output


Example timings

ASpli.Rcheck/ASpli-Ex.timings

nameusersystemelapsed
ASpli-package135.620 0.276135.213
DUreport000
DUreport.norm000
DUreport.offset000
DUreportBinSplice-method000
acc_AS0.0000.0000.001
acc_DU000
acc_counts000
acc_features0.2680.0000.265
binGenome4.1240.0004.471
containsJunctions-function000
example_data000
exportIntegratedSignals71.156 0.77671.040
exportSplicingReports72.676 0.32472.179
filterDU-method000
filterSignals000
gbCounts60.992 0.08060.069
gbDUreport-method68.672 0.08067.886
getConditions-function000
integrateSignals74.176 0.02873.354
jCounts-methods71.480 0.02470.569
jDUreport72.420 0.01671.513
junctionDUreport000
loadBAM000
mergeBinDUAS-method000
plotBins000
plotGenomicRegions0.0040.0000.001
rds000
splicingReport75.668 0.04474.649
subset-methods0.0040.0000.001