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CHECK report for ASpli on merida1

This page was generated on 2020-08-13 11:55:11 -0400 (Thu, 13 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: 2020-08-12 14:52:00 -0400 (Wed, 12 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  OK 
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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ASpli.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASpli_1.99.2.tar.gz
StartedAt: 2020-08-13 02:30:46 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 02:49:17 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 1111.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ASpli.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ASpli.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASpli_1.99.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ASpli.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
ASpli-package           135.402  0.679 136.875
exportIntegratedSignals  71.731  0.309  72.742
jCounts-methods          71.745  0.171  71.974
splicingReport           71.583  0.191  71.893
integrateSignals         71.375  0.196  71.646
exportSplicingReports    70.926  0.367  71.586
jDUreport                70.367  0.164  70.603
gbDUreport-method        65.668  0.174  65.918
gbCounts                 58.204  0.166  58.451
* 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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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ASpli
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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-package135.402 0.679136.875
DUreport0.0010.0010.001
DUreport.norm000
DUreport.offset0.0010.0000.000
DUreportBinSplice-method0.0000.0010.000
acc_AS0.0000.0010.001
acc_DU0.0010.0010.001
acc_counts0.0000.0010.001
acc_features0.4020.0010.403
binGenome4.9220.0204.948
containsJunctions-function000
example_data0.0010.0010.000
exportIntegratedSignals71.731 0.30972.742
exportSplicingReports70.926 0.36771.586
filterDU-method0.0010.0020.002
filterSignals000
gbCounts58.204 0.16658.451
gbDUreport-method65.668 0.17465.918
getConditions-function0.0000.0000.001
integrateSignals71.375 0.19671.646
jCounts-methods71.745 0.17171.974
jDUreport70.367 0.16470.603
junctionDUreport000
loadBAM000
mergeBinDUAS-method0.0000.0010.001
plotBins0.0010.0010.001
plotGenomicRegions0.0000.0010.001
rds0.0000.0010.000
splicingReport71.583 0.19171.893
subset-methods0.0000.0010.001