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CHECK report for ASpli on merida2

This page was generated on 2018-10-17 08:56:55 -0400 (Wed, 17 Oct 2018).

Package 77/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 1.6.0
Estefania Mancini
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ASpli
Branch: RELEASE_3_7
Last Commit: 2d246b3
Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ASpli
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2018-10-16 19:56:25 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:02:46 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 381.1 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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ASpli.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.0’
* 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 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 or elapsed time > 5s
                             user system elapsed
plotGenomicRegions         17.325  0.104  17.619
plotBins                   11.492  0.067  11.694
ASpli-package               8.786  0.263   9.135
mergeBinDUAS-method         8.598  0.027   8.729
subset-methods              7.195  0.024   7.267
AsDiscover-methods          6.481  0.069   6.591
containsJunctions-function  5.519  0.020   5.596
rds                         5.291  0.019   5.371
junctionDUreport            5.270  0.018   5.337
DUreportBinSplice-method    5.210  0.023   5.275
readCounts                  5.157  0.022   5.224
filterDU-method             5.004  0.017   5.069
* 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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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ASpli
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ASpli’ ...
** 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
* DONE (ASpli)

Tests output


Example timings

ASpli.Rcheck/ASpli-Ex.timings

nameusersystemelapsed
ASpli-package8.7860.2639.135
AsDiscover-methods6.4810.0696.591
DUreport4.8490.0204.904
DUreportBinSplice-method5.2100.0235.275
acc_AS0.0240.0020.026
acc_DU0.0120.0010.014
acc_counts0.0240.0020.027
acc_features0.2010.0000.204
binGenome2.8080.0102.846
containsJunctions-function5.5190.0205.596
example_data0.5520.0120.572
filterDU-method5.0040.0175.069
getConditions-function0.0140.0000.014
junctionDUreport5.2700.0185.337
loadBAM0.1710.0040.175
mergeBinDUAS-method8.5980.0278.729
plotBins11.492 0.06711.694
plotGenomicRegions17.325 0.10417.619
rds5.2910.0195.371
readCounts5.1570.0225.224
subset-methods7.1950.0247.267