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CHECK report for ASpli on machv2

This page was generated on 2020-10-17 11:58:04 -0400 (Sat, 17 Oct 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 92/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 1.14.0
Estefania Mancini
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ASpli
Branch: RELEASE_3_11
Last Commit: 912b01b
Last Changed Date: 2020-04-27 15:00:04 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ASpli
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2020-10-16 22:44:59 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:00:33 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 934.0 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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ASpli.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.14.0’
* 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 (user + system) or elapsed time > 5s
                             user system elapsed
mergeBinDUAS-method        14.227  0.045  14.290
ASpli-package              12.866  0.398  13.395
AsDiscover-methods         10.734  0.120  10.868
subset-methods             10.081  0.093  10.611
containsJunctions-function  8.441  0.032   8.479
DUreport                    8.372  0.038   8.423
junctionDUreport            8.312  0.042   8.448
DUreportBinSplice-method    8.147  0.038   8.195
filterDU-method             8.025  0.035   8.071
rds                         7.884  0.036   7.935
readCounts                  7.757  0.030   7.796
* 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-package12.866 0.39813.395
AsDiscover-methods10.734 0.12010.868
DUreport8.3720.0388.423
DUreportBinSplice-method8.1470.0388.195
acc_AS0.0360.0040.042
acc_DU0.0130.0020.015
acc_counts0.0270.0040.031
acc_features0.4620.0010.465
binGenome4.2090.0194.232
containsJunctions-function8.4410.0328.479
example_data0.8320.0160.854
filterDU-method8.0250.0358.071
getConditions-function0.0090.0010.010
junctionDUreport8.3120.0428.448
loadBAM0.2120.0040.217
mergeBinDUAS-method14.227 0.04514.290
rds7.8840.0367.935
readCounts7.7570.0307.796
subset-methods10.081 0.09310.611