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CHECK report for ASpediaFI on malbec1

This page was generated on 2020-08-07 11:50:25 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ASpediaFI PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 88/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpediaFI 1.3.0
Doyeong Yu
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/ASpediaFI
Branch: master
Last Commit: 1255415
Last Changed Date: 2020-04-27 15:31:42 -0400 (Mon, 27 Apr 2020)
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 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ASpediaFI
Version: 1.3.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ASpediaFI.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ASpediaFI_1.3.0.tar.gz
StartedAt: 2020-08-07 05:13:07 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 05:20:30 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 443.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ASpediaFI.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:ASpediaFI.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ASpediaFI_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ASpediaFI.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 ‘ASpediaFI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASpediaFI’ version ‘1.3.0’
* package encoding: UTF-8
* 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 ‘ASpediaFI’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
annotateASevents 55.82    0.3  56.203
* 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

ASpediaFI.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ASpediaFI
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ASpediaFI’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'as.table' in package 'ASpediaFI'
** 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 (ASpediaFI)

Tests output


Example timings

ASpediaFI.Rcheck/ASpediaFI-Ex.timings

nameusersystemelapsed
ASpediaFI-accessor0.1280.0080.136
ASpediaFI-class0.0440.0000.042
GSE114922.fpkm0.0320.0000.029
GSE114922.psi0.0840.0000.083
analyzeFI0.1920.0080.200
annotateASevents55.820 0.30056.203
exportNetwork0.0240.0000.041
quantifyPSI0.0160.0000.014
visualize000