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CHECK report for ASpli on malbec2

This page was generated on 2020-10-17 11:54:23 -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: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ASpli_1.14.0.tar.gz
StartedAt: 2020-10-16 22:57:56 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:05:33 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 457.1 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-3.11-bioc/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ASpli_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/ASpli.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.14.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
mergeBinDUAS-method        10.426  0.032  10.458
ASpli-package               9.137  0.168  13.329
junctionDUreport            7.125  0.000   7.125
subset-methods              7.067  0.004   7.071
AsDiscover-methods          6.633  0.000   6.638
DUreportBinSplice-method    6.025  0.020   6.057
readCounts                  6.040  0.004   6.045
containsJunctions-function  6.023  0.000   6.024
DUreport                    5.693  0.012   5.710
filterDU-method             5.233  0.000   5.233
rds                         5.060  0.000   5.061
* 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-3.11-bioc/R/bin/R CMD INSTALL ASpli
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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-package 9.137 0.16813.329
AsDiscover-methods6.6330.0006.638
DUreport5.6930.0125.710
DUreportBinSplice-method6.0250.0206.057
acc_AS0.0190.0040.023
acc_DU0.0070.0000.007
acc_counts0.0080.0080.016
acc_features0.3170.0000.317
binGenome2.7560.0042.760
containsJunctions-function6.0230.0006.024
example_data0.5590.0080.568
filterDU-method5.2330.0005.233
getConditions-function0.0050.0000.005
junctionDUreport7.1250.0007.125
loadBAM0.1360.0040.141
mergeBinDUAS-method10.426 0.03210.458
rds5.0600.0005.061
readCounts6.0400.0046.045
subset-methods7.0670.0047.071