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CHECK report for ASpli on merida1

This page was generated on 2020-04-15 12:44:02 -0400 (Wed, 15 Apr 2020).

Package 91/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 1.12.0
Estefania Mancini
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ASpli
Branch: RELEASE_3_10
Last Commit: 23929ac
Last Changed Date: 2019-10-29 13:09:57 -0400 (Tue, 29 Oct 2019)
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 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ASpli
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2020-04-15 00:29:26 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:37:04 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 458.1 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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ASpli.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.0’
* 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         21.069  0.156  21.469
plotBins                   14.178  0.045  14.366
ASpli-package              11.276  0.292  11.693
mergeBinDUAS-method        11.093  0.097  11.303
AsDiscover-methods          8.490  0.042   8.637
subset-methods              7.836  0.023   7.954
junctionDUreport            6.733  0.021   6.804
readCounts                  6.439  0.065   6.566
containsJunctions-function  6.442  0.023   6.501
rds                         6.425  0.024   6.534
DUreportBinSplice-method    6.399  0.022   6.466
DUreport                    6.226  0.024   6.312
filterDU-method             6.114  0.022   6.169
* 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/3.6/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-package11.276 0.29211.693
AsDiscover-methods8.4900.0428.637
DUreport6.2260.0246.312
DUreportBinSplice-method6.3990.0226.466
acc_AS0.0220.0020.024
acc_DU0.0080.0010.009
acc_counts0.0170.0010.020
acc_features0.3060.0010.308
binGenome3.1680.0133.208
containsJunctions-function6.4420.0236.501
example_data0.7620.0110.790
filterDU-method6.1140.0226.169
getConditions-function0.0100.0010.010
junctionDUreport6.7330.0216.804
loadBAM0.1770.0030.184
mergeBinDUAS-method11.093 0.09711.303
plotBins14.178 0.04514.366
plotGenomicRegions21.069 0.15621.469
rds6.4250.0246.534
readCounts6.4390.0656.566
subset-methods7.8360.0237.954