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CHECK report for ASpli on malbec2

This page was generated on 2019-10-16 12:09:24 -0400 (Wed, 16 Oct 2019).

Package 87/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 1.10.0
Estefania Mancini
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ASpli
Branch: RELEASE_3_9
Last Commit: d96e718
Last Changed Date: 2019-05-02 11:54:03 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ASpli
Version: 1.10.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ASpli_1.10.0.tar.gz
StartedAt: 2019-10-15 23:51:19 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 23:57:41 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 382.0 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-3.9-bioc/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ASpli_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ASpli.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.10.0’
* 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 or elapsed time > 5s
                             user system elapsed
plotGenomicRegions         17.087  0.047  17.209
plotBins                    9.217  0.007   9.261
ASpli-package               8.933  0.200   9.181
mergeBinDUAS-method         8.801  0.008   8.843
subset-methods              6.232  0.012   6.289
junctionDUreport            5.707  0.004   5.753
containsJunctions-function  5.589  0.001   5.605
rds                         5.318  0.005   5.322
readCounts                  5.243  0.004   5.258
filterDU-method             5.153  0.004   5.171
AsDiscover-methods          5.088  0.012   5.108
* 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:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ASpli
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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-package8.9330.2009.181
AsDiscover-methods5.0880.0125.108
DUreport4.5990.0084.613
DUreportBinSplice-method4.5810.0004.604
acc_AS0.0230.0040.060
acc_DU0.0090.0000.019
acc_counts0.0210.0000.030
acc_features0.2450.0000.246
binGenome2.8030.0002.806
containsJunctions-function5.5890.0015.605
example_data0.6030.0090.633
filterDU-method5.1530.0045.171
getConditions-function0.0070.0000.008
junctionDUreport5.7070.0045.753
loadBAM0.1820.0080.191
mergeBinDUAS-method8.8010.0088.843
plotBins9.2170.0079.261
plotGenomicRegions17.087 0.04717.209
rds5.3180.0055.322
readCounts5.2430.0045.258
subset-methods6.2320.0126.289