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CHECK report for acde on malbec1

This page was generated on 2020-10-01 10:45:28 -0400 (Thu, 01 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE acde PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 11/1923HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
acde 1.19.0
Juan Pablo Acosta
Snapshot Date: 2020-09-30 14:42:00 -0400 (Wed, 30 Sep 2020)
URL: https://git.bioconductor.org/packages/acde
Branch: master
Last Commit: b0efcae
Last Changed Date: 2020-04-27 14:49:17 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  NA 

Summary

Package: acde
Version: 1.19.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:acde.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings acde_1.19.0.tar.gz
StartedAt: 2020-10-01 02:29:28 -0400 (Thu, 01 Oct 2020)
EndedAt: 2020-10-01 02:30:48 -0400 (Thu, 01 Oct 2020)
EllapsedTime: 80.2 seconds
RetCode: 0
Status:  OK 
CheckDir: acde.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:acde.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings acde_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/acde.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 ‘acde/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘acde’ version ‘1.19.0’
* 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 ‘acde’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
bcaFDR 47.364  0.084  47.537
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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

acde.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL acde
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘acde’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (acde)

Tests output

acde.Rcheck/tests/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("acde")


RUNIT TEST PROTOCOL -- Thu Oct  1 02:30:44 2020 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
acde RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.172   0.056   1.235 

Example timings

acde.Rcheck/acde-Ex.timings

nameusersystemelapsed
ac0.3240.0240.346
acde-package2.9600.0162.982
bcaFDR47.364 0.08447.537
fdr0.4080.0080.417
phytophthora0.0200.0000.018
plot.STP0.5200.0000.521
plot.TC2.2960.0082.309
print.STP0.6240.0000.628
print.TC1.5680.0001.571
qval0.7560.0000.761
stp0.520.000.52
tc1.8560.0001.859