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CHECK report for dagLogo on malbec1

This page was generated on 2021-05-06 12:27:18 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the dagLogo package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 421/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dagLogo 1.28.1  (landing page)
Jianhong Ou
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/dagLogo
Branch: RELEASE_3_12
Last Commit: 28e6088
Last Changed Date: 2020-12-03 08:26:09 -0400 (Thu, 03 Dec 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: dagLogo
Version: 1.28.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:dagLogo.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings dagLogo_1.28.1.tar.gz
StartedAt: 2021-05-06 00:38:36 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:42:33 -0400 (Thu, 06 May 2021)
EllapsedTime: 236.3 seconds
RetCode: 0
Status:   OK  
CheckDir: dagLogo.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:dagLogo.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings dagLogo_1.28.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/dagLogo.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dagLogo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dagLogo’ version ‘1.28.1’
* 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 ‘dagLogo’ 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
testDAU              33.352  0.080  33.488
buildBackgroundModel 10.536  0.028  10.603
formatSequence        7.400  0.000   7.414
dagLogo               6.556  0.036   6.607
* 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

dagLogo.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL dagLogo
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘dagLogo’ ...
** 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 (dagLogo)

Tests output

dagLogo.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> require("dagLogo") || stop("unable to load Package:dagLogo")
Loading required package: dagLogo
Loading required package: grid
[1] TRUE
> require("Biostrings") || stop("unable to load Package:Biostrings")
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

[1] TRUE
> require("biomaRt") || stop("unable to load Package:biomaRt")
Loading required package: biomaRt
[1] TRUE
> data(seq.example)
> data(proteome.example)
> library(testthat)
> 
> test_check("dagLogo")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (4)

[ FAIL 0 | WARN 0 | SKIP 4 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
  9.568   0.240  11.505 

Example timings

dagLogo.Rcheck/dagLogo-Ex.timings

nameusersystemelapsed
addScheme0.0040.0000.001
buildBackgroundModel10.536 0.02810.603
cleanPeptides0.0080.0000.015
colorsets0.0040.0000.000
dagHeatmap1.3120.0281.353
dagLogo-package2.5720.0242.611
dagLogo6.5560.0366.607
ecoli.proteome0.0880.0040.093
fetchSequence0.0000.0000.003
formatSequence7.4000.0007.414
getGroupingSymbol000
prepareProteome000
prepareProteomeByFTP0.0080.0040.012
prepareProteomeByUniProtWS000
proteome.example0.0120.0000.012
seq.example0.0080.0000.005
testDAU33.352 0.08033.488