Package: dagLogo

Version: 1.22.3

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:dagLogo.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings dagLogo_1.22.3.tar.gz

StartedAt: 2019-10-16 00:56:58 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:02:40 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 341.8 seconds

RetCode: 0

Status:  OK

CheckDir: dagLogo.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:dagLogo.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings dagLogo_1.22.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/dagLogo.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 ‘dagLogo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dagLogo’ version ‘1.22.3’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘UniProt.ws’
  All declared Imports should be used.
* 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 or elapsed time > 5s
                       user system elapsed
testDAU              39.649  0.044  40.006
buildBackgroundModel 10.804  0.076  10.976
dagLogo               8.547  0.083   8.730
formatSequence        8.415  0.000   8.430
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/dagLogo.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL dagLogo
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘dagLogo’ ...
** using staged installation
** R
** data
** 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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: biomaRt
Loading required package: grImport2
Loading required package: grid
Loading required package: motifStack
Loading required package: MotIV
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, which.max, which.min


Attaching package: 'MotIV'

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

    filter

Loading required package: ade4

Attaching package: 'ade4'

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

    score

Loading required package: Biostrings
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("Biostrings") || stop("unable to load Package:Biostrings")
[1] TRUE
> require("biomaRt") || stop("unable to load Package:biomaRt")
[1] TRUE
> data(seq.example)
> data(proteome.example)
> library(testthat)
> 
> test_check("dagLogo")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 3 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 16.179   0.513  16.865 

name	user	system	elapsed
addScheme	0.001	0.000	0.001
buildBackgroundModel	10.804	0.076	10.976
cleanPeptides	0.005	0.000	0.096
colorsets	0.001	0.000	0.000
dagHeatmap	1.528	0.008	1.546
dagLogo-package	3.336	0.064	3.405
dagLogo	8.547	0.083	8.730
ecoli.proteome	0.246	0.000	0.247
fetchSequence	0.001	0.003	0.004
formatSequence	8.415	0.000	8.430
getGroupingSymbol	0	0	0
prepareProteome	0.001	0.000	0.000
proteome.example	0.061	0.000	0.061
seq.example	0.024	0.000	0.023
testDAU	39.649	0.044	40.006