Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:11 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for dagLogo on tokay2


To the developers/maintainers of the dagLogo package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dagLogo.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 446/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dagLogo 1.32.0  (landing page)
Jianhong Ou
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/dagLogo
git_branch: RELEASE_3_14
git_last_commit: 5a04a5f
git_last_commit_date: 2021-10-26 12:10:15 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  NO, package depends on 'UniProt.ws' which is not available
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: dagLogo
Version: 1.32.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dagLogo.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings dagLogo_1.32.0.tar.gz
StartedAt: 2022-01-20 18:23:39 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 18:28:27 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 288.5 seconds
RetCode: 0
Status:   OK  
CheckDir: dagLogo.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dagLogo.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings dagLogo_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/dagLogo.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dagLogo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dagLogo' version '1.32.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
testDAU              30.60   0.22   30.81
buildBackgroundModel 10.26   0.07   10.75
formatSequence       10.03   0.00   10.03
dagLogo               5.14   0.06    5.20
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
testDAU              28.41   0.06   28.48
buildBackgroundModel  8.50   0.00    8.50
formatSequence        6.50   0.00    6.50
dagLogo               5.05   0.08    5.12
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/dagLogo_1.32.0.tar.gz && rm -rf dagLogo.buildbin-libdir && mkdir dagLogo.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dagLogo.buildbin-libdir dagLogo_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL dagLogo_1.32.0.zip && rm dagLogo_1.32.0.tar.gz dagLogo_1.32.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 52 2032k   52 1062k    0     0  2223k      0 --:--:-- --:--:-- --:--:-- 2223k
100 2032k  100 2032k    0     0  2834k      0 --:--:-- --:--:-- --:--:-- 2835k

install for i386

* 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
  converting help for package 'dagLogo'
    finding HTML links ... done
    Proteome-class                          html  
    addScheme                               html  
    availableSchemes                        html  
    buildBackgroundModel                    html  
    buildZTestBackgroundModel               html  
    cleanPeptides                           html  
    colorsets                               html  
    colorsets2                              html  
    dagBackground-class                     html  
    dagHeatmap                              html  
    dagLogo-package                         html  
    dagLogo                                 html  
    dagPeptides-class                       html  
    ecoli.proteome                          html  
    fetchSequence                           html  
    formatSequence                          html  
    getData                                 html  
    getGroupingSymbol                       html  
    initiateBackgroundModel                 html  
    nameHash                                html  
    prepareProteome                         html  
    finding level-2 HTML links ... done

    prepareProteomeByFTP                    html  
    prepareProteomeByUniProtWS              html  
    proteome.example                        html  
    seq.example                             html  
    testDAU                                 html  
    testDAUresults-class                    html  
** 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

install for x64

* installing *source* package 'dagLogo' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dagLogo' as dagLogo_1.32.0.zip
* DONE (dagLogo)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'dagLogo' successfully unpacked and MD5 sums checked

Tests output

dagLogo.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

Attaching package: 'BiocGenerics'

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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    pattern

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 
   7.50    0.50    7.98 

dagLogo.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'BiocGenerics'

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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    pattern

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 
   7.26    0.42    7.67 

Example timings

dagLogo.Rcheck/examples_i386/dagLogo-Ex.timings

nameusersystemelapsed
addScheme000
buildBackgroundModel10.26 0.0710.75
cleanPeptides000
colorsets000
dagHeatmap0.910.020.92
dagLogo-package1.780.191.97
dagLogo5.140.065.20
ecoli.proteome0.060.030.10
fetchSequence000
formatSequence10.03 0.0010.03
getGroupingSymbol000
prepareProteome000
prepareProteomeByFTP0.020.000.01
prepareProteomeByUniProtWS000
proteome.example0.030.000.04
seq.example0.010.000.01
testDAU30.60 0.2230.81

dagLogo.Rcheck/examples_x64/dagLogo-Ex.timings

nameusersystemelapsed
addScheme000
buildBackgroundModel8.50.08.5
cleanPeptides000
colorsets000
dagHeatmap0.590.030.63
dagLogo-package1.920.112.03
dagLogo5.050.085.12
ecoli.proteome0.060.000.07
fetchSequence000
formatSequence6.50.06.5
getGroupingSymbol000
prepareProteome000
prepareProteomeByFTP0.020.000.01
prepareProteomeByUniProtWS000
proteome.example0.010.000.02
seq.example000
testDAU28.41 0.0628.48