Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:57 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 traseR on machv2


To the developers/maintainers of the traseR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/traseR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1991/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
traseR 1.24.0  (landing page)
li chen
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/traseR
git_branch: RELEASE_3_14
git_last_commit: 5cb7974
git_last_commit_date: 2021-10-26 12:21:40 -0400 (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  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: traseR
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:traseR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings traseR_1.24.0.tar.gz
StartedAt: 2022-04-12 19:34:09 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:40:19 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 369.9 seconds
RetCode: 0
Status:   OK  
CheckDir: traseR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:traseR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings traseR_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/traseR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘traseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘traseR’ version ‘1.24.0’
* 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 ‘traseR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
* 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 ... NOTE
enrichTest: no visible global function definition for ‘chisq.test’
enrichTest: no visible global function definition for ‘binom.test’
enrichTest: no visible global function definition for ‘phyper’
plotContext: no visible global function definition for ‘subjectHits’
plotContext: no visible global function definition for ‘pie’
plotContext: no visible global function definition for ‘rainbow’
plotGene: no visible global function definition for ‘mtext’
plotGene: no visible global function definition for ‘axis’
plotGene: no visible global function definition for ‘box’
plotGene: no visible global function definition for ‘points’
plotGene: no visible global function definition for ‘text’
plotGene: no visible global function definition for ‘arrows’
plotGene: no visible global function definition for ‘segments’
plotInterval: no visible global function definition for ‘subjectHits’
plotInterval: no visible global function definition for ‘mtext’
plotInterval: no visible global function definition for ‘axis’
plotInterval: no visible global function definition for ‘box’
plotInterval: no visible global function definition for ‘points’
plotInterval: no visible global function definition for ‘text’
plotInterval: no visible global function definition for ‘arrows’
plotInterval: no visible global function definition for ‘segments’
plotPvalue: no visible global function definition for ‘boxplot’
plotPvalue: no visible global function definition for ‘density’
plotPvalue: no visible global function definition for ‘lines’
plotPvalue: no visible global function definition for ‘legend’
plotPvalue: no visible global function definition for ‘subjectHits’
plotSNP: no visible global function definition for ‘mtext’
plotSNP: no visible global function definition for ‘axis’
plotSNP: no visible global function definition for ‘box’
plotSNP: no visible global function definition for ‘points’
plotSNP: no visible global function definition for ‘text’
plotSNP: no visible global function definition for ‘arrows’
plotSNP: no visible global function definition for ‘segments’
queryKeyword: no visible global function definition for ‘subjectHits’
querySNP: no visible global function definition for ‘subjectHits’
traseR: no visible global function definition for ‘seqlengths’
traseR: no visible global function definition for ‘subjectHits’
traseR: no visible global function definition for ‘runif’
traseR: no visible global function definition for ‘Rle’
traseR: no visible global function definition for ‘queryHits’
traseR: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  Rle arrows axis binom.test box boxplot chisq.test density legend
  lines mtext p.adjust phyper pie points queryHits rainbow runif
  segments seqlengths subjectHits text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "arrows", "axis", "box", "boxplot", "legend",
             "lines", "mtext", "pie", "points", "segments", "text")
  importFrom("stats", "binom.test", "chisq.test", "density", "p.adjust",
             "phyper", "runif")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
print.traseR 8.193  0.226   8.423
traseR       6.591  0.085   6.681
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/traseR.Rcheck/00check.log’
for details.



Installation output

traseR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL traseR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘traseR’ ...
** 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 (traseR)

Tests output

traseR.Rcheck/tests/runTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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("traseR")

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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


Attaching package: 'Biostrings'

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

    strsplit

There are  128094211 bp in the query region, accounting for  0.0421875469310327  of the genome.
There are  573 traits in the analysis.
There are  33 trait class in the analysis.
100 traits have been tested!
200 traits have been tested!
300 traits have been tested!
400 traits have been tested!
500 traits have been tested!
10 trait class have been tested!
20 trait class have been tested!
30 trait class have been tested!


RUNIT TEST PROTOCOL -- Tue Apr 12 19:40:10 2022 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
traseR 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 
 27.534   0.950  28.485 

Example timings

traseR.Rcheck/traseR-Ex.timings

nameusersystemelapsed
plots1.5920.0511.645
print.traseR8.1930.2268.423
querys1.5010.0341.536
traseR6.5910.0856.681