Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:40 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 plethy on nebbiolo1


To the developers/maintainers of the plethy package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plethy.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 1464/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plethy 1.34.0  (landing page)
Daniel Bottomly
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/plethy
git_branch: RELEASE_3_15
git_last_commit: 6c951e4
git_last_commit_date: 2022-04-26 11:14:59 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: plethy
Version: 1.34.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:plethy.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings plethy_1.34.0.tar.gz
StartedAt: 2022-10-18 21:09:31 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 21:11:35 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 123.7 seconds
RetCode: 0
Status:   OK  
CheckDir: plethy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:plethy.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings plethy_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/plethy.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plethy/DESCRIPTION’ ... OK
* this is package ‘plethy’ version ‘1.34.0’
* 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 ‘plethy’ 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘csv.to.table’ ‘find.break.ranges.integer’ ‘fix.time’ ‘multi.grep’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
generate.sample.buxco : <anonymous> : <anonymous> : <anonymous> :
  <anonymous>: no visible global function definition for ‘rnorm’
make.db.package: no visible global function definition for
  ‘packageDescription’
mvtsplot.data.frame: no visible global function definition for ‘colors’
mvtsplot.data.frame: no visible global function definition for ‘par’
mvtsplot.data.frame: no visible global function definition for ‘layout’
mvtsplot.data.frame: no visible global function definition for
  ‘strwidth’
mvtsplot.data.frame: no visible global function definition for ‘abline’
mvtsplot.data.frame: no visible global function definition for ‘mtext’
mvtsplot.data.frame: no visible global function definition for ‘bxp’
mvtsplot.data.frame : <anonymous>: no visible binding for global
  variable ‘median’
mvtsplot.data.frame: no visible global function definition for ‘lines’
mvtsplot.data.frame: no visible global function definition for ‘Axis’
mvtsplot.data.frame: no visible global function definition for ‘legend’
retrieveMatrix,BuxcoDB: no visible global function definition for
  ‘terms’
tsplot,BuxcoDB: no visible binding for global variable ‘Days’
tsplot,BuxcoDB: no visible binding for global variable ‘Value’
tsplot,BuxcoDB: no visible binding for global variable ‘Sample_Name’
Undefined global functions or variables:
  Axis Days Sample_Name Value abline bxp colors layout legend lines
  median mtext packageDescription par rnorm strwidth terms
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "Axis", "abline", "bxp", "layout", "legend",
             "lines", "mtext", "par", "strwidth")
  importFrom("stats", "median", "rnorm", "terms")
  importFrom("utils", "packageDescription")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/plethy.Rcheck/00check.log’
for details.



Installation output

plethy.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL plethy
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘plethy’ ...
** using staged installation
** R
** 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 (plethy)

Tests output

plethy.Rcheck/tests/runTests.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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("plethy")

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

Loading required package: reshape2
Processing /tmp/RtmpnSvFZu/file18bc4943039e89 in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_1
Sample written
Processing breakpoint 2
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Processing breakpoint 3
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Sample written
Processing breakpoint 5
Starting sample sample_1
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Sample written
Processing breakpoint 6
Starting sample sample_2
Sample written
Starting sample sample_3
Sample written
Reached the end of the file, writing remaining data
Starting sample sample_3
Sample written
Processing /tmp/RtmpnSvFZu/file18bc493f1ecbcf in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_1
Sample written
Reached the end of the file, writing remaining data
Starting sample sample_1
Sample written
Starting sample sample_2
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Sample written
Processing /tmp/RtmpnSvFZu/file18bc49335c384a in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_4
Sample written
Processing breakpoint 2
Starting sample sample_4
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Sample written
Reached the end of the file, writing remaining data
Starting sample sample_5
Sample written
Processing /tmp/RtmpnSvFZu/file18bc497915c0cc in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_1
Sample written
Processing breakpoint 2
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Reached the end of the file, writing remaining data
Starting sample sample_2
Sample written
Starting sample sample_5
Sample written
Processing /tmp/RtmpnSvFZu/file18bc496413a836 in chunks of 10000
Starting chunk 1
Reached breakpoint change
Processing breakpoint 1
Starting sample sample_1
Sample written
Processing breakpoint 2
Starting sample sample_2
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Processing breakpoint 3
Starting sample sample_1
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Processing breakpoint 7
Starting sample sample_1
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Reached the end of the file, writing remaining data
Starting sample sample_2
Sample written


RUNIT TEST PROTOCOL -- Tue Oct 18 21:11:31 2022 
*********************************************** 
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
plethy RUnit Tests - 23 test functions, 0 errors, 0 failures
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In is.data.frame(dta) && nrow(dta) == 1 && colnames(dta) == c("rat",  :
  'length(x) = 3 > 1' in coercion to 'logical(1)'
2: In is.data.frame(dta.2) && nrow(dta.2) == 1 && colnames(dta.2) ==  :
  'length(x) = 3 > 1' in coercion to 'logical(1)'
3: call dbDisconnect() when finished working with a connection 
4: In is.list(basic.result) && names(basic.result) == c("break.dta",  :
  'length(x) = 2 > 1' in coercion to 'logical(1)'
5: In is.list(bae.result) && names(bae.result) == c("break.dta", "break.at.end") :
  'length(x) = 2 > 1' in coercion to 'logical(1)'
6: In is.list(bim.ae.result) && names(bim.ae.result) == c("break.dta",  :
  'length(x) = 2 > 1' in coercion to 'logical(1)'
7: In is.list(bim.ae.single.result) && names(bim.ae.single.result) ==  :
  'length(x) = 2 > 1' in coercion to 'logical(1)'
8: In is.list(bim.result) && names(bim.result) == c("break.dta", "break.at.end") :
  'length(x) = 2 > 1' in coercion to 'logical(1)'
> 
> proc.time()
   user  system elapsed 
 33.127   3.789  36.908 

Example timings

plethy.Rcheck/plethy-Ex.timings

nameusersystemelapsed
BuxcoDB0.6260.0130.640
add_query_funcs0.2130.0070.220
dbImport0.3680.0120.381
parsing0.9330.2121.147
plethy0.9300.1801.111
utilities2.5920.2682.860