Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:08:05 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 genomicInstability on machv2


To the developers/maintainers of the genomicInstability package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genomicInstability.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 753/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genomicInstability 1.0.0  (landing page)
Mariano Alvarez
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/genomicInstability
git_branch: RELEASE_3_14
git_last_commit: 523d6a1
git_last_commit_date: 2021-10-26 13:11:49 -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    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: genomicInstability
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomicInstability.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomicInstability_1.0.0.tar.gz
StartedAt: 2022-01-18 13:22:13 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 13:25:55 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 221.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: genomicInstability.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomicInstability.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomicInstability_1.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/genomicInstability.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomicInstability/DESCRIPTION’ ... OK
* this is package ‘genomicInstability’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘genomicInstability’ 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 ... NOTE
mixGaussianFit : <anonymous>: warning in normalmixEM(x, lambda =
  param$lambda, mu = param$m, sd = param$sigma, epsilon = 1e-50):
  partial argument match of 'sd' to 'sd.constr'
aecdf1: no visible global function definition for ‘quantile’
aecdf1: no visible global function definition for ‘ecdf’
aecdf1: no visible binding for global variable ‘tl2’
aecdf1: no visible binding for global variable ‘iq2’
aecdf1: no visible global function definition for ‘epd’
aecdf1: no visible global function definition for ‘lm’
aecdf1: no visible global function definition for ‘predict’
aecdf1: no visible global function definition for ‘qnorm’
colorScale: no visible global function definition for ‘col2rgb’
colorScale : <anonymous>: no visible global function definition for
  ‘rgb’
generateChromosomeGeneSet: no visible global function definition for
  ‘data’
generateChromosomeGeneSet: no visible binding for global variable
  ‘hg38’
generateChromosomeGeneSet: no visible binding for global variable
  ‘mm10’
generateChromosomeGeneSet: no visible binding for global variable
  ‘genePosition’
getPeaks: no visible global function definition for ‘density’
getPeaks3: no visible global function definition for ‘density’
getPeaks3: no visible global function definition for ‘smooth.spline’
getPeaks3: no visible global function definition for ‘predict’
getPeaks3 : <anonymous>: no visible global function definition for
  ‘approx’
giDensityPlot: no visible global function definition for ‘density’
giDensityPlot: no visible global function definition for ‘lines’
giLikelihood: no visible global function definition for ‘sd’
giLikelihood: no visible global function definition for ‘predict’
mixGaussianFit : <anonymous> : <anonymous>: no visible global function
  definition for ‘dnorm’
mixGaussianFit: no visible global function definition for ‘density’
plot.inferCNV: no visible global function definition for ‘pdf’
plot.inferCNV: no visible global function definition for ‘png’
plot.inferCNV: no visible global function definition for ‘jpeg’
plot.inferCNV: no visible global function definition for ‘layout’
plot.inferCNV: no visible global function definition for ‘par’
plot.inferCNV: no visible global function definition for ‘axis’
plot.inferCNV: no visible global function definition for ‘dev.off’
plot.mgfit: no visible global function definition for ‘rainbow’
plot.mgfit: no visible global function definition for ‘density’
plot.mgfit: no visible global function definition for ‘dnorm’
plot.mgfit: no visible global function definition for ‘axis’
plot.mgfit: no visible global function definition for ‘polygon’
plot.mgfit: no visible global function definition for ‘lines’
plothm: no visible global function definition for ‘par’
plothm: no visible global function definition for ‘layout’
plothm: no visible global function definition for ‘axis’
plothm: no visible global function definition for ‘image’
plothm.: no visible global function definition for ‘image’
predict.mgfit : <anonymous>: no visible global function definition for
  ‘dnorm’
sREA: no visible global function definition for ‘qnorm’
sortRowsByHclust: no visible global function definition for ‘dist’
sortRowsByHclust: no visible global function definition for ‘hclust’
Undefined global functions or variables:
  approx axis col2rgb data density dev.off dist dnorm ecdf epd
  genePosition hclust hg38 image iq2 jpeg layout lines lm mm10 par pdf
  png polygon predict qnorm quantile rainbow rgb sd smooth.spline tl2
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "jpeg", "pdf", "png",
             "rainbow", "rgb")
  importFrom("graphics", "axis", "image", "layout", "lines", "par",
             "polygon")
  importFrom("stats", "approx", "density", "dist", "dnorm", "ecdf",
             "hclust", "lm", "predict", "qnorm", "quantile", "sd",
             "smooth.spline")
  importFrom("utils", "data")
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 ... ERROR
Running examples in ‘genomicInstability-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genomicInstabilityScore
> ### Title: Genomic Instability Analysis
> ### Aliases: genomicInstabilityScore
> 
> ### ** Examples
> 
> 
> eh <- ExperimentHub::ExperimentHub()
snapshotDate(): 2021-10-19
> dset <- eh[["EH5419"]]
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'GSE103322'
Error in UseMethod("conditionMessage") : 
  no applicable method for 'conditionMessage' applied to an object of class "character"
Calls: [[ ... tryCatchList -> tryCatchOne -> doTryCatch -> download.file
Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/genomicInstability.Rcheck/00check.log’
for details.


Installation output

genomicInstability.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘genomicInstability’ ...
** using staged installation
** R
** data
** 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 (genomicInstability)

Tests output


Example timings

genomicInstability.Rcheck/genomicInstability-Ex.timings

nameusersystemelapsed
generateChromosomeGeneSet0.1990.0140.212