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This page was generated on 2024-06-15 12:33 -0400 (Sat, 15 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4685
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4400
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4349
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

Package 221/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiSeq 1.45.0  (landing page)
Katja Hebestreit
Snapshot Date: 2024-06-14 14:00 -0400 (Fri, 14 Jun 2024)
git_url: https://git.bioconductor.org/packages/BiSeq
git_branch: devel
git_last_commit: cd005cd
git_last_commit_date: 2024-04-30 10:31:46 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for BiSeq on nebbiolo2

To the developers/maintainers of the BiSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiSeq.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BiSeq
Version: 1.45.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BiSeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BiSeq_1.45.0.tar.gz
StartedAt: 2024-06-14 21:01:20 -0400 (Fri, 14 Jun 2024)
EndedAt: 2024-06-14 21:07:25 -0400 (Fri, 14 Jun 2024)
EllapsedTime: 364.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BiSeq.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BiSeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BiSeq_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BiSeq.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BiSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiSeq’ version ‘1.45.0’
* 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 ‘BiSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘Formula’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Formula’
  All declared Imports should be used.
Package in Depends field not imported from: ‘Formula’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.betaRegression : inv.link: no visible global function definition for
  ‘pnorm’
.betaRegression : beta.regr: no visible global function definition for
  ‘as.formula’
.categorialColors: no visible global function definition for ‘colors’
.estLocCor: no visible global function definition for ‘combn’
.logisticRegression : inv.link: no visible global function definition
  for ‘pnorm’
.logisticRegression : logistic.regr: no visible global function
  definition for ‘lm’
.logisticRegression : logistic.regr: no visible global function
  definition for ‘as.formula’
.makeVariogram: no visible global function definition for ‘qnorm’
.plotBindingSites: no visible global function definition for
  ‘txtProgressBar’
.plotBindingSites: no visible global function definition for
  ‘setTxtProgressBar’
.plotBindingSites : <anonymous>: no visible global function definition
  for ‘ksmooth’
.plotBindingSites: no visible global function definition for ‘rainbow’
.plotBindingSites: no visible global function definition for ‘lines’
.plotBindingSites: no visible global function definition for ‘rgb’
.plotBindingSites: no visible global function definition for ‘col2rgb’
.plotMeth: no visible global function definition for ‘col2rgb’
.plotMeth: no visible global function definition for ‘rgb’
.plotMeth: no visible global function definition for ‘lines’
.plotMeth: no visible global function definition for ‘legend’
.plotMethMap: no visible global function definition for
  ‘colorRampPalette’
.plotMethMap: no visible binding for global variable ‘heatmap’
.plotSmoothMeth: no visible global function definition for ‘rainbow’
.plotSmoothMeth: no visible global function definition for ‘lines’
.predictMeth: no visible global function definition for
  ‘txtProgressBar’
.predictMeth: no visible global function definition for
  ‘setTxtProgressBar’
.testClusters: no visible global function definition for ‘pnorm’
.trimClusters : integrand: no visible global function definition for
  ‘pnorm’
.trimClusters : integrand: no visible global function definition for
  ‘qnorm’
.trimClusters : integrand: no visible global function definition for
  ‘dnorm’
.trimClusters: no visible global function definition for ‘integrate’
.trimClusters: no visible global function definition for ‘pnorm’
.trimClusters: no visible global function definition for ‘qnorm’
.variogram: no visible global function definition for ‘dist’
.variogram: no visible global function definition for ‘txtProgressBar’
.variogram: no visible global function definition for
  ‘setTxtProgressBar’
.writeBED_BSraw: no visible global function definition for ‘colorRamp’
.writeBED_BSraw: no visible global function definition for ‘rgb’
.writeBED_BSrel: no visible global function definition for ‘colorRamp’
.writeBED_BSrel: no visible global function definition for ‘rgb’
betaRegression,formula-character-BSrel-numeric : inv.link: no visible
  global function definition for ‘pnorm’
betaRegression,formula-character-BSrel-numeric : beta.regr: no visible
  global function definition for ‘as.formula’
estLocCor,list: no visible global function definition for ‘combn’
logisticRegression,formula-character-BSrel-numeric : inv.link: no
  visible global function definition for ‘pnorm’
logisticRegression,formula-character-BSrel-numeric : logistic.regr: no
  visible global function definition for ‘lm’
logisticRegression,formula-character-BSrel-numeric : logistic.regr: no
  visible global function definition for ‘as.formula’
makeVariogram,data.frame-logical-numeric-numeric: no visible global
  function definition for ‘qnorm’
plotMethMap,BSrel-GRanges-factor-logical: no visible global function
  definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-factor-logical: no visible binding for global
  variable ‘heatmap’
plotMethMap,BSrel-GRanges-factor-missing: no visible global function
  definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-factor-missing: no visible binding for global
  variable ‘heatmap’
plotMethMap,BSrel-GRanges-missing-logical: no visible global function
  definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-missing-logical: no visible binding for
  global variable ‘heatmap’
plotMethMap,BSrel-GRanges-missing-missing: no visible global function
  definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-missing-missing: no visible binding for
  global variable ‘heatmap’
predictMeth,BSraw-numeric-numeric-numeric: no visible global function
  definition for ‘txtProgressBar’
predictMeth,BSraw-numeric-numeric-numeric: no visible global function
  definition for ‘setTxtProgressBar’
testClusters,list-numeric: no visible global function definition for
  ‘pnorm’
trimClusters,list-numeric : integrand: no visible global function
  definition for ‘pnorm’
trimClusters,list-numeric : integrand: no visible global function
  definition for ‘qnorm’
trimClusters,list-numeric : integrand: no visible global function
  definition for ‘dnorm’
trimClusters,list-numeric: no visible global function definition for
  ‘integrate’
trimClusters,list-numeric: no visible global function definition for
  ‘pnorm’
trimClusters,list-numeric: no visible global function definition for
  ‘qnorm’
writeBED,BSraw-character-character: no visible global function
  definition for ‘colorRamp’
writeBED,BSraw-character-character: no visible global function
  definition for ‘rgb’
writeBED,BSrel-character-character: no visible global function
  definition for ‘colorRamp’
writeBED,BSrel-character-character: no visible global function
  definition for ‘rgb’
Undefined global functions or variables:
  as.formula col2rgb colorRamp colorRampPalette colors combn dist dnorm
  heatmap integrate ksmooth legend lines lm pnorm qnorm rainbow rgb
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "col2rgb", "colorRamp", "colorRampPalette",
             "colors", "rainbow", "rgb")
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "as.formula", "dist", "dnorm", "heatmap",
             "integrate", "ksmooth", "lm", "pnorm", "qnorm")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) DMRs.Rd:16: Lost braces
    16 | DMRs: \code{median.p}, code{median.meth.group1},
       |                            ^
checkRd: (-1) DMRs.Rd:17: Lost braces
    17 | code{median.meth.group2}, \code{median.meth.diff}.
       |     ^
* 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 (user + system) or elapsed time > 5s
                 user system elapsed
betaRegression 14.096  0.404  14.500
globalTest     11.716  0.028  11.744
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/BiSeq.Rcheck/00check.log’
for details.


Installation output

BiSeq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BiSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘BiSeq’ ...
** 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 (BiSeq)

Tests output


Example timings

BiSeq.Rcheck/BiSeq-Ex.timings

nameusersystemelapsed
BSraw-class0.2050.0120.217
BSrel-class0.1470.0200.167
DMRs0.0230.0040.027
annotateGRanges0.1600.0240.184
betaRegression14.096 0.40414.500
betaResults0.0050.0000.006
betaResultsNull0.0040.0000.003
binomLikelihoodSmooth0.0030.0000.003
clusterSites0.3830.0040.387
clusterSitesToGR0.4340.0000.434
compareTwoSamples3.6400.0443.685
covBoxplots0.0760.0000.077
covStatistics0.0360.0000.036
estLocCor3.3920.0083.400
filterByCov0.1030.0000.102
filterBySharedRegions0.1400.0040.144
findDMRs0.3740.0040.378
globalTest11.716 0.02811.744
limitCov0.4640.0000.464
logisticRegression1.1930.0001.193
makeVariogram3.4290.0323.461
plotBindingSites1.2900.0241.315
plotMeth0.1820.0000.182
plotMethMap0.1760.0040.179
plotSmoothMeth0.1180.0000.118
predictMeth1.1320.0001.131
predictedMeth0.0040.0040.008
promoters0.0450.0000.045
rawToRel0.0610.0040.065
readBismark0.0670.0000.067
rrbs0.0340.0000.033
smoothVariogram0.0460.0040.050
summarizeRegions2.4530.0402.493
testClusters0.0760.0000.075
trimClusters0.2540.0200.273
vario0.0000.0010.002
writeBED0.1790.0090.188