Multiple platform build/check report for BioC 3.21 - CHECK results for BiSeq on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4748
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4459
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	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*

CHECK results for BiSeq on lconway

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: 1.47.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiSeq_1.47.0.tar.gz

StartedAt: 2024-11-24 20:04:53 -0500 (Sun, 24 Nov 2024)

EndedAt: 2024-11-24 20:13:18 -0500 (Sun, 24 Nov 2024)

EllapsedTime: 505.2 seconds

RetCode: 0

Status: OK

CheckDir: BiSeq.Rcheck

Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiSeq_1.47.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BiSeq.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiSeq’ version ‘1.47.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BSraw-class.Rd: RangedSummarizedExperiment-class,
    RangedSummarizedExperiment
  BSrel-class.Rd: RangedSummarizedExperiment-class,
    RangedSummarizedExperiment
  betaRegression.Rd: betareg
  globalTest.Rd: gt, GRanges-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
betaRegression 12.550  0.274  12.863
globalTest      9.664  0.050   9.742
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/BiSeq.Rcheck/00check.log’
for details.

Installation output

BiSeq.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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

name	user	system	elapsed
BSraw-class	0.169	0.007	0.176
BSrel-class	0.127	0.015	0.142
DMRs	0.020	0.003	0.024
annotateGRanges	0.156	0.008	0.165
betaRegression	12.550	0.274	12.863
betaResults	0.005	0.002	0.006
betaResultsNull	0.003	0.002	0.004
binomLikelihoodSmooth	0.002	0.000	0.002
clusterSites	0.312	0.004	0.317
clusterSitesToGR	0.365	0.004	0.371
compareTwoSamples	2.139	0.017	2.160
covBoxplots	0.051	0.005	0.056
covStatistics	0.030	0.003	0.034
estLocCor	3.488	0.511	4.027
filterByCov	0.082	0.001	0.084
filterBySharedRegions	0.118	0.003	0.121
findDMRs	0.250	0.005	0.256
globalTest	9.664	0.050	9.742
limitCov	0.379	0.005	0.385
logisticRegression	0.908	0.007	0.916
makeVariogram	2.743	0.380	3.131
plotBindingSites	1.016	0.009	1.030
plotMeth	0.196	0.033	0.230
plotMethMap	0.146	0.006	0.152
plotSmoothMeth	0.098	0.004	0.103
predictMeth	0.998	0.008	1.024
predictedMeth	0.008	0.002	0.009
promoters	0.037	0.003	0.040
rawToRel	0.054	0.002	0.056
readBismark	0.058	0.002	0.061
rrbs	0.026	0.002	0.028
smoothVariogram	0.032	0.005	0.038
summarizeRegions	2.058	0.013	2.078
testClusters	0.061	0.005	0.067
trimClusters	0.245	0.008	0.258
vario	0.002	0.002	0.003
writeBED	0.171	0.006	0.179