Multiple platform build/check report for BioC 3.21 - CHECK results for BiSeq on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4779
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4550
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4578
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4530
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4461
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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: BiSeq

Version: 1.47.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BiSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiSeq_1.47.0.tar.gz

StartedAt: 2025-03-24 04:34:13 -0000 (Mon, 24 Mar 2025)

EndedAt: 2025-03-24 04:41:30 -0000 (Mon, 24 Mar 2025)

EllapsedTime: 437.4 seconds

RetCode: 0

Status: OK

CheckDir: BiSeq.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BiSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiSeq_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BiSeq.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 ... 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
betaRegression    22.063  0.814  22.930
globalTest        19.828  0.303  20.179
compareTwoSamples  5.410  0.247   5.671
makeVariogram      5.475  0.076   5.563
estLocCor          5.436  0.048   5.498
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/BiSeq.Rcheck/00check.log’
for details.

Installation output

BiSeq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BiSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘BiSeq’ ...
** this is package ‘BiSeq’ version ‘1.47.0’
** 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	0.358	0.000	0.359
BSrel-class	0.230	0.000	0.231
DMRs	0.036	0.004	0.040
annotateGRanges	0.229	0.016	0.245
betaRegression	22.063	0.814	22.930
betaResults	0.007	0.000	0.007
betaResultsNull	0.004	0.000	0.005
binomLikelihoodSmooth	0.004	0.000	0.005
clusterSites	0.622	0.000	0.624
clusterSitesToGR	0.717	0.008	0.727
compareTwoSamples	5.410	0.247	5.671
covBoxplots	0.093	0.000	0.093
covStatistics	0.050	0.004	0.054
estLocCor	5.436	0.048	5.498
filterByCov	0.173	0.000	0.173
filterBySharedRegions	0.253	0.012	0.265
findDMRs	0.571	0.020	0.592
globalTest	19.828	0.303	20.179
limitCov	0.777	0.004	0.783
logisticRegression	2.102	0.024	2.132
makeVariogram	5.475	0.076	5.563
plotBindingSites	2.173	0.068	2.246
plotMeth	0.263	0.000	0.263
plotMethMap	0.278	0.000	0.280
plotSmoothMeth	0.191	0.000	0.192
predictMeth	1.980	0.028	2.014
predictedMeth	0.012	0.000	0.012
promoters	0.05	0.00	0.05
rawToRel	0.099	0.000	0.100
readBismark	0.113	0.000	0.115
rrbs	0.038	0.004	0.042
smoothVariogram	0.046	0.000	0.045
summarizeRegions	4.472	0.032	4.515
testClusters	0.102	0.000	0.101
trimClusters	0.432	0.032	0.466
vario	0.000	0.001	0.002
writeBED	0.266	0.005	0.272