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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:deltaGseg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings deltaGseg_1.45.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/deltaGseg.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deltaGseg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘deltaGseg’ version ‘1.45.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'ggplot2', 'changepoint', 'wavethresh', 'tseries', 'pvclust',
'fBasics', 'grid', 'reshape', 'scales'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘deltaGseg’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
boot.hclust_new: no visible global function definition for ‘hclust’
dist.pvclust: no visible global function definition for ‘as.dist’
dist.pvclust: no visible global function definition for ‘cor’
dist.pvclust: no visible global function definition for ‘na.omit’
dist.pvclust: no visible global function definition for ‘dist’
distw.pvclust: no visible global function definition for ‘as.dist’
mydist: no visible global function definition for ‘dist’
mydist: no visible global function definition for ‘as.dist’
parseTraj: no visible global function definition for ‘read.table’
pvclust_new: no visible global function definition for ‘hclust’
segden1: no visible global function definition for ‘quantile’
text.pvclust: no visible global function definition for ‘par’
text.pvclust: no visible global function definition for ‘text’
clusterSegments,SegTrajectories: no visible global function definition
for ‘hclust’
clusterSegments,SegTrajectories: no visible global function definition
for ‘layout’
clusterSegments,SegTrajectories: no visible global function definition
for ‘lines’
clusterSegments,SegTrajectories: no visible global function definition
for ‘points’
clusterSegments,SegTrajectories: no visible global function definition
for ‘abline’
clusterSegments,SegTrajectories: no visible global function definition
for ‘text’
clusterSegments,SegTrajectories: no visible global function definition
for ‘identify’
clusterSegments,SegTrajectories: no visible global function definition
for ‘par’
clusterSegments,SegTrajectories: no visible global function definition
for ‘locator’
clusterSegments,SegTrajectories: no visible global function definition
for ‘cutree’
clusterSegments,SegTrajectories: no visible global function definition
for ‘mtext’
clusterSegments,SegTrajectories: no visible global function definition
for ‘median’
denoiseSegments,Trajectories: no visible global function definition for
‘txtProgressBar’
denoiseSegments,Trajectories: no visible global function definition for
‘setTxtProgressBar’
diagnosticPlots,SegSeriesTrajectories: no visible binding for global
variable ‘residuals’
diagnosticPlots,SegSeriesTrajectories: no visible global function
definition for ‘acf’
diagnosticPlots,SegSeriesTrajectories: no visible global function
definition for ‘qnorm’
diagnosticPlots,SegSeriesTrajectories: no visible binding for global
variable ‘lag’
Undefined global functions or variables:
abline acf as.dist cor cutree dist hclust identify lag layout lines
locator median mtext na.omit par points qnorm quantile read.table
residuals setTxtProgressBar text txtProgressBar
Consider adding
importFrom("graphics", "abline", "identify", "layout", "lines",
"locator", "mtext", "par", "points", "text")
importFrom("stats", "acf", "as.dist", "cor", "cutree", "dist",
"hclust", "lag", "median", "na.omit", "qnorm", "quantile",
"residuals")
importFrom("utils", "read.table", "setTxtProgressBar",
"txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) SegSeriesTrajectories-class.Rd:40: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:41: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:42: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:43: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:44: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:50: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:51: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:52: \item in \describe must have non-empty label
checkRd: (5) SegSeriesTrajectories-class.Rd:53: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:37: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:38: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:39: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:40: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:41: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:47: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:48: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:49: \item in \describe must have non-empty label
checkRd: (5) SegTrajectories-class.Rd:50: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:25: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:26: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:27: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:28: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:35: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:36: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:37: \item in \describe must have non-empty label
checkRd: (5) Trajectories-class.Rd:38: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:34: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:35: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:36: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:37: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:44: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:45: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:46: \item in \describe must have non-empty label
checkRd: (5) TransTrajectories-class.Rd:47: \item in \describe must have non-empty label
* 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 installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
‘diagplots.png’, ‘simclust.png’, ‘simtraj.png’, ‘simtrajtr.png’,
‘simtrajtr2.png’, ‘traj1.png’, ‘traj1break.png’, ‘traj1ss0.png’,
‘traj1ss1.png’, ‘traj1tr.png’
Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
clusterPV 102.021 11.935 114.792
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... NOTE
Package vignette with \VignetteEngine{} not specifying an engine package:
‘deltaGseg.Rnw’
Engines should be specified as \VignetteEngine{PKG::ENG}.
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/deltaGseg.Rcheck/00check.log’
for details.
