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R CMD BUILD
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* checking for file wavFeatExt/DESCRIPTION ... OK
* preparing wavFeatExt:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted LazyData from DESCRIPTION
* building wavFeatExt_0.99.0.tar.gz
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BiocCheckGitClone('wavFeatExt')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4076/wavFeatExt_20260306190328/wavFeatExt
BiocVersion: 3.23
Package: wavFeatExt
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4076/wavFeatExt_20260306190328/wavFeatExt.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4076/wavFeatExt_20260306190328/wavFeatExt
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
wavFeatExt.Rproj
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
BiocCheck v1.47.18 results
1 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
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R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/4076/wavFeatExt_20260306190328/wavFeatExt.Rcheck
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file wavFeatExt/DESCRIPTION ... OK
* checking extension type ... Package
* this is package wavFeatExt version 0.99.0
* 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 wavFeatExt can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking use of S3 registration ... 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 ... [11s/11s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 files in vignettes ... OK
* checking examples ... [175s/175s] ERROR
Running examples in wavFeatExt-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: classif.wavFeatExt
> ### Title: Classification on Wavelet-based Features
> ### Aliases: classif.wavFeatExt
> ### Keywords: classification wavelets
>
> ### ** Examples
>
> ## Not run:
> ## Generating simulated CNA data
> set.seed(10)
> sim.dat2 <- sim.CNA(n.sim = 2) # two simulated data sets
Simulating data set 1
Warning in read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :
cannot open compressed file '/home/biocbuild/bbs-3.23-bioc/R/site-library/DNAcopy/DESCRIPTION', probable reason 'No such file or directory'
Error in find.package(package, lib.loc, verbose = verbose) :
there is no package called DNAcopy
Calls: sim.CNA -> seg -> CBS -> segment -> data -> find.package
Execution halted
Error: failed to load sRGB colorspace file
Fatal error: error during cleanup
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
classif.pcaica 168.245 0.736 168.999
* checking package vignettes ... NOTE
Package has vignettes subdirectory but apparently no vignettes.
Perhaps the VignetteBuilder information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... [1s/0s] ERROR
Rd conversion errors:
During startup - Warning messages:
1: package "methods" in options("defaultPackages") was not found
2: package datasets in options("defaultPackages") was not found
3: package utils in options("defaultPackages") was not found
4: package grDevices in options("defaultPackages") was not found
5: package graphics in options("defaultPackages") was not found
6: package stats in options("defaultPackages") was not found
7: package methods in options("defaultPackages") was not found
Converting parsed Rd's to LaTeX Error : package utils does not have a namespace
* DONE
Status: 2 ERRORs, 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/4076/wavFeatExt_20260306190328/wavFeatExt.Rcheck/00check.log
for details.
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BiocCheck('wavFeatExt_0.99.0.tar.gz')
===============================
During startup - Warning messages:
1: package "methods" in options("defaultPackages") was not found
2: package datasets in options("defaultPackages") was not found
3: package utils in options("defaultPackages") was not found
4: package grDevices in options("defaultPackages") was not found
5: package graphics in options("defaultPackages") was not found
6: package stats in options("defaultPackages") was not found
7: package methods in options("defaultPackages") was not found
Error: package or namespace load failed for BiocCheck:
package methods does not have a namespace
Execution halted