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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PepsNMR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings PepsNMR_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/PepsNMR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘PepsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PepsNMR’ version ‘1.17.0’
* 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 ‘PepsNMR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 R 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) Normalization.Rd:47: Escaped LaTeX specials: \&
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘PepsNMR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PepsNMR-package
> ### Title: Metabolomic data pre-processing strategy for 1H NMR
> ###   spectroscopic data
> ### Aliases: PepsNMR-package PepsNMR
> ### Keywords: package
> 
> ### ** Examples
> 
> path <-  system.file("extdata", package = "PepsNMRData")
> dir(path)
[1] "Group_HS.csv" "HumanSerum"  
> 
> fidList <- ReadFids(file.path(path, "HumanSerum"))
> Fid_data <- fidList[["Fid_data"]]
> Fid_info <- fidList[["Fid_info"]]
> Fid_data <- GroupDelayCorrection(Fid_data, Fid_info)
> Fid_data <- SolventSuppression(Fid_data)
> Fid_data <- Apodization(Fid_data, Fid_info)
> Fid_data <- ZeroFilling(Fid_data)
> Spectrum_data <- FourierTransform(Fid_data, Fid_info)
> Spectrum_data <- ZeroOrderPhaseCorrection(Spectrum_data)
> Spectrum_data <- InternalReferencing(Spectrum_data, Fid_info)
> Spectrum_data <- BaselineCorrection(Spectrum_data)
> Spectrum_data <- NegativeValuesZeroing(Spectrum_data)
> Spectrum_data <- Warping(Spectrum_data)
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘PepsNMR_minimal_example.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘PepsNMR_minimal_example.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PepsNMR.Rcheck/vign_test/PepsNMR/vignettes/PepsNMR_minimal_example_files/figure-html/FIGRawFID-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PepsNMR.Rcheck/vign_test/PepsNMR/vignettes/PepsNMR_minimal_example_files/figure-html/unnamed-chunk-6-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PepsNMR.Rcheck/vign_test/PepsNMR/vignettes/PepsNMR_minimal_example_files/figure-html/unnamed-chunk-8-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PepsNMR.Rcheck/vign_test/PepsNMR/vignettes/PepsNMR_minimal_example_files/figure-html/unnamed-chunk-10-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PepsNMR.Rcheck/vign_test/PepsNMR/vignettes/PepsNMR_minimal_example_files/figure-html/unnamed-chunk-12-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PepsNMR.Rcheck/vign_test/PepsNMR/vignettes/PepsNMR_minimal_example_files/figure-html/unnamed-chunk-14-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PepsNMR.Rcheck/vign_test/PepsNMR/vignettes/PepsNMR_minimal_example_files/figure-html/unnamed-chunk-16-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PepsNMR.Rcheck/vign_test/PepsNMR/vignettes/PepsNMR_minimal_example_files/figure-html/unnamed-chunk-17-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PepsNMR.Rcheck/vign_test/PepsNMR/vignettes/PepsNMR_minimal_example_files/figure-html/unnamed-chunk-18-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PepsNMR.Rcheck/vign_test/PepsNMR/vignettes/PepsNMR_minimal_example_files/figure-html/unnamed-chunk-20-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PepsNMR.Rcheck/vign_test/PepsNMR/vignettes/PepsNMR_minimal_example_files/figure-html/unnamed-chunk-21-1.png" but not available.
Killed

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/PepsNMR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL PepsNMR
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘PepsNMR’ ...
** using staged installation
** R
** 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 (PepsNMR)