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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:proteasy.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings proteasy_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/proteasy.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘proteasy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proteasy’ version ‘1.4.0’
* 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 ‘proteasy’ 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 loading without being on the library search path ... 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 ... OK
* 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 ‘proteasy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cleavages
> ### Title: Access resulting object from 'findProteases' function.
> ### Aliases: cleavages cleavages-Cleavages cleavages,Cleavages-method
> 
> ### ** Examples
> 
> protein <- c("P02671", "P02671", "P68871", "P01011")
> peptide <- c("FEEVSGNVSPGTR", "FVSETESR", "LLVVYPW", "ITLLSAL")
> res <- findProtease(protein = protein, peptide = peptide,
+ organism = "Homo sapiens")
Error: To read gz and bz2 files directly, fread() requires 'R.utils' package which cannot be found. Please install 'R.utils' using 'install.packages('R.utils')'.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘proteasy.Rmd’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘proteasy.Rmd’
  ...

</style>

> library("proteasy")

> searchSubstrate(protein = "P01042", summarize = TRUE)

  When sourcing ‘proteasy.R’:
Error: To read gz and bz2 files directly, fread() requires 'R.utils' package which cannot be found. Please install 'R.utils' using 'install.packages('R.utils')'.
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
  ...
--- re-building ‘proteasy.Rmd’ using rmarkdown

Quitting from lines  at lines 101-116 [SearchSubstrate] (proteasy.Rmd)
Error: processing vignette 'proteasy.Rmd' failed with diagnostics:
To read gz and bz2 files directly, fread() requires 'R.utils' package which cannot be found. Please install 'R.utils' using 'install.packages('R.utils')'.
--- failed re-building ‘proteasy.Rmd’

SUMMARY: processing the following file failed:
  ‘proteasy.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/proteasy.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL proteasy
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘proteasy’ ...
** 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 (proteasy)