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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pepStat.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings pepStat_1.33.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/pepStat.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 ‘pepStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pepStat’ version ‘1.33.0’
* 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 ‘pepStat’ 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 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘pepStat’ for: ‘end’, ‘start’, ‘values’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
.findFDR : <anonymous>: no visible global function definition for
  ‘median’
.sanitize_mapping_file2: no visible global function definition for
  ‘read.csv’
create_db: no visible global function definition for ‘mcols<-’
create_db: no visible global function definition for ‘mcols’
getPlotCoords: no visible global function definition for ‘values’
getWeightedEstimator : <anonymous>: no visible global function
  definition for ‘lm.fit’
getWeightedEstimator : <anonymous>: no visible global function
  definition for ‘lm.wfit’
getWeightedEstimator : <anonymous> : <anonymous>: no visible global
  function definition for ‘sd’
getZpep: no visible global function definition for ‘values’
getZpep : <anonymous>: no visible global function definition for
  ‘values’
plotArrayImage: no visible global function definition for
  ‘dev.interactive’
plotArrayImage: no visible global function definition for
  ‘devAskNewPage’
plotArrayImage: no visible global function definition for ‘dev.hold’
plotArrayImage: no visible global function definition for ‘dev.flush’
plotArrayResiduals: no visible global function definition for
  ‘dev.interactive’
plotArrayResiduals: no visible global function definition for
  ‘devAskNewPage’
plotArrayResiduals: no visible global function definition for
  ‘dev.hold’
plotArrayResiduals: no visible global function definition for
  ‘dev.flush’
summarizePeptides: no visible global function definition for ‘values<-’
summarizePeptides: no visible global function definition for ‘values’
coerce,peptideSet-ExpressionSet: no visible global function definition
  for ‘annotation’
end,peptideSet: no visible global function definition for ‘end’
featureID,peptideSet: no visible global function definition for
  ‘values’
pepZscore,GRanges: no visible global function definition for ‘values’
peptide,peptideSet: no visible global function definition for ‘values’
peptide<-,peptideSet-character: no visible global function definition
  for ‘values’
peptide<-,peptideSet-character: no visible global function definition
  for ‘values<-’
position,peptideSet: no visible global function definition for ‘start’
position,peptideSet: no visible global function definition for ‘end’
start,peptideSet: no visible global function definition for ‘start’
values,peptideSet: no visible global function definition for ‘values’
values<-,peptideSet: no visible global function definition for
  ‘values<-’
write.pSet,peptideSet: no visible global function definition for
  ‘start’
write.pSet,peptideSet: no visible global function definition for ‘end’
write.pSet,peptideSet: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  annotation dev.flush dev.hold dev.interactive devAskNewPage end
  lm.fit lm.wfit mcols mcols<- median read.csv sd start values values<-
  write.csv
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold", "dev.interactive",
             "devAskNewPage")
  importFrom("stats", "end", "lm.fit", "lm.wfit", "median", "sd",
             "start")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
makeCalls         5.848  0.072   6.758
restab            5.514  0.015   6.423
normalizeArray    5.199  0.008   6.598
plotArray         5.154  0.008   6.247
summarizePeptides 5.126  0.008   5.671
slidingMean       5.069  0.012   5.466
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘pepStat.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘pepStat.Rnw’ using knitr
Killed

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

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/pepStat.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL pepStat
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘pepStat’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘GenomicRanges’ for request: ‘mcols<-’ when loading ‘pepStat’
No methods found in package ‘GenomicRanges’ for request: ‘mcols’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values<-’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘pepStat’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘GenomicRanges’ for request: ‘mcols<-’ when loading ‘pepStat’
No methods found in package ‘GenomicRanges’ for request: ‘mcols’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values<-’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘pepStat’
** testing if installed package can be loaded from final location
No methods found in package ‘GenomicRanges’ for request: ‘mcols<-’ when loading ‘pepStat’
No methods found in package ‘GenomicRanges’ for request: ‘mcols’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values<-’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘pepStat’
** testing if installed package keeps a record of temporary installation path
* DONE (pepStat)