Multiple platform build/check report for BioC 3.10 - CHECK report for pepStat on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:pepStat.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings pepStat_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/pepStat.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pepStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pepStat’ version ‘1.20.0’
* 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’

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’
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’
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’
coerce,peptideSet-ExpressionSet: no visible global function definition
  for ‘annotation’
end,peptideSet: no visible global function definition for ‘end’
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’
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 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 or elapsed time > 5s
                   user system elapsed
makeCalls         6.676  0.032   6.822
slidingMean       6.144  0.012   6.170
plotArray         5.904  0.012   5.924
summarizePeptides 5.596  0.020   5.634
restab            5.576  0.016   5.599
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/pepStat.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL pepStat
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* installing to library ‘/home/biocbuild/bbs-3.10-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’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘pepStat.Rnw’ 
** 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’
** 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’
** testing if installed package keeps a record of temporary installation path
* DONE (pepStat)

CHECK report for pepStat on malbec1

Summary

Command output

Installation output

Tests output

Example timings

name	user	system	elapsed
create_db	0.152	0.000	0.154
makeCalls	6.676	0.032	6.822
makePeptideSet	2.496	0.012	2.516
normalizeArray	4.928	0.008	4.940
plotArray	5.904	0.012	5.924
restab	5.576	0.016	5.599
shinyPepStat	0	0	0
slidingMean	6.144	0.012	6.170
summarizePeptides	5.596	0.020	5.634