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CHECK report for pepStat on merida1

This page was generated on 2019-04-16 11:57:45 -0400 (Tue, 16 Apr 2019).

Package 1142/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pepStat 1.16.0
Gregory C Imholte
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/pepStat
Branch: RELEASE_3_8
Last Commit: 3e2b046
Last Changed Date: 2018-10-30 11:41:54 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: pepStat
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pepStat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pepStat_1.16.0.tar.gz
StartedAt: 2019-04-16 01:51:47 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:54:24 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 156.3 seconds
RetCode: 0
Status:  OK 
CheckDir: pepStat.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pepStat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pepStat_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/pepStat.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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         6.149  0.108   6.310
slidingMean       5.814  0.050   5.916
summarizePeptides 5.799  0.051   5.924
normalizeArray    5.632  0.083   5.738
plotArray         5.652  0.051   5.736
restab            5.515  0.051   5.612
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/pepStat.Rcheck/00check.log’
for details.



Installation output

pepStat.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pepStat
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘pepStat’ ...
** 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
No methods found in package ‘GenomicRanges’ for request: ‘mcols<-’ when loading ‘pepStat’
No methods found in package ‘GenomicRanges’ for request: ‘mcols’ when loading ‘pepStat’
* DONE (pepStat)

Tests output


Example timings

pepStat.Rcheck/pepStat-Ex.timings

nameusersystemelapsed
create_db0.1020.0040.106
makeCalls6.1490.1086.310
makePeptideSet2.5560.0392.611
normalizeArray5.6320.0835.738
plotArray5.6520.0515.736
restab5.5150.0515.612
shinyPepStat000
slidingMean5.8140.0505.916
summarizePeptides5.7990.0515.924