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CHECK report for pepStat on celaya2

This page was generated on 2019-10-16 12:53:30 -0400 (Wed, 16 Oct 2019).

Package 1195/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pepStat 1.18.0
Gregory C Imholte
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/pepStat
Branch: RELEASE_3_9
Last Commit: f5541f4
Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: pepStat
Version: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2019-10-16 05:29:24 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:32:59 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 214.6 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_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/pepStat.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.18.0’
* 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 : : 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 : : no visible global function
  definition for ‘lm.fit’
getWeightedEstimator : : no visible global function
  definition for ‘lm.wfit’
getWeightedEstimator :  : : 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         8.196  0.231   8.462
normalizeArray    7.066  0.154   7.222
restab            7.065  0.119   7.186
plotArray         7.045  0.110   7.156
slidingMean       6.941  0.104   7.048
summarizePeptides 6.864  0.112   6.976
* 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-3.9-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/3.6/Resources/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)

Tests output


Example timings

pepStat.Rcheck/pepStat-Ex.timings

nameusersystemelapsed
create_db0.1370.0050.142
makeCalls8.1960.2318.462
makePeptideSet3.1520.0853.237
normalizeArray7.0660.1547.222
plotArray7.0450.1107.156
restab7.0650.1197.186
shinyPepStat0.0000.0000.001
slidingMean6.9410.1047.048
summarizePeptides6.8640.1126.976