Package: BRAIN

Version: 1.28.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BRAIN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BRAIN_1.28.1.tar.gz

StartedAt: 2019-04-15 22:41:07 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:42:17 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 70.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BRAIN.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BRAIN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BRAIN_1.28.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/BRAIN.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 ‘BRAIN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BRAIN’ version ‘1.28.1’
* 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 ‘BRAIN’ 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘Biostrings’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ... WARNING
Codoc mismatches from documentation object 'calculateIsotopicProbabilities':
calculateIsotopicProbabilities
  Code: function(aC, stopOption = "nrPeaks", nrPeaks = NULL, coverage =
                 NULL, abundantEstim = NULL, approx = FALSE,
                 approxStart = 1, approxParam = NULL)
  Docs: function(aC, stopOption = "nrPeaks", nrPeaks, coverage,
                 abundantEstim)
  Argument names in code not in docs:
    approx approxStart approxParam
  Mismatches in argument default values:
    Name: 'nrPeaks' Code: NULL Docs: 
    Name: 'coverage' Code: NULL Docs: 
    Name: 'abundantEstim' Code: NULL Docs: 

* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'useBRAIN2':
  useBRAIN2(aC, stopOption = "nrPeaks", nrPeaks, approxStart = 1, approxParam = NULL))

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/BRAIN.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BRAIN
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘BRAIN’ ...
** 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
* DONE (BRAIN)

name	user	system	elapsed
BRAIN-package	0.234	0.033	0.268
calculateAverageMass	0	0	0
calculateIsotopicProbabilities	0.032	0.006	0.038
calculateMonoisotopicMass	0.001	0.000	0.001
calculateNrPeaks	0.001	0.000	0.001
getAtomsFromSeq	0.005	0.001	0.005
useBRAIN	0.335	0.033	0.368
useBRAIN2	0.177	0.027	0.204