Package: BRAIN

Version: 1.28.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BRAIN.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BRAIN_1.28.1.tar.gz

StartedAt: 2019-04-13 00:53:14 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 00:55:24 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 129.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BRAIN.Rcheck

Warnings: 2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BRAIN.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BRAIN_1.28.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BRAIN.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/BRAIN.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/BRAIN_1.28.1.tar.gz && rm -rf BRAIN.buildbin-libdir && mkdir BRAIN.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BRAIN.buildbin-libdir BRAIN_1.28.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BRAIN_1.28.1.zip && rm BRAIN_1.28.1.tar.gz BRAIN_1.28.1.zip
###
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install for i386

* installing *source* package 'BRAIN' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BRAIN'
    finding HTML links ... done
    BRAIN-package                           html  
    calculateAverageMass                    html  
    calculateIsotopicProbabilities          html  
    calculateMonoisotopicMass               html  
    calculateNrPeaks                        html  
    getAtomsFromSeq                         html  
    useBRAIN                                html  
    useBRAIN2                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BRAIN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BRAIN' as BRAIN_1.28.1.zip
* DONE (BRAIN)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BRAIN' successfully unpacked and MD5 sums checked
In R CMD INSTALL