BioC 3.6: CHECK report for synapter on veracruz1

Package: synapter

Version: 2.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings synapter_2.1.0.tar.gz

StartedAt: 2017-08-16 09:03:30 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 09:07:08 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 217.8 seconds

RetCode: 0

Status:  OK

CheckDir: synapter.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings synapter_2.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/synapter.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘synapter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synapter’ version ‘2.1.0’
* 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 ‘synapter’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc   7.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
  Laurent Gatto <lg390@cam.ac.uk> [aut, cre]
  Sebastian Gibb <mail@sebastiangibb.de> [aut, cre]
* 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
Missing object imported by a ':::' call: ‘MSnbase:::utils.applyColumnwiseByGroup’
Unexported objects imported by ':::' calls:
  ‘MSnbase:::.plotSingleSpectrum’ ‘MSnbase:::Spectrum2_mz_sorted’
  ‘MSnbase:::commonPeaks’ ‘MSnbase:::numberOfCommonPeaks’
  ‘MSnbase:::relaxedMatch’ ‘MSnbase:::utils.list2ssv’
  ‘MSnbase:::utils.ssv2list’ ‘MSnbase:::utils.ssv2vec’
  ‘MSnbase:::utils.vec2ssv’
  See the note in ?`:::` about the use of this operator.
* 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
synergise 15.932  1.031  17.960
Synapter   5.502  0.193   5.838
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/synapter.Rcheck/00check.log’
for details.

* installing *source* package ‘synapter’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (synapter)

name	user	system	elapsed
MasterFdrResults-class	0.000	0.000	0.001
Synapter	5.502	0.193	5.838
createUniquePeptideDbRds	0.000	0.000	0.001
synapterTinyData	0.192	0.008	0.207
synergise	15.932	1.031	17.960
synergise2	0.000	0.000	0.001