BioC 2.12: CHECK report for isobar on pelham

Package: isobar

Version: 1.5.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch isobar_1.5.3.tar.gz

StartedAt: 2013-03-24 06:52:40 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 06:56:14 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 214.2 seconds

RetCode: 0

Status: OK

CheckDir: isobar.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/isobar.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'isobar/DESCRIPTION' ... OK
* this is package 'isobar' version '1.5.3'
* 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 'isobar' can be installed ... [12s/14s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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
.DEPR.get.seqlength: no visible global function definition for
  'read.fasta'
.IBSpectraAsConciseDataFrameNew: no visible binding for global variable
  'protein.group'
.add.quant.to.xls.tbl: no visible binding for global variable
  'ibspectra'
.add.quant.to.xls.tbl: no visible binding for global variable
  'protein.tbl'
.calc.w.na: no visible binding for global variable 'noise.model'
.calc.w.na: no visible binding for global variable 'sel.notna'
.calc.w.na: possible error in .calc.weighted.ratio(sel, i1, i2, var.i,
  remove.outliers, outliers.coef, outliers.trim, variance.function,
  preweights): unused arguments (remove.outliers, outliers.coef,
  outliers.trim, variance.function, preweights)
.calc.w.na: no visible binding for global variable 'var.i'
.calc.w.na: no visible binding for global variable 'remove.outliers'
.calc.w.na: no visible binding for global variable 'outliers.coef'
.calc.w.na: no visible binding for global variable 'outliers.trim'
.calc.w.na: no visible binding for global variable 'variance.function'
.calc.w.na: no visible binding for global variable 'preweights'
.create.xls.peptide.quant.tbl : <anonymous>: no visible binding for
  global variable 'peptide'
.create.xls.peptide.quant.tbl : <anonymous>: no visible binding for
  global variable 'modif'
.dissect.search.engines: no visible binding for global variable 'SC'
.get.merged.table : <anonymous>: no visible binding for global variable
  'quant.tbl'
.get.modif.pos.for.ac: no visible binding for global variable
  'ptm.info'
.get.modif.pos.for.ac : <anonymous>: no visible binding for global
  variable 'ptm.info'
.merge.identifications: no visible binding for global variable
  'identifcations'
.merge.identifications: no visible binding for global variable
  'identification'
.panel.cor: no visible global function definition for 'corr'
.parse.spectrum : <anonymous>: no visible binding for '<<-' assignment
  to 'observedMasses'
.parse.spectrum : <anonymous>: no visible binding for global variable
  'observedMasses'
.parse.spectrum : <anonymous>: no visible binding for '<<-' assignment
  to 'observedIntensities'
.parse.spectrum : <anonymous>: no visible binding for global variable
  'observedIntensities'
.plot.heatmaps: no visible binding for global variable
  'normalized.ratio.matrix'
.plot.heatmaps : <anonymous> : <anonymous>: no visible global function
  definition for 'corr'
.plot.heatmaps : <anonymous> : <anonymous>: no visible binding for
  global variable 'variance.matrix'
.plot.heatmaps.gd : <anonymous> : <anonymous>: no visible global
  function definition for 'corr'
.plot.heatmaps.gd : <anonymous> : <anonymous>: no visible binding for
  global variable 'variance.matrix'
.plot.pairs: no visible binding for global variable 'variance.matrix'
.plot.pairs: no visible binding for global variable 'ratio.matrix'
.resolve.conflicts: no visible binding for global variable 'false'
create.meta.reports: no visible binding for global variable 'lratio'
create.meta.reports: no visible binding for global variable
  'p.value.rat'
create.meta.reports: no visible binding for global variable 'comp'
create.meta.reports: no visible binding for global variable 'x'
create.meta.reports: no visible binding for global variable 'y'
create.meta.reports: no visible binding for global variable 'TRUE'
fitGumbel : gumbel.fit: no visible global function definition for
  'Gumbel'
getProteinInfoFromBioDb: no visible global function definition for
  'dbConnect'
getProteinInfoFromBioDb: no visible global function definition for
  'dbGetQuery'
getProteinInfoFromBioDb: no visible global function definition for
  'dbDisconnect'
ratiosReshapeWide: no visible binding for global variable 'class1'
sequence.coverage: no visible binding for global variable 'peptide'
sequence.coverage : <anonymous> : <anonymous>: no visible binding for
  global variable 'protein'
shared.ratios.sign: no visible binding for global variable 'ratio'
shared.ratios.sign: no visible binding for global variable 'proteins'
shared.ratios.sign: no visible binding for global variable 'g'
spectra.count2: no visible binding for global variable 'peptide'
write.xls.report: no visible binding for global variable 'accession'
writePhosphoRSInput: no visible global function definition for
  'sum.bool.c'
ProteinGroup,data.frame-ProteinGroup: no visible binding for global
  variable 'peptide'
ProteinGroup,data.frame-ProteinGroup: no visible binding for global
  variable 'accession'
coerce,IBSpectra-MSnSet: no visible binding for global variable
  'ibspiked_set1'
coerce,IBSpectra-MSnSet: no visible binding for global variable 'o'
reporterIntensityPlot,IBSpectra: no visible binding for global variable
  'tag'
reporterIntensityPlot,IBSpectra: no visible binding for global variable
  'normalized'
reporterMassPrecision,IBSpectra-logical: no visible binding for global
  variable 'mass'
reporterMassPrecision,IBSpectra-logical: no visible binding for global
  variable 'reporter'
* 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 examples ... [68s/69s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
NoiseModel-class 22.729  1.069  24.082
peptide.count     6.806  0.339   7.202
calculate.dNSAF   6.435  0.275   6.734
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/isobar.Rcheck/00check.log'
for details.

* installing *source* package 'isobar' ...
** R
** data
** inst
** preparing package for lazy loading
in method for 'coerce' with signature '"MSnSet","IBSpectra"': no definition for class "MSnSet"
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "MSnSet"
** help
*** installing help indices
** building package indices
** installing vignettes
   'isobar-devel.Rnw' 
   'isobar-ptm.Rnw' using 'UTF-8' 
   'isobar.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (isobar)

name	user	system	elapsed
IBSpectra-class	0.976	0.056	1.038
NoiseModel-class	22.729	1.069	24.082
ProteinGroup-class	0.455	0.043	0.506
TlsParameter-class	0.004	0.003	0.007
Tlsd-class	0.012	0.004	0.017
calculate-pvalues	0.046	0.008	0.054
calculate.dNSAF	6.435	0.275	6.734
calculate.emPAI	0.604	0.037	0.641
fit-distr	1.815	0.095	1.986
getPtmInfo	0.005	0.006	0.011
groupMemberPeptides	0.505	0.042	0.550
isobar-analysis	0.485	0.058	0.558
isobar-data	0.345	0.031	0.378
isobar-import	1.823	0.136	1.960
isobar-log	3.834	0.089	3.938
isobar-plots	3.034	0.164	3.317
isobar-preprocessing	3.338	0.154	3.543
number.ranges	0.012	0.006	0.018
observedKnownSites	0.759	0.017	0.788
peptide.count	6.806	0.339	7.202
proteinInfo-methods	0.337	0.034	0.371
proteinNameAndDescription	0.363	0.038	0.401
ratio-summ	0.587	0.046	0.638
sanitize	0.010	0.005	0.015
spectra.count2	0.606	0.038	0.650
subsetIBSpectra	4.446	0.151	4.613
utils	0.003	0.003	0.005

Summary

Command output