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Package 290/553HostnameOS / ArchBUILDCHECKBUILD BIN
isobar 1.2.1
Florian P Breitwieser
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/isobar
Last Changed Rev: 66903 / Revision: 69725
Last Changed Date: 2012-06-21 02:55:12 -0700 (Thu, 21 Jun 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: isobar
Version: 1.2.1
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings isobar_1.2.1.tar.gz
StartedAt: 2012-09-24 01:48:26 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 01:50:50 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 144.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: isobar.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/isobar.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘isobar/DESCRIPTION’ ... OK
* this is package ‘isobar’ version ‘1.2.1’
* 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 whether package ‘isobar’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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’
.IBSpectraAsConciseDataFrame: no visible global function definition for
  ‘.convertPeptideModif’
.IBSpectraAsConciseDataFrame: no visible global function definition for
  ‘.convertModifToPos’
.IBSpectraAsConciseDataFrame: no visible binding for global variable
  ‘protein.group’
.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 argument(s) (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.or.load.xls.peptide.tbl : <anonymous>: no visible binding for
  global variable ‘quant.tbl’
.create.or.load.xls.quant.tbl : <anonymous>: no visible global function
  definition for ‘.convertPeptideModif’
.create.or.load.xls.quant.tbl : <anonymous>: no visible global function
  definition for ‘.convertModifToPos’
.create.or.load.xls.quant.tbl : <anonymous> : <anonymous>: no visible
  binding for global variable ‘peptide’
.create.or.load.xls.quant.tbl : <anonymous> : <anonymous>: no visible
  binding for global variable ‘modif’
.create.or.load.xls.quant.tbl : <anonymous>: no visible binding for
  global variable ‘ibspectra’
.create.or.load.xls.quant.tbl : <anonymous>: no visible binding for
  global variable ‘protein.tbl’
.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’
.proteinGroupAsConciseDataFrame: no visible binding for global variable
  ‘pep.n.prot’
.proteinGroupAsConciseDataFrame : <anonymous> : <anonymous>: no visible
  binding for global variable ‘modif.pos’
.proteinGroupAsConciseDataFrame : <anonymous> : <anonymous>: no visible
  global function definition for ‘.convertModifToPos’
.proteinGroupAsConciseDataFrame : <anonymous> : <anonymous> :
  <anonymous>: no visible binding for global variable ‘ptm.info’
.proteinGroupAsConciseDataFrame : <anonymous> : <anonymous> :
  <anonymous> : <anonymous>: no visible binding for global variable
  ‘ptm.info’
create.meta.reports: no visible global function definition for
  ‘get.merged.table’
create.meta.reports: no visible binding for global variable ‘r1’
create.meta.reports: no visible binding for global variable ‘sdf’
create.meta.reports: no visible binding for global variable ‘y’
create.meta.reports: no visible binding for global variable ‘x’
create.meta.reports: no visible global function definition for ‘+<-’
create.meta.reports: no visible binding for global variable ‘geom’
create.meta.reports: no visible global function definition for ‘tile’
create.meta.reports: no visible binding for global variable ‘height’
create.meta.reports: no visible global function definition for
  ‘gradientn’
create.meta.reports: no visible binding for global variable ‘breaks’
create.meta.reports: no visible global function definition for
  ‘plot.heatmaps’
create.meta.reports: no visible global function definition for
  ‘plot.pairs’
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’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘%inrange%’ ‘opts_isobar’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/isobar.Rcheck/00check.log’
for details.

isobar.Rcheck/00install.out:

* installing *source* package ‘isobar’ ...
** R
** data
** inst
** preparing package for lazy loading
in method for ‘coerce’ with signature ‘"ProteinGroup","data.frame.concise"’: no definition for class “data.frame.concise”
in method for ‘coerce’ with signature ‘"IBSpectra","data.frame.concise"’: no definition for class “data.frame.concise”
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.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded

* DONE (isobar)

isobar.Rcheck/isobar-Ex.timings:

nameusersystemelapsed
IBSpectra-class0.7440.0200.764
NoiseModel-class25.425 0.18826.582
ProteinGroup-class0.2520.0120.282
calculate.dNSAF0.7400.0040.762
calculate.emPAI0.5560.0120.567
fit-distr1.1800.0521.308
groupMemberPeptides0.4330.0120.443
isobar-analysis0.2400.0040.245
isobar-data0.2040.0040.204
isobar-import12.444 0.08412.667
isobar-log2.5040.0042.511
isobar-plots1.8770.0241.899
isobar-preprocessing1.7640.0321.800
number.ranges000
peptide.count0.5360.0120.554
proteinInfo-methods0.1880.0080.195
ratio-summ0.2680.0200.288
sanitize0.0000.0000.001
subsetIBSpectra3.3280.0083.399