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BioC 2.12: CHECK report for isobar on petty

This page was generated on 2013-10-09 09:40:05 -0700 (Wed, 09 Oct 2013).

Package 348/671HostnameOS / ArchBUILDCHECKBUILD BIN
isobar 1.6.6
Florian P Breitwieser
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/isobar
Last Changed Rev: 80152 / Revision: 81334
Last Changed Date: 2013-09-09 04:03:28 -0700 (Mon, 09 Sep 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: isobar
Version: 1.6.6
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch isobar_1.6.6.tar.gz
StartedAt: 2013-10-08 22:52:08 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:56:27 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 258.8 seconds
RetCode: 0
Status:  OK 
CheckDir: isobar.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/isobar.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '1.6.6'
* 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 ... [14s/17s] 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'
.build.protein.group: no visible binding for global variable 'peptide'
.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'
.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'
.scatter.plot: no visible binding for global variable 'lratio.x'
.scatter.plot: no visible binding for global variable 'lratio.y'
.scatter.plot: no visible binding for global variable 'comp'
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'
initialize.env: no visible binding for global variable 'ibspectra'
load.tex.properties : get.property: no visible binding for global
  variable 'properties.env'
load.tex.properties: possible error in initialize.env(env, "protein",
  properties.env): unused argument (properties.env)
load.tex.properties: no visible binding for global variable
  'properties.env'
ratiosReshapeWide: no visible binding for global variable 'class1'
read.mzid : <anonymous>: no visible binding for global variable
  'modParams'
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'
twodistr.plot: no visible binding for global variable 'x'
twodistr.plot: no visible binding for global variable 'Distribution'
write.tex.commands: no visible global function definition for
  'get.property'
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 'TMT10'
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.difference'
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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [77s/78s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
NoiseModel-class 25.084  1.102  26.517
peptide.count     7.477  0.257   7.804
calculate.dNSAF   7.196  0.221   7.449
subsetIBSpectra   5.146  0.142   5.351
* 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.

isobar.Rcheck/00install.out:

* 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
** testing if installed package can be loaded
* DONE (isobar)

isobar.Rcheck/isobar-Ex.timings:

nameusersystemelapsed
IBSpectra-class1.2970.0621.381
NoiseModel-class25.084 1.10226.517
ProteinGroup-class0.5080.0390.550
TlsParameter-class0.0040.0020.005
Tlsd-class0.0090.0040.013
calculate-pvalues0.0280.0060.035
calculate.dNSAF7.1960.2217.449
calculate.emPAI0.7210.0400.762
distr-methods0.5140.0290.562
fit-distr1.9200.0752.162
getPtmInfo0.0180.0030.025
groupMemberPeptides0.7400.0400.789
isobar-analysis0.5480.0510.612
isobar-data0.4070.0330.444
isobar-import2.2700.0952.397
isobar-log4.6880.0764.807
isobar-plots3.3120.1433.609
isobar-preprocessing3.6080.1333.818
number.ranges0.0020.0010.004
observedKnownSites0.8390.0160.859
peptide.count7.4770.2577.804
proteinInfo-methods0.3990.0370.436
proteinNameAndDescription0.4230.0350.459
ratio-summ0.7250.0400.766
sanitize0.0020.0030.006
spectra.count20.6430.0350.685
subsetIBSpectra5.1460.1425.351
utils0.0020.0030.005