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BioC 2.13: CHECK report for isobar on moscato1

This page was generated on 2014-04-05 09:50:32 -0700 (Sat, 05 Apr 2014).

Package 380/750HostnameOS / ArchBUILDCHECKBUILD BIN
isobar 1.8.1
Florian P Breitwieser
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/isobar
Last Changed Rev: 82968 / Revision: 88450
Last Changed Date: 2013-11-05 22:10:42 -0800 (Tue, 05 Nov 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: isobar
Version: 1.8.1
Command: rm -rf isobar.buildbin-libdir && mkdir isobar.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=isobar.buildbin-libdir isobar_1.8.1.tar.gz >isobar-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=isobar.buildbin-libdir --install="check:isobar-install.out" --force-multiarch --no-vignettes --timings isobar_1.8.1.tar.gz && mv isobar.buildbin-libdir/* isobar.Rcheck/ && rmdir isobar.buildbin-libdir
StartedAt: 2014-04-05 04:43:49 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:47:53 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 243.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: isobar.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/isobar.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'isobar/DESCRIPTION' ... OK
* this is package 'isobar' version '1.8.1'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'isobar' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'distr'
A package should be listed in only one of these fields.
* 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: 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.as.matrix' '.as.vect' '.convertPeptideModif'
  '.proteinGroupAsConciseDataFrame' '.read.idfile' '.sum.bool'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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'
.create.or.load.quant.table : <anonymous> : <anonymous>: possible error
  in correct.peptide.ratios(..., protein.quant.tbl = protein.quant.tbl,
  protein.group = correct.protein.group, correlation =
  property("peptide.protein.correlation", properties.env)): unused
  argument (protein.group = correct.protein.group)
.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.pairs: possible error in
  png(sprintf("pairwise_correlation_%s.png", name), title = "Pairwise
  Correlation plot", width = 1000, height = 1000, pointsize = 14):
  unused argument (title = "Pairwise Correlation plot")
.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 ... WARNING
Codoc mismatches from documentation object 'distr-methods':
calcProbXDiffNormals
  Code: function(X, mu_Y, sd_Y, ..., alternative = "greater", progress
                 = FALSE)
  Docs: function(X, mu_Y, sd_Y, ..., alternative = "greater")
  Argument names in code not in docs:
    progress

Codoc mismatches from documentation object 'getPeptideModifContext':
getPeptideModifContext
  Code: function(protein.group, modif, n.aa.up = 7, n.aa.down = 7)
  Docs: function(protein.group, modif, n.aa.up = 5, n.aa.down = 5)
  Mismatches in argument default values:
    Name: 'n.aa.up' Code: 7 Docs: 5
    Name: 'n.aa.down' Code: 7 Docs: 5

* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'isobar-devel.Rnw', 'isobar-ptm.Rnw', 'isobar.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [50s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
NoiseModel-class 18.73   0.06   18.79
calculate.dNSAF   5.24   0.00    5.28
** running examples for arch 'x64' ... [47s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
NoiseModel-class 17.36   0.04   17.39
* 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

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/isobar.Rcheck/00check.log'
for details.

isobar.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'isobar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'isobar' as isobar_1.8.1.zip
* DONE (isobar)

isobar.Rcheck/examples_i386/isobar-Ex.timings:

nameusersystemelapsed
IBSpectra-class0.710.020.72
NoiseModel-class18.73 0.0618.79
ProteinGroup-class0.470.000.48
TlsParameter-class0.010.000.02
Tlsd-class000
calculate-pvalues0.030.000.04
calculate.dNSAF5.240.005.28
calculate.emPAI0.470.000.47
distr-methods0.220.020.24
fit-distr1.060.031.09
getPtmInfo000
groupMemberPeptides0.560.010.58
isobar-analysis0.520.000.52
isobar-data0.330.040.35
isobar-import1.480.001.53
isobar-log2.390.002.39
isobar-plots2.450.012.63
isobar-preprocessing2.650.022.67
number.ranges000
observedKnownSites0.450.000.45
peptide.count4.180.004.18
proteinInfo-methods0.290.000.28
proteinNameAndDescription0.260.000.28
ratio-summ0.420.010.44
sanitize0.090.000.09
spectra.count20.440.000.44
subsetIBSpectra2.600.002.61
utils000

isobar.Rcheck/examples_x64/isobar-Ex.timings:

nameusersystemelapsed
IBSpectra-class0.880.000.87
NoiseModel-class17.36 0.0417.39
ProteinGroup-class0.400.000.41
TlsParameter-class000
Tlsd-class000
calculate-pvalues0.050.000.05
calculate.dNSAF3.680.003.68
calculate.emPAI0.430.010.45
distr-methods0.270.020.29
fit-distr0.980.031.01
getPtmInfo000
groupMemberPeptides0.340.000.34
isobar-analysis0.310.000.31
isobar-data0.250.000.25
isobar-import1.300.031.33
isobar-log2.780.012.79
isobar-plots2.480.002.50
isobar-preprocessing2.340.052.39
number.ranges000
observedKnownSites0.470.000.46
peptide.count4.410.024.44
proteinInfo-methods0.240.000.23
proteinNameAndDescription0.250.000.25
ratio-summ0.420.000.42
sanitize0.010.000.02
spectra.count20.350.010.35
subsetIBSpectra3.260.003.26
utils000