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 |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/isobar.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.8.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘isobar’ can be installed ... [7s/7s] 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
* 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’
.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 ... [38s/39s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
NoiseModel-class 14.557 0.032 14.62
* 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
‘/home/biocbuild/bbs-2.13-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
** testing if installed package can be loaded
* DONE (isobar)