isobar 1.5.0
Florian P Breitwieser
| Snapshot Date: 2012-12-03 17:01:51 -0800 (Mon, 03 Dec 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/isobar | | Last Changed Rev: 70825 / Revision: 71622 | | Last Changed Date: 2012-10-29 07:23:47 -0700 (Mon, 29 Oct 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 |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | ERROR | |
* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/isobar.Rcheck’
* using R Under development (unstable) (2012-10-31 r61060)
* 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 ‘1.5.0’
* 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 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 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 global function definition
for ‘.convertPeptideModif’
.IBSpectraAsConciseDataFrameNew: no visible global function definition
for ‘.convertModifToPos’
.IBSpectraAsConciseDataFrameNew: 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 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.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 : <anonymous> : <anonymous>: no visible
global function definition for ‘.convertModifToPos’
.read.mapping: no visible binding for global variable ‘id.file.domap’
.read.mapping: no visible binding for global variable ‘id.format’
.read.mapping: no visible binding for global variable ‘decode.titles’
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’
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 ... WARNING
Codoc mismatches from documentation object 'calculate.emPAI':
observable.peptides
Code: function(seq, nmc = 1, min.length = 6, min.mass = 600, max.mass
= 4000, custom = list(code = c("B", "Z", "J", "U"),
mass = c(164.554862, 278.61037, 213.12392,
150.953636)), ...)
Docs: function(seq, nmc = 1, min.length = 6, min.mass = 600, max.mass
= 4000, custom = list(code = "U", mass = 150.953636),
...)
Mismatches in argument default values:
Name: 'custom'
Code: list(code = c("B", "Z", "J", "U"), mass = c(164.554862, 278.61037,
213.12392, 150.953636))
Docs: list(code = "U", mass = 150.953636)
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
NoiseModel-class 23.673 0.040 23.731
isobar-import 14.789 0.056 14.852
* 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-2.12-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 ‘"ProteinGroup","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)