isobar 1.5.3
Florian P Breitwieser
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/isobar | | Last Changed Rev: 74452 / Revision: 74774 | | Last Changed Date: 2013-03-16 08:53:37 -0700 (Sat, 16 Mar 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/isobar.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.5.3’
* 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/14s] 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’
.add.quant.to.xls.tbl: no visible binding for global variable
‘protein.tbl’
.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.xls.peptide.quant.tbl : <anonymous>: no visible binding for
global variable ‘peptide’
.create.xls.peptide.quant.tbl : <anonymous>: no visible binding for
global variable ‘modif’
.dissect.search.engines: no visible binding for global variable ‘SC’
.get.merged.table : <anonymous>: no visible binding for global variable
‘quant.tbl’
.get.modif.pos.for.ac: no visible binding for global variable
‘ptm.info’
.get.modif.pos.for.ac : <anonymous>: no visible binding for global
variable ‘ptm.info’
.merge.identifications: no visible binding for global variable
‘identifcations’
.merge.identifications: no visible binding for global variable
‘identification’
.panel.cor: no visible global function definition for ‘corr’
.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.heatmaps: no visible binding for global variable
‘normalized.ratio.matrix’
.plot.heatmaps : <anonymous> : <anonymous>: no visible global function
definition for ‘corr’
.plot.heatmaps : <anonymous> : <anonymous>: no visible binding for
global variable ‘variance.matrix’
.plot.heatmaps.gd : <anonymous> : <anonymous>: no visible global
function definition for ‘corr’
.plot.heatmaps.gd : <anonymous> : <anonymous>: no visible binding for
global variable ‘variance.matrix’
.plot.pairs: no visible binding for global variable ‘variance.matrix’
.plot.pairs: no visible binding for global variable ‘ratio.matrix’
.resolve.conflicts: no visible binding for global variable ‘false’
create.meta.reports: no visible binding for global variable ‘lratio’
create.meta.reports: no visible binding for global variable
‘p.value.rat’
create.meta.reports: no visible binding for global variable ‘comp’
create.meta.reports: no visible binding for global variable ‘x’
create.meta.reports: no visible binding for global variable ‘y’
create.meta.reports: no visible binding for global variable ‘TRUE’
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’
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 ‘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 ... WARNING
package ‘MSnbase’ exists but was not installed under R >= 2.10.0 so xrefs cannot be checked
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [74s/76s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
NoiseModel-class 30.342 0.092 31.606
calculate.dNSAF 5.664 0.028 5.693
peptide.count 5.493 0.032 5.589
* 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
‘/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 ‘"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-ptm.Rnw’ using ‘UTF-8’
‘isobar.Rnw’ using ‘UTF-8’
** testing if installed package can be loaded
* DONE (isobar)