isobar 1.12.2
Florian P Breitwieser
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/isobar | | Last Changed Rev: 98146 / Revision: 102249 | | Last Changed Date: 2015-01-07 13:43:38 -0800 (Wed, 07 Jan 2015) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch isobar_1.12.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/isobar.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘isobar/DESCRIPTION’ ... OK
* this is package ‘isobar’ version ‘1.12.2’
* 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 ... [9s/9s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘DBI’ ‘Hmisc’ ‘MSnbase’ ‘OrgMassSpecR’ ‘RColorBrewer’ ‘RJSONIO’ ‘XML’
‘boot’ ‘distr’ ‘ggplot2’ ‘gplots’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
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’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.IBSpectraAsConciseDataFrameNew: no visible global function definition
for ‘fData’
.calculate.mw : <anonymous> : <anonymous>: no visible global function
definition for ‘MolecularWeight’
.calculate.mw : <anonymous> : <anonymous>: no visible global function
definition for ‘ConvertPeptide’
.call.estimateRatio: no visible global function definition for
‘assayDataElementNames’
.call.estimateRatio: no visible global function definition for ‘fData’
.create.or.load.ibspectra: no visible global function definition for
‘fData’
.create.or.load.ibspectra: no visible global function definition for
‘fData<-’
.create.or.load.quant.table : <anonymous>: no visible global function
definition for ‘fData’
.create.or.load.quant.table : <anonymous>: no visible global function
definition for ‘fData<-’
.gg_element_text: no visible global function definition for
‘element_text’
.gg_element_text: no visible global function definition for
‘theme_text’
.gg_theme: no visible global function definition for ‘theme’
.gg_theme: no visible global function definition for ‘opts’
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
.panel.txt: no visible global function definition for ‘brewer.pal’
.plot.heatmaps: no visible global function definition for ‘heatmap.2’
.plot.heatmaps: no visible global function definition for ‘greenred’
.plot.heatmaps.gd: no visible global function definition for
‘heatmap.2’
.plot.heatmaps.gd: no visible global function definition for ‘greenred’
.scatter.plot: no visible global function definition for ‘ggplot’
.scatter.plot: no visible global function definition for ‘geom_point’
.scatter.plot: no visible global function definition for ‘aes_string’
.scatter.plot: no visible global function definition for ‘facet_wrap’
.sel.outliers: no visible global function definition for ‘wtd.quantile’
getProteinInfoFromBioDb: no visible global function definition for
‘dbConnect’
getProteinInfoFromBioDb: no visible global function definition for
‘dbGetQuery’
getProteinInfoFromBioDb: no visible global function definition for
‘dbDisconnect’
getProteinInfoFromEntrez: no visible global function definition for
‘xmlToList’
getPtmInfoFromNextprot : <anonymous>: no visible global function
definition for ‘fromJSON’
ibSpectra.as.concise.data.frame: no visible global function definition
for ‘fData’
initialize.env: no visible global function definition for ‘fData’
initialize.env: no visible global function definition for ‘fData<-’
observable.peptides: no visible global function definition for ‘Digest’
peptideRatiosNotQuant: no visible global function definition for
‘fData’
read.mzid: no visible global function definition for
‘xmlInternalTreeParse’
read.mzid: no visible global function definition for ‘xmlNamespace’
read.mzid: no visible global function definition for ‘xmlRoot’
read.mzid: no visible global function definition for ‘xpathSApply’
read.mzid: no visible binding for global variable ‘xmlGetAttr’
read.mzid: no visible global function definition for ‘xpathApply’
read.mzid : <anonymous>: no visible global function definition for
‘xmlAttrs’
read.mzid : <anonymous>: no visible global function definition for
‘getNodeSet’
read.mzid : <anonymous>: no visible global function definition for
‘xmlGetAttr’
read.mzid : <anonymous>: no visible global function definition for
‘xmlValue’
read.mzid : <anonymous>: no visible global function definition for
‘xpathSApply’
read.mzid : <anonymous> : <anonymous>: no visible global function
definition for ‘xmlGetAttr’
read.mzid : <anonymous>: no visible binding for global variable
‘xmlGetAttr’
read.mzid : <anonymous>: no visible global function definition for
‘xmlApply’
read.mzid : <anonymous> : <anonymous>: no visible global function
definition for ‘xpathSApply’
read.mzid : <anonymous> : <anonymous>: no visible binding for global
variable ‘xmlGetAttr’
read.mzid : <anonymous>: no visible global function definition for
‘xpathApply’
read.mzid: no visible binding for global variable ‘xmlAttrs’
read.mzid: no visible global function definition for ‘free’
readPhosphoRSOutput: no visible global function definition for
‘xmlTreeParse’
readPhosphoRSOutput: no visible global function definition for
‘xmlRoot’
readPhosphoRSOutput: no visible global function definition for
‘xmlApply’
readPhosphoRSOutput : <anonymous>: no visible global function
definition for ‘xmlAttrs’
readPhosphoRSOutput : <anonymous>: no visible global function
definition for ‘xmlApply’
readPhosphoRSOutput : <anonymous> : <anonymous>: no visible global
function definition for ‘xmlAttrs’
readPhosphoRSOutput : <anonymous> : <anonymous>: no visible global
function definition for ‘xmlSApply’
readPhosphoRSOutput : <anonymous> : <anonymous>: no visible binding for
global variable ‘xmlAttrs’
readPhosphoRSOutput : <anonymous> : <anonymous> : <anonymous>: no
visible global function definition for ‘xmlSApply’
readPhosphoRSOutput : <anonymous> : <anonymous> : <anonymous>: no
visible binding for global variable ‘xmlGetAttr’
readPhosphoRSOutput : <anonymous> : <anonymous> : <anonymous>: no
visible global function definition for ‘xmlAttrs’
readPhosphoRSOutput: no visible global function definition for
‘xmlChildren’
readPhosphoRSOutput: no visible binding for global variable
‘xmlGetAttr’
shared.ratios.sign: no visible global function definition for ‘ggplot’
shared.ratios.sign: no visible global function definition for
‘aes_string’
shared.ratios.sign: no visible global function definition for
‘geom_vline’
shared.ratios.sign: no visible global function definition for
‘geom_point’
shared.ratios.sign: no visible global function definition for
‘geom_errorbarh’
shared.ratios.sign: no visible global function definition for ‘aes’
shared.ratios.sign: no visible binding for global variable ‘ratio’
shared.ratios.sign: no visible binding for global variable ‘g’
shared.ratios.sign: no visible global function definition for
‘scale_x_continuous’
shared.ratios.sign: no visible global function definition for
‘scale_colour_manual’
shared.ratios.sign: no visible global function definition for
‘scale_shape’
shared.ratios.sign: no visible global function definition for
‘scale_size’
spectra.count2: no visible global function definition for ‘fData’
spectra.count2: no visible binding for global variable ‘peptide’
subsetIBSpectra: no visible global function definition for
‘assayDataElementNames’
subsetIBSpectra: no visible global function definition for
‘assayDataElement<-’
subsetIBSpectra: no visible global function definition for
‘assayDataElement’
subsetIBSpectra: no visible global function definition for ‘fData’
subsetIBSpectra: no visible global function definition for
‘featureData<-’
twodistr.plot: no visible global function definition for ‘ggplot’
twodistr.plot: no visible global function definition for ‘geom_line’
twodistr.plot: no visible global function definition for ‘aes_string’
twodistr.plot: no visible global function definition for ‘ggtitle’
writeData: no visible global function definition for ‘sampleNames’
classLabels,IBSpectra: no visible global function definition for
‘phenoData’
classLabels<-,IBSpectra: no visible global function definition for
‘phenoData’
classLabels<-,IBSpectra: no visible global function definition for
‘phenoData<-’
coerce,IBSpectra-MSnSet: no visible global function definition for
‘assayDataElementNames’
coerce,IBSpectra-MSnSet : get.elem: no visible global function
definition for ‘assayDataElement’
coerce,IBSpectra-MSnSet: no visible binding for global variable
‘iTRAQ4’
coerce,IBSpectra-MSnSet: no visible binding for global variable
‘iTRAQ8’
coerce,IBSpectra-MSnSet: no visible binding for global variable ‘TMT6’
coerce,IBSpectra-MSnSet: no visible global function definition for ‘mz’
coerce,IBSpectra-MSnSet: no visible binding for global variable ‘o’
coerce,IBSpectra-MSnSet: no visible global function definition for
‘fData’
coerce,IBSpectra-data.frame: no visible global function definition for
‘fData’
coerce,MSnSet-IBSpectra: no visible global function definition for
‘exprs’
coerce,MSnSet-IBSpectra: no visible global function definition for
‘qual’
coerce,MSnSet-IBSpectra: no visible global function definition for
‘fData’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘ggplot’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘aes_string’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘geom_boxplot’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘position_dodge’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘xlab’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘scale_y_log10’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘theme_bw’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘scale_color_hue’
show,IBSpectra: no visible global function definition for ‘fData’
spectrumTitles,IBSpectra : <anonymous>: no visible global function
definition for ‘fData’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [39s/42s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
NoiseModel-class 11.899 0.22 12.698
* 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
* DONE
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-3.0-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)