MSstats 3.7.0
Meena Choi
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSstats | | Last Changed Rev: 122712 / Revision: 127142 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| toluca2 | Mac OS X Mavericks (10.9.5) / 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 MSstats_3.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MSstats.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘3.7.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstats’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘MSnbase’ ‘Rcpp’ ‘data.table’ ‘limma’ ‘minpack.lm’ ‘preprocessCore’
‘reshape’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.iter.wls.fit.model: no visible binding for global variable ‘weight’
.multiplot: no visible global function definition for ‘grid.newpage’
.multiplot: no visible global function definition for ‘pushViewport’
.multiplot: no visible global function definition for ‘grid.layout’
.runQuantification: no visible binding for global variable
‘datafeature’
dataProcess: no visible global function definition for
‘normalize.quantiles’
dataProcess: no visible binding for global variable ‘RUN’
dataProcess: no visible binding for global variable ‘LABEL’
dataProcessPlots: no visible binding for global variable ‘RUN’
dataProcessPlots: no visible binding for global variable ‘ABUNDANCE’
dataProcessPlots: no visible binding for global variable ‘Name’
dataProcessPlots: no visible binding for global variable ‘analysis’
dataProcessPlots: no visible binding for global variable ‘Mean’
dataProcessPlots: no visible binding for global variable ‘ciw’
groupComparisonPlots: no visible binding for global variable ‘Protein’
groupComparisonPlots: no visible binding for global variable ‘logFC’
groupComparisonPlots: no visible binding for global variable ‘ciw’
linear_quantlim: no visible binding for global variable ‘label’
linear_quantlim: no visible global function definition for ‘nlsLM’
linear_quantlim: no visible global function definition for
‘nls.lm.control’
modelBasedQCPlots: no visible binding for global variable ‘residual’
nonlinear_quantlim: no visible binding for global variable ‘label’
nonlinear_quantlim: no visible global function definition for ‘nlsLM’
nonlinear_quantlim: no visible global function definition for
‘nls.lm.control’
plot_quantlim: no visible binding for global variable ‘x’
plot_quantlim: no visible binding for global variable ‘y’
plot_quantlim: no visible binding for global variable ‘ymin’
plot_quantlim: no visible binding for global variable ‘ymax’
plot_quantlim: no visible binding for global variable ‘shape’
transformMSnSetToMSstats: no visible global function definition for
‘pData’
transformMSnSetToMSstats: no visible global function definition for
‘fData’
transformMSnSetToMSstats: no visible global function definition for
‘exprs’
transformMSstatsToMSnSet: no visible global function definition for
‘MSnSet’
transformMSstatsToMSnSet: no visible global function definition for
‘sampleNames<-’
transformMSstatsToMSnSet: no visible global function definition for
‘featureNames<-’
transformMSstatsToMSnSet: no visible global function definition for
‘fData’
Undefined global functions or variables:
ABUNDANCE LABEL MSnSet Mean Name Protein RUN analysis ciw datafeature
exprs fData featureNames<- grid.layout grid.newpage label logFC
nls.lm.control nlsLM normalize.quantiles pData pushViewport residual
sampleNames<- shape weight x y ymax ymin
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_quantlim 19.095 0.990 20.141
nonlinear_quantlim 18.649 1.054 19.715
dataProcessPlots 12.516 0.059 12.586
linear_quantlim 9.415 0.642 10.063
groupComparisonPlots 5.943 0.046 6.080
transformMSnSetToMSstats 4.427 0.225 7.502
* 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
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/MSstats.Rcheck/00check.log’
for details.