BioC 3.4: CHECK report for MSstats on malbec1

Package: MSstats

Version: 3.6.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MSstats_3.6.0.tar.gz

StartedAt: 2017-04-15 00:02:09 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:04:14 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 124.9 seconds

RetCode: 0

Status:  OK

CheckDir: MSstats.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MSstats_3.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/MSstats.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘3.6.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
nonlinear_quantlim       13.324  0.288  13.644
plot_quantlim            12.996  0.320  13.344
linear_quantlim           7.392  0.296   7.702
dataProcessPlots          6.184  0.032   6.229
transformMSnSetToMSstats  4.500  0.132   7.147
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/MSstats.Rcheck/00check.log’
for details.

* installing *source* package ‘MSstats’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSstats)

name	user	system	elapsed
DDARawData	0.008	0.000	0.007
DDARawData.Skyline	0.004	0.000	0.005
DIARawData	0.000	0.004	0.003
SRMRawData	0.004	0.000	0.003
SpikeInDataLinear	0.012	0.000	0.012
SpikeInDataNonLinear	0.008	0.000	0.008
dataProcess	0.628	0.076	0.731
dataProcessPlots	6.184	0.032	6.229
designSampleSize	0.388	0.044	0.437
designSampleSizePlots	0.448	0.020	0.474
groupComparison	0.328	0.040	0.373
groupComparisonPlots	3.140	0.044	3.193
linear_quantlim	7.392	0.296	7.702
modelBasedQCPlots	0.840	0.024	0.872
nonlinear_quantlim	13.324	0.288	13.644
plot_quantlim	12.996	0.320	13.344
quantification	0.288	0.036	0.327
transformMSnSetToMSstats	4.500	0.132	7.147
transformMSstatsToMSnSet	0.22	0.00	0.22