Package: MSstats

Version: 3.10.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSstats_3.10.6.tar.gz

StartedAt: 2018-04-12 06:48:54 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 06:54:00 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 305.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MSstats.Rcheck

Warnings: 1

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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_3.10.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MSstats.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘3.10.6’
* 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 ‘MSstats’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘foreach::accumulate’ by ‘purrr::accumulate’ when loading ‘MSstats’
  Warning: replacing previous import ‘foreach::when’ by ‘purrr::when’ when loading ‘MSstats’
See ‘/Users/biocbuild/bbs-3.6-bioc/meat/MSstats.Rcheck/00install.out’ for details.
* 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 ... OK
* 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’
DIAUmpiretoMSstatsFormat: no visible binding for global variable
  ‘Selected_fragments’
DIAUmpiretoMSstatsFormat: no visible binding for global variable
  ‘Selected_peptides’
DIAUmpiretoMSstatsFormat: no visible binding for global variable ‘fea’
DIAUmpiretoMSstatsFormat: no visible binding for global variable
  ‘Intensity’
OpenSWATHtoMSstatsFormat: no visible binding for global variable
  ‘missing.col’
OpenSWATHtoMSstatsFormat: no visible binding for global variable
  ‘aggr_Fragment_Annotation’
OpenSWATHtoMSstatsFormat: no visible binding for global variable
  ‘aggr_Peak_Area’
OpenSWATHtoMSstatsFormat: no visible binding for global variable ‘fea’
OpenSWATHtoMSstatsFormat: no visible binding for global variable
  ‘Intensity’
OpenSWATHtoMSstatsFormat: no visible binding for global variable
  ‘PeptideSequence’
OpenSWATHtoMSstatsFormat: no visible binding for global variable
  ‘ProteinName’
SkylinetoMSstatsFormat: no visible binding for global variable
  ‘PeptideSequence’
SkylinetoMSstatsFormat: no visible binding for global variable
  ‘ProteinName’
SkylinetoMSstatsFormat: no visible binding for global variable ‘fea’
SkylinetoMSstatsFormat: no visible binding for global variable
  ‘Intensity’
SpectronauttoMSstatsFormat: no visible binding for global variable
  ‘missing.col’
SpectronauttoMSstatsFormat: no visible binding for global variable
  ‘fea’
SpectronauttoMSstatsFormat: no visible binding for global variable
  ‘Intensity’
SpectronauttoMSstatsFormat: no visible binding for global variable
  ‘PeptideSequence’
SpectronauttoMSstatsFormat: no visible binding for global variable
  ‘ProteinName’
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’
modelBasedQCPlots: no visible binding for global variable ‘residual’
nonlinear_quantlim: no visible binding for global variable ‘label’
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
  ‘exprs’
transformMSstatsToMSnSet: no visible global function definition for
  ‘sampleNames<-’
transformMSstatsToMSnSet: no visible global function definition for
  ‘featureNames<-’
Undefined global functions or variables:
  ABUNDANCE Intensity LABEL Mean Name PeptideSequence Protein
  ProteinName RUN Selected_fragments Selected_peptides
  aggr_Fragment_Annotation aggr_Peak_Area analysis ciw datafeature
  exprs fea featureNames<- grid.layout grid.newpage label logFC
  missing.col 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
dataProcessPlots      12.424  0.074  20.682
dataProcess            5.922  0.075  29.558
groupComparisonPlots   5.477  0.095  13.079
designSampleSize       3.018  0.033  11.100
modelBasedQCPlots      1.851  0.036   9.741
designSampleSizePlots  1.170  0.026   9.520
quantification         1.106  0.024   9.270
groupComparison        0.930  0.023   8.507
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-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
Warning: replacing previous import ‘foreach::accumulate’ by ‘purrr::accumulate’ when loading ‘MSstats’
Warning: replacing previous import ‘foreach::when’ by ‘purrr::when’ when loading ‘MSstats’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘foreach::accumulate’ by ‘purrr::accumulate’ when loading ‘MSstats’
Warning: replacing previous import ‘foreach::when’ by ‘purrr::when’ when loading ‘MSstats’
* DONE (MSstats)

name	user	system	elapsed
DDARawData	0.009	0.001	0.010
DDARawData.Skyline	0.007	0.002	0.009
DIARawData	0.005	0.001	0.006
DIAUmpiretoMSstatsFormat	0.005	0.001	0.004
MaxQtoMSstatsFormat	0.004	0.000	0.004
OpenSWATHtoMSstatsFormat	0.001	0.001	0.000
PDtoMSstatsFormat	0.004	0.000	0.004
ProgenesistoMSstatsFormat	0.005	0.001	0.004
SRMRawData	0.004	0.000	0.005
SkylinetoMSstatsFormat	0.003	0.000	0.003
SpectronauttoMSstatsFormat	0.004	0.001	0.006
SpikeInDataLinear	0.645	0.006	0.697
SpikeInDataNonLinear	0.290	0.001	0.298
dataProcess	5.922	0.075	29.558
dataProcessPlots	12.424	0.074	20.682
designSampleSize	3.018	0.033	11.100
designSampleSizePlots	1.170	0.026	9.520
groupComparison	0.930	0.023	8.507
groupComparisonPlots	5.477	0.095	13.079
linear_quantlim	0.072	0.001	0.074
modelBasedQCPlots	1.851	0.036	9.741
nonlinear_quantlim	0.062	0.000	0.067
plot_quantlim	0.063	0.001	0.066
quantification	1.106	0.024	9.270
transformMSnSetToMSstats	0.876	0.149	1.458
transformMSstatsToMSnSet	0.392	0.007	0.411