Package: MSstats

Version: 3.15.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstats_3.15.1.tar.gz

StartedAt: 2019-04-09 03:49:10 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:02:08 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 778.5 seconds

RetCode: 0

Status:  OK

CheckDir: MSstats.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstats_3.15.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MSstats.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘3.15.1’
* 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 ... 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 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’
.runQuantification: no visible binding for global variable
  ‘datafeature’
.runQuantification: no visible binding for global variable ‘ount’
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’
OpenMStoMSstatsFormat: no visible binding for global variable
  ‘missing.col’
OpenMStoMSstatsFormat: no visible binding for global variable ‘fea’
OpenMStoMSstatsFormat: no visible binding for global variable
  ‘Intensity’
OpenMStoMSstatsFormat: no visible binding for global variable
  ‘PeptideSequence’
OpenMStoMSstatsFormat: no visible binding for global variable
  ‘ProteinName’
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’
PDtoMSstatsFormat: no visible binding for global variable ‘fea’
PDtoMSstatsFormat: no visible binding for global variable ‘Intensity’
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 ‘FEATURE’
dataProcess: no visible binding for global variable ‘ncount’
dataProcess: no visible binding for global variable ‘ABUNDANCE’
dataProcess: no visible binding for global variable ‘RUN’
dataProcess: no visible binding for global variable ‘FRACTION’
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’
designSampleSizeClassificationPlots: no visible binding for global
  variable ‘Train_size’
designSampleSizeClassificationPlots: no visible binding for global
  variable ‘Protein_number’
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’
Undefined global functions or variables:
  ABUNDANCE FEATURE FRACTION Intensity LABEL Mean Name PeptideSequence
  Protein ProteinName Protein_number RUN Selected_fragments
  Selected_peptides Train_size aggr_Fragment_Annotation aggr_Peak_Area
  analysis ciw datafeature fea label logFC missing.col ncount ount
  residual 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                       user system elapsed
designSampleSizeClassification      286.630 16.829 302.376
designSampleSizeClassificationPlots 285.901 16.824 309.483
dataProcessPlots                     11.187  0.221  11.640
groupComparisonPlots                  5.626  0.842   4.917
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/MSstats.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MSstats
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MSstats’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstats)

name	user	system	elapsed
DDARawData	0.010	0.001	0.011
DDARawData.Skyline	0.010	0.002	0.011
DIARawData	0.007	0.001	0.007
DIAUmpiretoMSstatsFormat	0.006	0.001	0.007
MaxQtoMSstatsFormat	0.005	0.001	0.006
OpenMStoMSstatsFormat	0.001	0.000	0.000
OpenSWATHtoMSstatsFormat	0.000	0.001	0.000
PDtoMSstatsFormat	0.006	0.001	0.007
ProgenesistoMSstatsFormat	0.005	0.001	0.006
SRMRawData	0.005	0.001	0.007
SkylinetoMSstatsFormat	0.005	0.001	0.007
SpectronauttoMSstatsFormat	0.005	0.002	0.006
SpikeInDataLinear	0.554	0.017	0.573
SpikeInDataNonLinear	0.086	0.001	0.087
dataProcess	1.165	0.148	1.314
dataProcessPlots	11.187	0.221	11.640
designSampleSize	0.996	0.192	0.901
designSampleSizeClassification	286.630	16.829	302.376
designSampleSizeClassificationPlots	285.901	16.824	309.483
designSampleSizePlots	1.614	0.035	0.626
groupComparison	1.110	0.256	0.510
groupComparisonPlots	5.626	0.842	4.917
linear_quantlim	0.073	0.002	0.074
modelBasedQCPlots	1.874	0.489	1.473
nonlinear_quantlim	0.061	0.001	0.062
plot_quantlim	0.073	0.001	0.075
quantification	0.355	0.020	0.377