Package: MSstats

Version: 3.12.3

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_3.12.3.tar.gz

StartedAt: 2018-10-16 22:49:18 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:02:17 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 779.1 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_3.12.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MSstats.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘3.12.3’
* 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
designSampleSizeClassificationPlots 317.900  8.488 332.273
designSampleSizeClassification      306.782  8.551 318.270
dataProcessPlots                      8.412  0.082   8.651
* 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-3.7-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/3.5/Resources/library’
* installing *source* package ‘MSstats’ ...
** 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
* DONE (MSstats)

name	user	system	elapsed
DDARawData	0.009	0.001	0.010
DDARawData.Skyline	0.006	0.001	0.007
DIARawData	0.006	0.001	0.007
DIAUmpiretoMSstatsFormat	0.005	0.001	0.005
MaxQtoMSstatsFormat	0.006	0.001	0.006
OpenMStoMSstatsFormat	0.001	0.000	0.001
OpenSWATHtoMSstatsFormat	0.002	0.000	0.002
PDtoMSstatsFormat	0.005	0.000	0.006
ProgenesistoMSstatsFormat	0.006	0.001	0.006
SRMRawData	0.004	0.001	0.004
SkylinetoMSstatsFormat	0.005	0.000	0.005
SpectronauttoMSstatsFormat	0.005	0.001	0.006
SpikeInDataLinear	0.316	0.006	0.324
SpikeInDataNonLinear	0.054	0.000	0.055
dataProcess	1.276	0.071	1.374
dataProcessPlots	8.412	0.082	8.651
designSampleSize	0.882	0.025	1.052
designSampleSizeClassification	306.782	8.551	318.270
designSampleSizeClassificationPlots	317.900	8.488	332.273
designSampleSizePlots	0.610	0.047	0.661
groupComparison	0.567	0.028	0.604
groupComparisonPlots	4.271	0.035	4.354
linear_quantlim	0.063	0.001	0.063
modelBasedQCPlots	1.284	0.025	1.325
nonlinear_quantlim	0.061	0.001	0.061
plot_quantlim	0.056	0.000	0.059
quantification	0.400	0.021	0.432