Package: MSstats

Version: 3.10.6

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MSstats_3.10.6.tar.gz

StartedAt: 2018-04-12 01:20:03 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:24:13 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 249.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MSstats.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MSstats_3.10.6.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/MSstats.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘3.10.6’
* 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 ‘/home/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 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      8.792  0.068  15.360
dataProcess           5.116  0.308  25.569
groupComparisonPlots  4.192  0.100  10.801
designSampleSize      2.904  0.108   9.524
modelBasedQCPlots     1.732  0.136   8.646
designSampleSizePlots 1.060  0.076   7.667
quantification        0.828  0.072   7.553
groupComparison       0.792  0.064   7.273
* 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
  ‘/home/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	0.004	0.000	0.005
DDARawData.Skyline	0.012	0.000	0.013
DIARawData	0.000	0.000	0.003
DIAUmpiretoMSstatsFormat	0.004	0.000	0.002
MaxQtoMSstatsFormat	0.004	0.000	0.002
OpenSWATHtoMSstatsFormat	0	0	0
PDtoMSstatsFormat	0.004	0.000	0.002
ProgenesistoMSstatsFormat	0.004	0.000	0.002
SRMRawData	0.000	0.000	0.003
SkylinetoMSstatsFormat	0.000	0.000	0.003
SpectronauttoMSstatsFormat	0.004	0.000	0.003
SpikeInDataLinear	0.408	0.000	0.409
SpikeInDataNonLinear	0.208	0.000	0.208
dataProcess	5.116	0.308	25.569
dataProcessPlots	8.792	0.068	15.360
designSampleSize	2.904	0.108	9.524
designSampleSizePlots	1.060	0.076	7.667
groupComparison	0.792	0.064	7.273
groupComparisonPlots	4.192	0.100	10.801
linear_quantlim	0.064	0.004	0.068
modelBasedQCPlots	1.732	0.136	8.646
nonlinear_quantlim	0.044	0.000	0.043
plot_quantlim	0.040	0.000	0.042
quantification	0.828	0.072	7.553
transformMSnSetToMSstats	0.704	0.120	1.060
transformMSstatsToMSnSet	0.324	0.004	0.332