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BioC 3.5: CHECK report for MSstats on tokay2

This page was generated on 2017-10-16 14:23:06 -0400 (Mon, 16 Oct 2017).

Package 864/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstats 3.8.6
Meena Choi
Snapshot Date: 2017-10-15 17:01:01 -0400 (Sun, 15 Oct 2017)
URL: https://git.bioconductor.org/packages/MSstats
Branch: RELEASE_3_5
Last Commit: e0cb9f5
Last Changed Date: 2017-10-12 01:02:08 -0400 (Thu, 12 Oct 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSstats
Version: 3.8.6
Command: rm -rf MSstats.buildbin-libdir MSstats.Rcheck && mkdir MSstats.buildbin-libdir MSstats.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSstats.buildbin-libdir MSstats_3.8.6.tar.gz >MSstats.Rcheck\00install.out 2>&1 && cp MSstats.Rcheck\00install.out MSstats-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MSstats.buildbin-libdir --install="check:MSstats-install.out" --force-multiarch --no-vignettes --timings MSstats_3.8.6.tar.gz
StartedAt: 2017-10-16 01:54:04 -0400 (Mon, 16 Oct 2017)
EndedAt: 2017-10-16 01:59:08 -0400 (Mon, 16 Oct 2017)
EllapsedTime: 304.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: MSstats.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MSstats.buildbin-libdir MSstats.Rcheck && mkdir MSstats.buildbin-libdir MSstats.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSstats.buildbin-libdir MSstats_3.8.6.tar.gz >MSstats.Rcheck\00install.out 2>&1 && cp MSstats.Rcheck\00install.out MSstats-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MSstats.buildbin-libdir --install="check:MSstats-install.out" --force-multiarch --no-vignettes --timings MSstats_3.8.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MSstats.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSstats/DESCRIPTION' ... OK
* this is package 'MSstats' version '3.8.6'
* 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 whether package 'MSstats' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'MSnbase::image' by 'graphics::image' when loading 'MSstats'
See 'C:/Users/biocbuild/bbs-3.5-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
SpectronauttoMSstatsFormat: no visible binding for global variable
  'missing.col'
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
  'pData'
Undefined global functions or variables:
  ABUNDANCE LABEL Mean Name Protein RUN analysis ciw datafeature
  grid.layout grid.newpage label logFC missing.col pData pushViewport
  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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
dataProcessPlots         7.66   0.03    7.69
transformMSnSetToMSstats 1.12   0.05    7.60
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
dataProcessPlots         9.80   0.05    9.91
transformMSnSetToMSstats 0.86   0.03   10.08
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/MSstats.Rcheck/00check.log'
for details.


MSstats.Rcheck/00install.out:


install for i386

* installing *source* package 'MSstats' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: replacing previous import 'MSnbase::image' by 'graphics::image' when loading 'MSstats'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'MSnbase::image' by 'graphics::image' when loading 'MSstats'

install for x64

* installing *source* package 'MSstats' ...
** testing if installed package can be loaded
Warning: replacing previous import 'MSnbase::image' by 'graphics::image' when loading 'MSstats'
* MD5 sums
packaged installation of 'MSstats' as MSstats_3.8.6.zip
* DONE (MSstats)

MSstats.Rcheck/examples_i386/MSstats-Ex.timings:

nameusersystemelapsed
DDARawData000
DDARawData.Skyline000
DIARawData000
MaxQtoMSstatsFormat000
PDtoMSstatsFormat0.020.000.02
ProgenesistoMSstatsFormat000
SRMRawData000
SkylinetoMSstatsFormat000
SpectronauttoMSstatsFormat000
SpikeInDataLinear0.070.000.06
SpikeInDataNonLinear0.090.000.09
dataProcess3.470.103.56
dataProcessPlots7.660.037.69
designSampleSize1.670.001.67
designSampleSizePlots0.480.010.50
groupComparison0.240.020.25
groupComparisonPlots3.450.063.52
linear_quantlim000
modelBasedQCPlots0.750.020.76
nonlinear_quantlim0.020.000.02
plot_quantlim0.020.000.01
quantification0.250.030.28
transformMSnSetToMSstats1.120.057.60
transformMSstatsToMSnSet0.330.030.36

MSstats.Rcheck/examples_x64/MSstats-Ex.timings:

nameusersystemelapsed
DDARawData0.010.000.01
DDARawData.Skyline000
DIARawData000
MaxQtoMSstatsFormat000
PDtoMSstatsFormat000
ProgenesistoMSstatsFormat0.020.000.01
SRMRawData000
SkylinetoMSstatsFormat000
SpectronauttoMSstatsFormat000
SpikeInDataLinear0.090.000.10
SpikeInDataNonLinear0.110.000.11
dataProcess3.840.063.93
dataProcessPlots9.800.059.91
designSampleSize1.800.011.81
designSampleSizePlots0.540.030.58
groupComparison0.280.000.28
groupComparisonPlots3.740.073.80
linear_quantlim000
modelBasedQCPlots1.340.001.56
nonlinear_quantlim0.020.000.02
plot_quantlim0.010.000.01
quantification0.410.000.41
transformMSnSetToMSstats 0.86 0.0310.08
transformMSstatsToMSnSet0.360.030.39