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CHECK report for MSstats on tokay1

This page was generated on 2019-04-13 11:23:18 -0400 (Sat, 13 Apr 2019).

Package 1013/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstats 3.14.1
Meena Choi
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/MSstats
Branch: RELEASE_3_8
Last Commit: 3dfe3d7
Last Changed Date: 2019-01-04 13:41:02 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSstats
Version: 3.14.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MSstats_3.14.1.tar.gz
StartedAt: 2019-04-13 04:02:42 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:23:51 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 1268.7 seconds
RetCode: 0
Status:  OK  
CheckDir: MSstats.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MSstats_3.14.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MSstats.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '3.14.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... 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
* 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
* 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
designSampleSizeClassificationPlots 295.83   0.36  296.21
designSampleSizeClassification      277.73   0.51  278.44
dataProcessPlots                      5.44   0.06    5.50
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
designSampleSizeClassificationPlots 253.12   0.09  253.25
designSampleSizeClassification      251.84   0.20  252.06
dataProcessPlots                      5.92   0.02    5.94
* 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/MSstats.Rcheck/00check.log'
for details.



Installation output

MSstats.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MSstats_3.14.1.tar.gz && rm -rf MSstats.buildbin-libdir && mkdir MSstats.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSstats.buildbin-libdir MSstats_3.14.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MSstats_3.14.1.zip && rm MSstats_3.14.1.tar.gz MSstats_3.14.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  202k  100  202k    0     0  5857k      0 --:--:-- --:--:-- --:--:-- 6527k

install for i386

* installing *source* package 'MSstats' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSstats'
    finding HTML links ... done
    DDARawData                              html  
    DDARawData.Skyline                      html  
    DIARawData                              html  
    DIAUmpiretoMSstatsFormat                html  
    MSstats-package                         html  
    MaxQtoMSstatsFormat                     html  
    OpenMStoMSstatsFormat                   html  
    OpenSWATHtoMSstatsFormat                html  
    PDtoMSstatsFormat                       html  
    ProgenesistoMSstatsFormat               html  
    SRMRawData                              html  
    SkylinetoMSstatsFormat                  html  
    SpectronauttoMSstatsFormat              html  
    SpikeInDataLinear                       html  
    SpikeInDataNonLinear                    html  
    dataProcess                             html  
    dataProcessPlots                        html  
    designSampleSize                        html  
    designSampleSizeClassification          html  
    designSampleSizeClassificationPlots     html  
    designSampleSizePlots                   html  
    groupComparison                         html  
    groupComparisonPlots                    html  
    linear_quantlim                         html  
    modelBasedQCPlots                       html  
    nonlinear_quantlim                      html  
    plot_quantlim                           html  
    quantification                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MSstats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSstats' as MSstats_3.14.1.zip
* DONE (MSstats)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MSstats' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

MSstats.Rcheck/examples_i386/MSstats-Ex.timings

nameusersystemelapsed
DDARawData0.010.000.02
DDARawData.Skyline000
DIARawData000
DIAUmpiretoMSstatsFormat000
MaxQtoMSstatsFormat000
OpenMStoMSstatsFormat000
OpenSWATHtoMSstatsFormat000
PDtoMSstatsFormat000
ProgenesistoMSstatsFormat0.010.000.02
SRMRawData000
SkylinetoMSstatsFormat000
SpectronauttoMSstatsFormat000
SpikeInDataLinear0.210.060.26
SpikeInDataNonLinear0.040.000.05
dataProcess0.860.030.89
dataProcessPlots5.440.065.50
designSampleSize0.550.020.56
designSampleSizeClassification277.73 0.51278.44
designSampleSizeClassificationPlots295.83 0.36296.21
designSampleSizePlots0.380.050.42
groupComparison0.370.000.37
groupComparisonPlots2.530.022.55
linear_quantlim0.050.000.05
modelBasedQCPlots0.800.010.81
nonlinear_quantlim0.030.000.03
plot_quantlim0.040.000.05
quantification0.280.020.29

MSstats.Rcheck/examples_x64/MSstats-Ex.timings

nameusersystemelapsed
DDARawData000
DDARawData.Skyline000
DIARawData000
DIAUmpiretoMSstatsFormat000
MaxQtoMSstatsFormat000
OpenMStoMSstatsFormat000
OpenSWATHtoMSstatsFormat000
PDtoMSstatsFormat000
ProgenesistoMSstatsFormat000
SRMRawData000
SkylinetoMSstatsFormat000
SpectronauttoMSstatsFormat000
SpikeInDataLinear0.220.030.25
SpikeInDataNonLinear0.050.000.04
dataProcess0.840.060.91
dataProcessPlots5.920.025.94
designSampleSize0.550.030.56
designSampleSizeClassification251.84 0.20252.06
designSampleSizeClassificationPlots253.12 0.09253.25
designSampleSizePlots0.440.000.43
groupComparison0.370.030.41
groupComparisonPlots3.570.003.56
linear_quantlim0.080.000.08
modelBasedQCPlots1.420.041.45
nonlinear_quantlim0.040.000.05
plot_quantlim0.050.000.05
quantification0.490.060.55