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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MSstats_3.22.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MSstats.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '3.22.1'
* package encoding: UTF-8
* 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 ... 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'
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'
PhilosophertoMSstatsFormat: no visible binding for global variable
  'fea'
PhilosophertoMSstatsFormat: 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'
calc_fvar: no visible binding for global variable '.resid'
calc_fvar: no visible binding for global variable 'is_olr'
calc_fvar: no visible binding for global variable 'log2inty'
calc_fvar: no visible binding for global variable 'feature'
calc_fvar: no visible binding for global variable 'nb_run'
calc_fvar: no visible binding for global variable 'resid_null'
calc_fvar: no visible binding for global variable 'svar_feature'
calc_fvar: no visible binding for global variable 'svar_ref'
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 'PROTEIN'
dataProcess: no visible binding for global variable 'INTENSITY'
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'
flag_noninf_data: no visible binding for global variable 'PROTEIN'
flag_noninf_data: no visible binding for global variable 'PEPTIDE'
flag_noninf_data: no visible binding for global variable 'FEATURE'
flag_noninf_data: no visible binding for global variable 'originalRUN'
flag_noninf_data: no visible binding for global variable 'LABEL'
flag_noninf_data: no visible binding for global variable 'ABUNDANCE'
flag_noninf_data: no visible binding for global variable 'censored'
flag_noninf_data: no visible binding for global variable 'log2inty'
flag_noninf_data: no visible binding for global variable 'is_censored'
flag_noninf_data: no visible binding for global variable 'is_obs'
flag_noninf_data: no visible binding for global variable 'protein'
flag_noninf_data: no visible binding for global variable 'peptide'
flag_noninf_data: no visible binding for global variable 'feature'
flag_noninf_data: no visible binding for global variable 'run'
flag_noninf_data: no visible binding for global variable 'label'
flag_noninf_data: no visible binding for global variable 'nb_run'
flag_noninf_data: no visible binding for global variable 'nb_feature'
flag_noninf_data: no visible binding for global variable 'nb_obs'
flag_noninf_data: no visible binding for global variable 'nb_full'
flag_noninf_data: no visible binding for global variable 'pi_obs'
flag_noninf_data: no visible binding for global variable 'min_obs'
flag_noninf_data: no visible binding for global variable 'is_lowcvr'
flag_noninf_data: no visible binding for global variable
  'cover_feature'
flag_noninf_data: no visible binding for global variable 'rlm_fit'
flag_noninf_data: no visible binding for global variable 's_resid'
flag_noninf_data: no visible binding for global variable 'df_resid'
flag_noninf_data: no visible binding for global variable 'var_resid_eb'
flag_noninf_data: no visible binding for global variable 's_resid_eb'
flag_noninf_data: no visible binding for global variable 'is_olr'
flag_noninf_data: no visible binding for global variable 'var_feature'
flag_noninf_data: no visible binding for global variable 'svar_feature'
flag_noninf_data_nbftr: no visible binding for global variable
  'PROTEIN'
flag_noninf_data_nbftr: no visible binding for global variable
  'PEPTIDE'
flag_noninf_data_nbftr: no visible binding for global variable
  'FEATURE'
flag_noninf_data_nbftr: no visible binding for global variable
  'originalRUN'
flag_noninf_data_nbftr: no visible binding for global variable 'LABEL'
flag_noninf_data_nbftr: no visible binding for global variable
  'ABUNDANCE'
flag_noninf_data_nbftr: no visible binding for global variable
  'censored'
flag_noninf_data_nbftr: no visible binding for global variable
  'log2inty'
flag_noninf_data_nbftr: no visible binding for global variable
  'is_censored'
flag_noninf_data_nbftr: no visible binding for global variable 'is_obs'
flag_noninf_data_nbftr: no visible binding for global variable
  'protein'
flag_noninf_data_nbftr: no visible binding for global variable
  'peptide'
flag_noninf_data_nbftr: no visible binding for global variable
  'feature'
flag_noninf_data_nbftr: no visible binding for global variable 'run'
flag_noninf_data_nbftr: no visible binding for global variable 'label'
flag_noninf_data_nbftr: no visible binding for global variable
  'nb_feature'
flag_noninf_data_nbftr: no visible binding for global variable 'nb_run'
flag_noninf_data_nbftr: no visible binding for global variable 'nb_obs'
flag_noninf_data_nbftr: no visible binding for global variable
  'nb_full'
flag_noninf_data_nbftr: no visible binding for global variable 'pi_obs'
flag_noninf_data_nbftr: no visible binding for global variable
  'min_obs'
flag_noninf_data_nbftr: no visible binding for global variable
  'is_lowcvr'
flag_noninf_data_nbftr: no visible binding for global variable
  'cover_feature'
flag_noninf_data_nbftr: no visible binding for global variable
  'rlm_fit'
flag_noninf_data_nbftr: no visible binding for global variable
  's_resid'
flag_noninf_data_nbftr: no visible binding for global variable
  'df_resid'
flag_noninf_data_nbftr: no visible binding for global variable
  'var_resid_eb'
flag_noninf_data_nbftr: no visible binding for global variable
  's_resid_eb'
flag_noninf_data_nbftr: no visible binding for global variable 'is_olr'
flag_noninf_data_nbftr: no visible binding for global variable
  'var_feature'
flag_noninf_data_nbftr: no visible binding for global variable
  'svar_feature'
flag_outlier: no visible binding for global variable '.resid'
flag_outlier: no visible binding for global variable 'run'
flag_outlier: no visible binding for global variable 'feature'
flag_outlier: no visible binding for global variable 'is_olr'
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:
  .resid ABUNDANCE FEATURE FRACTION INTENSITY Intensity LABEL Mean Name
  PEPTIDE PROTEIN PeptideSequence Protein ProteinName RUN
  Selected_fragments Selected_peptides aggr_Fragment_Annotation
  aggr_Peak_Area analysis censored ciw cover_feature datafeature
  df_resid fea feature is_censored is_lowcvr is_obs is_olr label
  log2inty logFC min_obs missing.col nb_feature nb_full nb_obs nb_run
  ncount originalRUN peptide pi_obs protein resid_null residual rlm_fit
  run s_resid s_resid_eb shape svar_feature svar_ref var_feature
  var_resid_eb 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
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
dataProcessPlots 7.35   0.05     7.4
* 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-3.12-bioc/meat/MSstats.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MSstats_3.22.1.tar.gz && rm -rf MSstats.buildbin-libdir && mkdir MSstats.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSstats.buildbin-libdir MSstats_3.22.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MSstats_3.22.1.zip && rm MSstats_3.22.1.tar.gz MSstats_3.22.1.zip
###
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install for i386

* 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
  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  
    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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MSstats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSstats' as MSstats_3.22.1.zip
* DONE (MSstats)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MSstats' successfully unpacked and MD5 sums checked