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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MSstats_3.22.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/MSstats.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘3.22.1’
* 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 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’
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
dataProcessPlots 6.728  0.016   6.756
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/MSstats.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL MSstats
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* 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
** 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
* DONE (MSstats)