Package: MSstats

Version: 3.16.2

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MSstats_3.16.2.tar.gz

StartedAt: 2019-10-16 03:24:05 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:34:59 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 653.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MSstats.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MSstats_3.16.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MSstats.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘3.16.2’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘MASS::select’ by ‘dplyr::select’ when loading ‘MSstats’
See ‘/home/biocbuild/bbs-3.9-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’
.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’
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’
designSampleSizeClassificationPlots: no visible binding for global
  variable ‘Train_size’
designSampleSizeClassificationPlots: no visible binding for global
  variable ‘Protein_number’
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 Protein_number
  RUN Selected_fragments Selected_peptides Train_size
  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 ount 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 or elapsed time > 5s
                                       user system elapsed
designSampleSizeClassification      275.035  0.207 276.448
designSampleSizeClassificationPlots 258.440  0.036 260.273
groupComparisonPlots                  5.275  0.024   4.581
dataProcessPlots                      5.086  0.012   5.106
* 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-3.9-bioc/meat/MSstats.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MSstats
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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
Warning: replacing previous import ‘MASS::select’ by ‘dplyr::select’ when loading ‘MSstats’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘MASS::select’ by ‘dplyr::select’ when loading ‘MSstats’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘MASS::select’ by ‘dplyr::select’ when loading ‘MSstats’
** testing if installed package keeps a record of temporary installation path
* DONE (MSstats)

name	user	system	elapsed
DDARawData	0.006	0.000	0.006
DDARawData.Skyline	0.005	0.000	0.005
DIARawData	0.003	0.000	0.002
DIAUmpiretoMSstatsFormat	0.002	0.000	0.002
MaxQtoMSstatsFormat	0.002	0.000	0.002
OpenMStoMSstatsFormat	0	0	0
OpenSWATHtoMSstatsFormat	0	0	0
PDtoMSstatsFormat	0.002	0.000	0.002
ProgenesistoMSstatsFormat	0.003	0.000	0.002
SRMRawData	0.002	0.000	0.002
SkylinetoMSstatsFormat	0.002	0.000	0.002
SpectronauttoMSstatsFormat	0.002	0.000	0.002
SpikeInDataLinear	0.331	0.003	0.334
SpikeInDataNonLinear	0.034	0.000	0.034
dataProcess	0.846	0.044	0.891
dataProcessPlots	5.086	0.012	5.106
designSampleSize	1.357	0.009	1.048
designSampleSizeClassification	275.035	0.207	276.448
designSampleSizeClassificationPlots	258.440	0.036	260.273
designSampleSizePlots	1.171	0.008	0.575
groupComparison	0.649	0.004	0.451
groupComparisonPlots	5.275	0.024	4.581
linear_quantlim	0.041	0.004	0.045
modelBasedQCPlots	1.449	0.004	1.254
nonlinear_quantlim	0.033	0.000	0.033
plot_quantlim	0.032	0.000	0.033
quantification	0.312	0.004	0.324