Mac ARM64 build report for BioC 3.19 - CHECK results for DAPAR on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4461
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DAPAR_1.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/DAPAR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.36.0’
* 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 ‘DAPAR’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 code 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 whether startup messages can be suppressed ... 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
aggregateIterParallel: no visible binding for global variable ‘cond’
averageIntensities: no visible binding for global variable ‘condition’
averageIntensities: no visible binding for global variable ‘feature’
averageIntensities: no visible binding for global variable ‘intensity’
Check_Dataset_Validity: no visible global function definition for
  ‘exprs’
createMSnset: no visible global function definition for
  ‘installed.packages’
createMSnset: no visible binding for global variable ‘Prostar.loc’
createMSnset2: no visible global function definition for
  ‘installed.packages’
createMSnset2: no visible binding for global variable ‘Prostar.loc’
diffAnaVolcanoplot_rCharts: no visible binding for global variable ‘x’
diffAnaVolcanoplot_rCharts: no visible binding for global variable ‘y’
diffAnaVolcanoplot_rCharts: no visible binding for global variable ‘g’
display.CC.visNet: no visible binding for global variable
  ‘layout_nicely’
getTextForGOAnalysis: no visible binding for global variable
  ‘textGOParams’
getTextForGOAnalysis: no visible binding for global variable ‘input’
globalAdjPval: no visible global function definition for ‘stack’
heatmapForMissingValues: no visible binding for global variable ‘par’
limmaCompleteTest: no visible binding for global variable ‘A’
limmaCompleteTest: no visible binding for global variable ‘B’
limmaCompleteTest: no visible binding for global variable ‘P.Value’
OWAnova: no visible global function definition for ‘aov’
pepa.test: no visible global function definition for ‘nodes<-’
testAnovaModels : <anonymous>: no visible global function definition
  for ‘TukeyHSD’
visualizeClusters: no visible binding for global variable
  ‘adjusted_pvalues’
visualizeClusters: no visible binding for global variable ‘Condition’
visualizeClusters: no visible binding for global variable ‘Intensity’
visualizeClusters: no visible binding for global variable
  ‘FDR_threshold’
visualizeClusters: no visible binding for global variable ‘feature’
wrapperClassic1wayAnova: no visible binding for global variable
  ‘Pr(>F)1’
wrapperRunClustering: no visible global function definition for ‘str_c’
Undefined global functions or variables:
  A adjusted_pvalues aov B cond condition Condition exprs FDR_threshold
  feature g input installed.packages intensity Intensity layout_nicely
  nodes<- P.Value par Pr(>F)1 Prostar.loc stack str_c textGOParams
  TukeyHSD x y
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "aov", "TukeyHSD")
  importFrom("utils", "installed.packages", "stack")
to your NAMESPACE file.
* 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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
wrapper.compareNormalizationD_HC 13.470  8.383  21.847
wrapper.dapar.impute.mi           5.038  0.509   5.550
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/DAPAR.Rcheck/00check.log’
for details.

Installation output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DAPAR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘DAPAR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (DAPAR)

Tests output


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(DAPAR)

This is the 'DAPAR' version 1.36.0.

  To get started, visit
    http://www.prostar-proteomics.org/


> 
> test_check("DAPAR")

 Iterations: 

 1 / 1  - Imputation MNAR OK - 
Imputation MCAR in progress - 
3 % - 6 % - 9 % - 12 % - 15 % - 18 % - 21 % - 24 % - 27 % - 30 % - 33 % - 36 % - 39 % - 42 % - 45 % - 48 % - 51 % - 54 % - 57 % - 60 % - 63 % - 66 % - 69 % - 72 % - 75 % - 78 % - 81 % - 84 % - 87 % - 90 % - 93 % - 96 % - 100 % - 
 Iterations: 

 1 / 1  - Imputation MNAR OK - 
Imputation MCAR in progress - 
3 % - 6 % - 9 % - 12 % - 15 % - 18 % - 21 % - 24 % - 27 % - 30 % - 33 % - 36 % - 39 % - 42 % - 45 % - 48 % - 51 % - 54 % - 57 % - 60 % - 63 % - 66 % - 69 % - 72 % - 75 % - 78 % - 81 % - 84 % - 87 % - 90 % - 93 % - 96 % - 100 % - 
 Imputation in condition  1 ...
 In progress: 10 % - 20 % - 30 % - 40 % - 50 % - 60 % - 70 % - 80 % - 90 % - 100 % - 
 Imputation in condition  2 ...
 In progress: 10 % - 20 % - 30 % - 40 % - 50 % - 60 % - 70 % - 80 % - 90 % - 100 % - [ FAIL 0 | WARN 17 | SKIP 0 | PASS 66 ]

[ FAIL 0 | WARN 17 | SKIP 0 | PASS 66 ]
> 
> proc.time()
   user  system elapsed 
 11.679   0.830  12.514

Example timings

name	user	system	elapsed
AggregateMetacell	0.520	0.003	0.525
BuildAdjacencyMatrix	0.118	0.001	0.121
BuildColumnToProteinDataset	0.140	0.001	0.142
BuildMetaCell	0.212	0.008	0.223
CVDistD_HC	1.068	0.048	1.123
Children	0.001	0.000	0.001
CountPep	0.125	0.002	0.128
ExtendPalette	0.008	0.001	0.008
GOAnalysisSave	0	0	0
GetCC	0.946	0.010	0.956
GetColorsForConditions	0.111	0.001	0.113
GetDetailedNbPeptides	0.120	0.002	0.125
GetDetailedNbPeptidesUsed	0	0	0
GetIndices_BasedOnConditions	0.119	0.001	0.121
GetIndices_MetacellFiltering	0.118	0.000	0.120
GetIndices_WholeLine	0.117	0.002	0.119
GetIndices_WholeMatrix	0.115	0.001	0.117
GetKeyId	0.111	0.001	0.113
GetMatAdj	0.126	0.002	0.127
GetMetacell	0	0	0
GetMetacellTags	0.113	0.002	0.115
GetNbPeptidesUsed	0.117	0.001	0.118
GetNbTags	0	0	0
GetSoftAvailables	0	0	0
GetTypeofData	0.110	0.002	0.113
Get_AllComparisons	0.072	0.001	0.073
GlobalQuantileAlignment	0.132	0.006	0.137
GraphPepProt	0.119	0.002	0.121
LH0	0.000	0.000	0.001
LH0.lm	0	0	0
LH1	0	0	0
LH1.lm	0	0	0
LOESS	0.409	0.007	0.417
MeanCentering	0.112	0.002	0.114
MetaCellFiltering	0.159	0.005	0.164
MetacellFilteringScope	0	0	0
Metacell_DIA_NN	0.186	0.004	0.195
Metacell_generic	0.163	0.005	0.169
Metacell_maxquant	0.173	0.009	0.185
Metacell_proline	0.165	0.005	0.172
NumericalFiltering	0.122	0.002	0.124
NumericalgetIndicesOfLinesToRemove	0.112	0.001	0.114
OWAnova	0.003	0.000	0.003
QuantileCentering	0.108	0.002	0.110
SetCC	0.888	0.006	0.894
SetMatAdj	0.119	0.002	0.122
Set_POV_MEC_tags	0.110	0.001	0.117
StringBasedFiltering	0.118	0.002	0.120
StringBasedFiltering2	0.118	0.002	0.120
SumByColumns	0.394	0.008	0.402
SymFilteringOperators	0	0	0
UpdateMetacellAfterImputation	0.115	0.001	0.117
aggregateIter	0.155	0.002	0.158
aggregateIterParallel	0	0	0
aggregateMean	0.136	0.002	0.138
aggregateSum	0.153	0.002	0.156
aggregateTopn	0.132	0.001	0.134
applyAnovasOnProteins	0.034	0.001	0.035
averageIntensities	0.189	0.034	0.225
barplotEnrichGO_HC	3.442	0.543	3.985
barplotGroupGO_HC	1.989	0.211	2.207
boxPlotD_HC	0.091	0.032	0.129
buildGraph	0.648	0.020	0.671
check.conditions	0.107	0.002	0.109
check.design	0.108	0.001	0.108
checkClusterability	1.066	0.878	1.902
classic1wayAnova	0	0	0
compareNormalizationD_HC	0.045	0.023	0.067
compute.selection.table	0.230	0.053	0.281
compute_t_tests	0.318	0.089	0.402
corrMatrixD_HC	0.140	0.021	0.162
createMSnset	0.620	0.038	0.665
createMSnset2	0.564	0.037	0.600
dapar_hc_ExportMenu	0.038	0.040	0.082
dapar_hc_chart	0.016	0.015	0.031
deleteLinesFromIndices	0.123	0.006	0.129
densityPlotD_HC	0.833	0.627	1.419
diffAnaComputeAdjustedPValues	0.052	0.012	0.063
diffAnaComputeFDR	0	0	0
diffAnaGetSignificant	0.072	0.016	0.087
diffAnaSave	0.070	0.014	0.083
diffAnaVolcanoplot	0.051	0.008	0.061
diffAnaVolcanoplot_rCharts	0.120	0.059	0.177
display.CC.visNet	0.706	0.020	0.728
enrich_GO	1.937	0.186	2.128
finalizeAggregation	0	0	0
findMECBlock	0.126	0.005	0.137
formatHSDResults	0	0	0
formatLimmaResult	0.049	0.011	0.060
formatPHResults	0	0	0
formatPHTResults	0	0	0
fudge2LRT	0	0	0
get.pep.prot.cc	0.680	0.017	0.697
getDesignLevel	0.107	0.002	0.109
getIndicesConditions	0.106	0.001	0.108
getIndicesOfLinesToRemove	0.117	0.004	0.122
getListNbValuesInLines	0.109	0.001	0.111
getNumberOf	0.114	0.004	0.118
getNumberOfEmptyLines	0.118	0.003	0.120
getPourcentageOfMV	0.116	0.005	0.121
getProcessingInfo	0.108	0.002	0.110
getProteinsStats	0.123	0.006	0.129
getQuantile4Imp	0.028	0.001	0.028
getTextForAggregation	0	0	0
getTextForAnaDiff	0	0	0
getTextForFiltering	0	0	0
getTextForGOAnalysis	0	0	0
getTextForHypothesisTest	0	0	0
getTextForNewDataset	0.001	0.000	0.000
getTextForNormalization	0	0	0
getTextForpeptideImputation	0	0	0
getTextForproteinImputation	0.001	0.001	0.000
globalAdjPval	0.124	0.014	0.138
group_GO	2.023	0.247	2.272
hc_logFC_DensityPlot	0.208	0.154	0.357
hc_mvTypePlot2	0.312	0.122	0.430
heatmapD	0.218	0.017	0.235
heatmapForMissingValues	0.069	0.010	0.079
histPValue_HC	0.067	0.023	0.091
impute.pa2	0.131	0.004	0.135
inner.aggregate.iter	0.135	0.006	0.141
inner.aggregate.topn	0.127	0.006	0.132
inner.mean	0.140	0.004	0.144
inner.sum	0.127	0.004	0.129
is.subset	0	0	0
limmaCompleteTest	0.411	0.022	0.432
listSheets	0	0	0
make.contrast	0.119	0.002	0.124
make.design.1	0.118	0.002	0.120
make.design.2	0.125	0.002	0.128
make.design.3	0.129	0.002	0.132
make.design	0.199	0.003	0.206
match.metacell	0.127	0.007	0.134
metacell.def	0.001	0.001	0.002
metacellHisto_HC	0.135	0.017	0.153
metacellPerLinesHistoPerCondition_HC	0.174	0.038	0.211
metacellPerLinesHisto_HC	0.201	0.084	0.283
metacombine	0.019	0.002	0.021
mvImage	0.663	0.057	0.717
my_hc_ExportMenu	0.037	0.038	0.076
my_hc_chart	0.037	0.040	0.079
nonzero	0.006	0.000	0.008
normalizeMethods.dapar	0	0	0
pepa.test	0.124	0.003	0.127
pkgs.require	0	0	0
plotJitter	0.718	0.028	0.745
plotJitter_rCharts	0.606	0.023	0.629
plotPCA_Eigen	0.143	0.011	0.154
plotPCA_Eigen_hc	0.108	0.001	0.109
plotPCA_Ind	0.112	0.003	0.114
plotPCA_Var	0.108	0.001	0.109
postHocTest	0	0	0
proportionConRev_HC	0.015	0.017	0.031
rbindMSnset	0.137	0.017	0.153
reIntroduceMEC	0.127	0.011	0.137
readExcel	0	0	0
removeLines	0.122	0.011	0.132
samLRT	0	0	0
saveParameters	0.110	0.002	0.111
scatterplotEnrichGO_HC	1.954	0.240	2.208
search.metacell.tags	0.002	0.000	0.002
separateAdjPval	0.059	0.003	0.063
splitAdjacencyMat	0.126	0.004	0.129
test.design	0.121	0.001	0.123
testAnovaModels	0.042	0.005	0.045
thresholdpval4fdr	0	0	0
translatedRandomBeta	0.001	0.002	0.002
univ_AnnotDbPkg	0.054	0.018	0.072
violinPlotD	0.120	0.006	0.126
visualizeClusters	0.337	0.052	0.388
vsn	0.217	0.011	0.230
wrapper.CVDistD_HC	0.670	0.433	1.087
wrapper.compareNormalizationD_HC	13.470	8.383	21.847
wrapper.corrMatrixD_HC	0.136	0.021	0.157
wrapper.dapar.impute.mi	5.038	0.509	5.550
wrapper.heatmapD	0.200	0.014	0.214
wrapper.impute.KNN	0.121	0.008	0.129
wrapper.impute.detQuant	0.137	0.014	0.149
wrapper.impute.fixedValue	0.144	0.015	0.159
wrapper.impute.mle	0.126	0.007	0.133
wrapper.impute.pa	0.042	0.009	0.051
wrapper.impute.pa2	0.127	0.011	0.137
wrapper.impute.slsa	0.168	0.017	0.184
wrapper.mvImage	0.046	0.006	0.052
wrapper.normalizeD	0.117	0.002	0.118
wrapper.pca	0.047	0.010	0.056
wrapperCalibrationPlot	0.064	0.011	0.075
wrapperClassic1wayAnova	0	0	0
wrapperRunClustering	0.620	0.170	0.782
write.excel	0.279	0.084	0.361
writeMSnsetToCSV	0.125	0.010	0.135
writeMSnsetToExcel	0.321	0.105	0.425

CHECK results for DAPAR on kjohnson3

Summary

Command output

Installation output

Tests output

Example timings