Multiple platform build/check report for BioC 3.21 - CHECK results for DAPAR on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4756
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4475
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4435
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4390
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4383
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*

CHECK results for DAPAR on kjohnson3

To the developers/maintainers of the DAPAR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DAPAR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: DAPAR

Version: 1.39.0

Command: /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_1.39.0.tar.gz

StartedAt: 2025-01-03 18:58:06 -0500 (Fri, 03 Jan 2025)

EndedAt: 2025-01-03 19:01:50 -0500 (Fri, 03 Jan 2025)

EllapsedTime: 223.7 seconds

RetCode: 0

Status: OK

CheckDir: DAPAR.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/DAPAR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.39.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Vignette dependency required without any vignettes: ‘knitr’
* 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
Check_Dataset_Validity: no visible global function definition for
  ‘exprs’
OWAnova: no visible global function definition for ‘aov’
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’
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’
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 B Condition FDR_threshold Intensity P.Value Pr(>F)1 Prostar.loc
  TukeyHSD adjusted_pvalues aov cond condition exprs feature g input
  installed.packages intensity layout_nicely nodes<- par stack str_c
  textGOParams x y
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "TukeyHSD", "aov")
  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 14.464  9.115  45.139
wrapper.dapar.impute.mi           5.846  0.685   7.359
* 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-3.21-bioc/meat/DAPAR.Rcheck/00check.log’
for details.

Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-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

DAPAR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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 1.39.0.

  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 18 | SKIP 0 | PASS 66 ]

[ FAIL 0 | WARN 18 | SKIP 0 | PASS 66 ]
> 
> proc.time()
   user  system elapsed 
 11.016   0.720  11.949

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

name	user	system	elapsed
AggregateMetacell	0.507	0.004	0.514
BuildAdjacencyMatrix	0.121	0.002	0.124
BuildColumnToProteinDataset	0.140	0.002	0.143
BuildMetaCell	0.218	0.010	0.231
CVDistD_HC	1.023	0.044	1.080
Children	0.001	0.000	0.002
CountPep	0.128	0.002	0.130
ExtendPalette	0.008	0.001	0.008
GOAnalysisSave	0	0	0
GetCC	0.923	0.008	0.935
GetColorsForConditions	0.112	0.001	0.113
GetDetailedNbPeptides	0.119	0.002	0.121
GetDetailedNbPeptidesUsed	0	0	0
GetIndices_BasedOnConditions	0.120	0.002	0.121
GetIndices_MetacellFiltering	0.121	0.002	0.123
GetIndices_WholeLine	0.117	0.002	0.120
GetIndices_WholeMatrix	0.116	0.002	0.119
GetKeyId	0.112	0.002	0.114
GetMatAdj	0.127	0.002	0.129
GetMetacell	0	0	0
GetMetacellTags	0.116	0.002	0.118
GetNbPeptidesUsed	0.118	0.001	0.120
GetNbTags	0	0	0
GetSoftAvailables	0	0	0
GetTypeofData	0.114	0.001	0.116
Get_AllComparisons	0.074	0.002	0.076
GlobalQuantileAlignment	0.139	0.005	0.144
GraphPepProt	0.121	0.002	0.123
LH0	0	0	0
LH0.lm	0	0	0
LH1	0.000	0.000	0.001
LH1.lm	0	0	0
LOESS	0.408	0.006	0.414
MeanCentering	0.114	0.002	0.117
MetaCellFiltering	0.162	0.006	0.168
MetacellFilteringScope	0	0	0
Metacell_DIA_NN	0.187	0.005	0.192
Metacell_generic	0.154	0.004	0.158
Metacell_maxquant	0.164	0.009	0.172
Metacell_proline	0.148	0.004	0.152
NumericalFiltering	0.118	0.002	0.119
NumericalgetIndicesOfLinesToRemove	0.112	0.001	0.114
OWAnova	0.002	0.001	0.002
QuantileCentering	0.109	0.002	0.110
SetCC	0.885	0.005	0.891
SetMatAdj	0.121	0.002	0.123
Set_POV_MEC_tags	0.112	0.002	0.113
StringBasedFiltering	0.121	0.002	0.122
StringBasedFiltering2	0.121	0.001	0.122
SumByColumns	0.375	0.005	0.379
SymFilteringOperators	0	0	0
UpdateMetacellAfterImputation	0.113	0.002	0.114
aggregateIter	0.159	0.002	0.161
aggregateIterParallel	0	0	0
aggregateMean	0.133	0.003	0.135
aggregateSum	0.139	0.002	0.141
aggregateTopn	0.126	0.002	0.129
applyAnovasOnProteins	0.033	0.001	0.033
averageIntensities	0.194	0.037	0.250
barplotEnrichGO_HC	3.041	0.471	3.574
barplotGroupGO_HC	2.411	0.248	2.734
boxPlotD_HC	0.072	0.023	0.108
buildGraph	0.651	0.017	0.674
check.conditions	0.107	0.001	0.109
check.design	0.109	0.002	0.110
checkClusterability	0.908	1.235	2.374
classic1wayAnova	0	0	0
compareNormalizationD_HC	0.044	0.015	0.074
compute.selection.table	0.206	0.055	0.260
compute_t_tests	0.291	0.079	0.370
corrMatrixD_HC	0.142	0.026	0.167
createMSnset	0.645	0.039	0.686
createMSnset2	0.624	0.034	0.658
dapar_hc_ExportMenu	0.036	0.045	0.114
dapar_hc_chart	0.016	0.017	0.048
deleteLinesFromIndices	0.123	0.006	0.129
densityPlotD_HC	0.771	0.476	1.245
diffAnaComputeAdjustedPValues	0.051	0.014	0.065
diffAnaComputeFDR	0	0	0
diffAnaGetSignificant	0.079	0.022	0.101
diffAnaSave	0.079	0.026	0.104
diffAnaVolcanoplot	0.055	0.013	0.067
diffAnaVolcanoplot_rCharts	0.115	0.055	0.169
display.CC.visNet	0.629	0.040	0.669
enrich_GO	1.737	0.188	1.939
finalizeAggregation	0.000	0.000	0.001
findMECBlock	0.128	0.005	0.140
formatHSDResults	0	0	0
formatLimmaResult	0.050	0.014	0.069
formatPHResults	0	0	0
formatPHTResults	0	0	0
fudge2LRT	0	0	0
get.pep.prot.cc	0.632	0.010	0.643
getDesignLevel	0.110	0.002	0.115
getIndicesConditions	0.109	0.001	0.111
getIndicesOfLinesToRemove	0.126	0.005	0.131
getListNbValuesInLines	0.119	0.003	0.121
getNumberOf	0.125	0.005	0.130
getNumberOfEmptyLines	0.134	0.004	0.138
getPourcentageOfMV	0.132	0.004	0.139
getProcessingInfo	0.118	0.002	0.121
getProteinsStats	0.140	0.006	0.146
getQuantile4Imp	0.032	0.002	0.033
getTextForAggregation	0.001	0.000	0.000
getTextForAnaDiff	0.000	0.000	0.001
getTextForFiltering	0.001	0.000	0.001
getTextForGOAnalysis	0	0	0
getTextForHypothesisTest	0	0	0
getTextForNewDataset	0.001	0.001	0.002
getTextForNormalization	0.000	0.000	0.001
getTextForpeptideImputation	0	0	0
getTextForproteinImputation	0	0	0
globalAdjPval	0.241	0.017	0.260
group_GO	1.961	0.306	2.408
hc_logFC_DensityPlot	0.178	0.178	0.420
hc_mvTypePlot2	0.388	0.128	0.518
heatmapD	0.326	0.028	0.357
heatmapForMissingValues	0.081	0.009	0.093
histPValue_HC	0.113	0.036	0.155
impute.pa2	0.163	0.010	0.173
inner.aggregate.iter	0.173	0.008	0.182
inner.aggregate.topn	0.163	0.007	0.170
inner.mean	0.141	0.005	0.148
inner.sum	0.145	0.005	0.151
is.subset	0.000	0.000	0.001
limmaCompleteTest	0.724	0.031	0.786
listSheets	0	0	0
make.contrast	0.164	0.003	0.168
make.design.1	0.143	0.002	0.147
make.design.2	0.131	0.002	0.135
make.design.3	0.128	0.003	0.135
make.design	0.132	0.003	0.135
match.metacell	0.146	0.007	0.155
metacell.def	0.003	0.001	0.004
metacellHisto_HC	0.171	0.035	0.214
metacellPerLinesHistoPerCondition_HC	0.244	0.064	0.436
metacellPerLinesHisto_HC	0.295	0.133	0.438
metacombine	0.080	0.004	0.089
mvImage	0.892	0.069	1.296
my_hc_ExportMenu	0.055	0.053	0.440
my_hc_chart	0.041	0.053	0.565
nonzero	0.007	0.000	0.011
normalizeMethods.dapar	0	0	0
pepa.test	0.136	0.006	0.168
pkgs.require	0	0	0
plotJitter	0.725	0.019	0.759
plotJitter_rCharts	0.607	0.037	0.751
plotPCA_Eigen	0.146	0.015	0.253
plotPCA_Eigen_hc	0.119	0.002	0.125
plotPCA_Ind	0.129	0.003	0.135
plotPCA_Var	0.116	0.002	0.119
postHocTest	0	0	0
proportionConRev_HC	0.025	0.028	0.054
rbindMSnset	0.170	0.016	0.185
reIntroduceMEC	0.153	0.012	0.169
readExcel	0.000	0.000	0.001
removeLines	0.143	0.009	0.152
samLRT	0.001	0.000	0.000
saveParameters	0.130	0.003	0.135
scatterplotEnrichGO_HC	2.393	0.271	2.918
search.metacell.tags	0.002	0.000	0.004
separateAdjPval	0.059	0.008	0.101
splitAdjacencyMat	0.140	0.009	0.154
test.design	0.124	0.002	0.127
testAnovaModels	0.055	0.011	0.066
thresholdpval4fdr	0	0	0
translatedRandomBeta	0.001	0.005	0.006
univ_AnnotDbPkg	0.074	0.028	0.147
violinPlotD	0.086	0.008	0.114
visualizeClusters	0.402	0.097	0.827
vsn	0.291	0.027	0.348
wrapper.CVDistD_HC	0.598	0.587	2.551
wrapper.compareNormalizationD_HC	14.464	9.115	45.139
wrapper.corrMatrixD_HC	0.196	0.037	0.239
wrapper.dapar.impute.mi	5.846	0.685	7.359
wrapper.heatmapD	0.186	0.012	0.204
wrapper.impute.KNN	0.121	0.009	0.132
wrapper.impute.detQuant	0.134	0.018	0.159
wrapper.impute.fixedValue	0.150	0.022	0.178
wrapper.impute.mle	0.126	0.009	0.134
wrapper.impute.pa	0.044	0.008	0.051
wrapper.impute.pa2	0.129	0.011	0.139
wrapper.impute.slsa	0.166	0.016	0.181
wrapper.mvImage	0.050	0.011	0.061
wrapper.normalizeD	0.114	0.004	0.118
wrapper.pca	0.046	0.013	0.063
wrapperCalibrationPlot	0.070	0.014	0.084
wrapperClassic1wayAnova	0.000	0.000	0.001
wrapperRunClustering	0.562	0.126	0.955
write.excel	0.227	0.052	0.364
writeMSnsetToCSV	0.119	0.012	0.133
writeMSnsetToExcel	0.297	0.134	0.463