Multiple platform build/check report for BioC 3.20 - CHECK results for DAPAR on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4505
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4538
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4486
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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: 1.38.0

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_1.38.0.tar.gz

StartedAt: 2024-11-09 00:22:02 -0500 (Sat, 09 Nov 2024)

EndedAt: 2024-11-09 00:28:31 -0500 (Sat, 09 Nov 2024)

EllapsedTime: 388.8 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_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DAPAR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.38.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
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 12.404  5.148  17.559
wrapper.dapar.impute.mi           4.888  0.520   5.409
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-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

DAPAR.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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 1.38.0.

  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 
  9.901   0.791  10.694

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

name	user	system	elapsed
AggregateMetacell	0.145	0.003	0.148
BuildAdjacencyMatrix	0.118	0.002	0.119
BuildColumnToProteinDataset	0.133	0.002	0.136
BuildMetaCell	0.194	0.009	0.204
CVDistD_HC	0.701	0.041	0.750
Children	0.001	0.000	0.002
CountPep	0.126	0.002	0.128
ExtendPalette	0.009	0.001	0.009
GOAnalysisSave	0	0	0
GetCC	1.128	0.005	1.134
GetColorsForConditions	0.097	0.001	0.099
GetDetailedNbPeptides	0.104	0.001	0.105
GetDetailedNbPeptidesUsed	0	0	0
GetIndices_BasedOnConditions	0.104	0.001	0.106
GetIndices_MetacellFiltering	0.106	0.002	0.109
GetIndices_WholeLine	0.105	0.001	0.107
GetIndices_WholeMatrix	0.105	0.002	0.106
GetKeyId	0.102	0.001	0.103
GetMatAdj	0.118	0.001	0.120
GetMetacell	0	0	0
GetMetacellTags	0.102	0.002	0.104
GetNbPeptidesUsed	0.102	0.002	0.103
GetNbTags	0	0	0
GetSoftAvailables	0	0	0
GetTypeofData	0.097	0.001	0.099
Get_AllComparisons	0.070	0.006	0.076
GlobalQuantileAlignment	0.108	0.002	0.109
GraphPepProt	0.104	0.001	0.106
LH0	0.000	0.000	0.001
LH0.lm	0	0	0
LH1	0	0	0
LH1.lm	0	0	0
LOESS	0.372	0.007	0.381
MeanCentering	0.107	0.007	0.115
MetaCellFiltering	0.136	0.002	0.139
MetacellFilteringScope	0	0	0
Metacell_DIA_NN	0.161	0.004	0.165
Metacell_generic	0.133	0.004	0.137
Metacell_maxquant	0.143	0.005	0.148
Metacell_proline	0.132	0.003	0.135
NumericalFiltering	0.107	0.001	0.109
NumericalgetIndicesOfLinesToRemove	0.097	0.001	0.099
OWAnova	0.002	0.000	0.003
QuantileCentering	0.095	0.002	0.096
SetCC	0.825	0.006	0.832
SetMatAdj	0.109	0.001	0.111
Set_POV_MEC_tags	0.102	0.001	0.103
StringBasedFiltering	0.108	0.001	0.109
StringBasedFiltering2	0.106	0.001	0.107
SumByColumns	0.349	0.006	0.355
SymFilteringOperators	0.000	0.001	0.000
UpdateMetacellAfterImputation	0.105	0.001	0.106
aggregateIter	0.146	0.002	0.149
aggregateIterParallel	0	0	0
aggregateMean	0.118	0.001	0.120
aggregateSum	0.123	0.002	0.124
aggregateTopn	0.116	0.001	0.117
applyAnovasOnProteins	0.030	0.001	0.030
averageIntensities	0.175	0.026	0.201
barplotEnrichGO_HC	2.816	0.386	3.197
barplotGroupGO_HC	1.713	0.165	1.877
boxPlotD_HC	0.064	0.020	0.083
buildGraph	0.591	0.020	0.611
check.conditions	0.095	0.001	0.096
check.design	0.093	0.001	0.094
checkClusterability	0.985	0.426	1.410
classic1wayAnova	0	0	0
compareNormalizationD_HC	0.040	0.013	0.053
compute.selection.table	0.192	0.032	0.222
compute_t_tests	0.256	0.045	0.298
corrMatrixD_HC	0.143	0.020	0.163
createMSnset	0.576	0.021	0.598
createMSnset2	0.568	0.028	0.595
dapar_hc_ExportMenu	0.035	0.037	0.071
dapar_hc_chart	0.015	0.012	0.027
deleteLinesFromIndices	0.120	0.004	0.124
densityPlotD_HC	0.747	0.270	1.015
diffAnaComputeAdjustedPValues	0.047	0.007	0.054
diffAnaComputeFDR	0	0	0
diffAnaGetSignificant	0.069	0.011	0.079
diffAnaSave	0.065	0.010	0.075
diffAnaVolcanoplot	0.048	0.005	0.052
diffAnaVolcanoplot_rCharts	0.098	0.025	0.122
display.CC.visNet	0.614	0.020	0.635
enrich_GO	1.665	0.120	1.788
finalizeAggregation	0	0	0
findMECBlock	0.107	0.005	0.112
formatHSDResults	0	0	0
formatLimmaResult	0.038	0.006	0.045
formatPHResults	0	0	0
formatPHTResults	0	0	0
fudge2LRT	0	0	0
get.pep.prot.cc	0.608	0.019	0.626
getDesignLevel	0.096	0.001	0.097
getIndicesConditions	0.095	0.002	0.096
getIndicesOfLinesToRemove	0.101	0.002	0.103
getListNbValuesInLines	0.094	0.001	0.095
getNumberOf	0.099	0.002	0.101
getNumberOfEmptyLines	0.102	0.002	0.103
getPourcentageOfMV	0.101	0.003	0.104
getProcessingInfo	0.094	0.001	0.095
getProteinsStats	0.105	0.003	0.108
getQuantile4Imp	0.025	0.000	0.025
getTextForAggregation	0.000	0.000	0.001
getTextForAnaDiff	0	0	0
getTextForFiltering	0	0	0
getTextForGOAnalysis	0	0	0
getTextForHypothesisTest	0	0	0
getTextForNewDataset	0.001	0.000	0.001
getTextForNormalization	0	0	0
getTextForpeptideImputation	0	0	0
getTextForproteinImputation	0	0	0
globalAdjPval	0.116	0.008	0.124
group_GO	1.655	0.129	1.786
hc_logFC_DensityPlot	0.162	0.061	0.223
hc_mvTypePlot2	0.258	0.057	0.314
heatmapD	0.197	0.012	0.208
heatmapForMissingValues	0.058	0.004	0.063
histPValue_HC	0.060	0.017	0.077
impute.pa2	0.117	0.004	0.121
inner.aggregate.iter	0.119	0.004	0.124
inner.aggregate.topn	0.130	0.004	0.133
inner.mean	0.110	0.002	0.113
inner.sum	0.109	0.003	0.111
is.subset	0	0	0
limmaCompleteTest	0.379	0.014	0.393
listSheets	0	0	0
make.contrast	0.107	0.002	0.109
make.design.1	0.106	0.002	0.107
make.design.2	0.160	0.008	0.168
make.design.3	0.103	0.002	0.106
make.design	0.103	0.002	0.106
match.metacell	0.110	0.003	0.114
metacell.def	0.001	0.000	0.002
metacellHisto_HC	0.120	0.015	0.136
metacellPerLinesHistoPerCondition_HC	0.151	0.028	0.178
metacellPerLinesHisto_HC	0.177	0.061	0.237
metacombine	0.018	0.001	0.019
mvImage	0.614	0.047	0.662
my_hc_ExportMenu	0.034	0.035	0.069
my_hc_chart	0.034	0.034	0.067
nonzero	0.006	0.000	0.006
normalizeMethods.dapar	0	0	0
pepa.test	0.113	0.004	0.116
pkgs.require	0	0	0
plotJitter	0.582	0.032	0.615
plotJitter_rCharts	0.512	0.016	0.528
plotPCA_Eigen	0.127	0.009	0.136
plotPCA_Eigen_hc	0.096	0.001	0.097
plotPCA_Ind	0.100	0.002	0.101
plotPCA_Var	0.097	0.001	0.099
postHocTest	0.000	0.001	0.000
proportionConRev_HC	0.012	0.011	0.022
rbindMSnset	0.122	0.007	0.129
reIntroduceMEC	0.114	0.005	0.119
readExcel	0	0	0
removeLines	0.109	0.004	0.114
samLRT	0.001	0.000	0.000
saveParameters	0.097	0.001	0.099
scatterplotEnrichGO_HC	1.662	0.123	1.784
search.metacell.tags	0.001	0.000	0.002
separateAdjPval	0.055	0.003	0.058
splitAdjacencyMat	0.122	0.003	0.124
test.design	0.115	0.001	0.116
testAnovaModels	0.036	0.002	0.037
thresholdpval4fdr	0	0	0
translatedRandomBeta	0.001	0.001	0.003
univ_AnnotDbPkg	0.049	0.016	0.065
violinPlotD	0.081	0.004	0.085
visualizeClusters	0.344	0.038	0.380
vsn	0.193	0.006	0.198
wrapper.CVDistD_HC	0.489	0.175	0.663
wrapper.compareNormalizationD_HC	12.404	5.148	17.559
wrapper.corrMatrixD_HC	0.126	0.015	0.140
wrapper.dapar.impute.mi	4.888	0.520	5.409
wrapper.heatmapD	0.165	0.010	0.174
wrapper.impute.KNN	0.107	0.004	0.111
wrapper.impute.detQuant	0.117	0.006	0.123
wrapper.impute.fixedValue	0.117	0.006	0.125
wrapper.impute.mle	0.144	0.042	0.188
wrapper.impute.pa	0.037	0.003	0.040
wrapper.impute.pa2	0.114	0.006	0.120
wrapper.impute.slsa	0.143	0.008	0.151
wrapper.mvImage	0.041	0.004	0.046
wrapper.normalizeD	0.101	0.004	0.104
wrapper.pca	0.040	0.004	0.044
wrapperCalibrationPlot	0.057	0.007	0.064
wrapperClassic1wayAnova	0	0	0
wrapperRunClustering	0.546	0.092	0.637
write.excel	0.216	0.032	0.248
writeMSnsetToCSV	0.114	0.009	0.125
writeMSnsetToExcel	0.261	0.043	0.307