Samuel Wieczorek
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/DAPAR |
| Branch: RELEASE_3_12 |
| Last Commit: 0e5ad9b |
| Last Changed Date: 2021-04-30 02:40:56 -0400 (Fri, 30 Apr 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:30:35 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the DAPAR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 425/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DAPAR 1.22.9 (landing page) Samuel Wieczorek
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: DAPAR |
| Version: 1.22.9 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAPAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DAPAR_1.22.9.tar.gz |
| StartedAt: 2021-05-06 01:58:23 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:11:37 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 793.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DAPAR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAPAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DAPAR_1.22.9.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/DAPAR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DAPAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DAPAR' version '1.22.9'
* 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 whether package 'DAPAR' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Namespaces in Imports field not imported from:
'Cairo' 'DAPARdata' 'clusterProfiler' 'igraph' 'knitr' 'lattice'
'norm' 'parallel' 'pcaMethods' 'png' 'scales' 'siggenes' 'tidyverse'
'tmvtnorm'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
heatmap.DAPAR: warning in axis(1, 1:nc, label = labCol, las = 2, line =
-0.5 + offsetCol, tick = 0, cex.axis = cexCol, hadj = NA, padj = 0):
partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(1, 1:nc, label = rep("", nc), las = 2,
tick = 0): partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(4, iy, label = labRow, las = 5, line =
-0.5 + offsetRow, tick = 0, cex.axis = cexRow, hadj = 0, padj = NA):
partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(4, iy, label = rep("", nr), las = 2,
line = -0.5, tick = 0): partial argument match of 'label' to 'labels'
BuildColumnToProteinDataset_par: no visible global function definition
for '%dopar%'
aggregateIterParallel: no visible global function definition for
'%dopar%'
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'
barplotEnrichGO_HC : <anonymous>: no visible global function definition
for 'last'
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'
enrich_GO: no visible global function definition for 'bitr'
enrich_GO: no visible global function definition for 'enrichGO'
getTextForGOAnalysis: no visible binding for global variable
'textGOParams'
getTextForGOAnalysis: no visible binding for global variable 'input'
group_GO: no visible global function definition for 'bitr'
group_GO: no visible global function definition for 'groupGO'
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<-'
visualizeClusters: no visible global function definition for 'desc'
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'
wrapperClassic1wayAnova: no visible binding for global variable
'post_hoc'
wrapperRunClustering: no visible global function definition for 'str_c'
Undefined global functions or variables:
%dopar% A B Condition FDR_threshold P.Value Pr(>F)1 adjusted_pvalues
bitr cond condition desc enrichGO feature g groupGO input intensity
last layout_nicely nodes<- post_hoc str_c textGOParams x y
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
buildGraph 64.91 0.86 65.78
display.CC.visNet 63.00 0.65 63.80
checkClusterability 15.44 0.73 16.23
wrapper.dapar.impute.mi 8.92 0.27 9.19
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
buildGraph 63.56 0.80 64.36
display.CC.visNet 58.47 0.62 59.17
checkClusterability 14.84 0.20 15.05
wrapper.dapar.impute.mi 12.01 0.09 12.57
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/DAPAR.Rcheck/00check.log'
for details.
DAPAR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/DAPAR_1.22.9.tar.gz && rm -rf DAPAR.buildbin-libdir && mkdir DAPAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DAPAR.buildbin-libdir DAPAR_1.22.9.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL DAPAR_1.22.9.zip && rm DAPAR_1.22.9.tar.gz DAPAR_1.22.9.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 3973k 100 3973k 0 0 31.6M 0 --:--:-- --:--:-- --:--:-- 31.8M
install for i386
* installing *source* package 'DAPAR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DAPAR'
finding HTML links ... done
BuildAdjacencyMatrix html
BuildColumnToProteinDataset html
BuildColumnToProteinDataset_par html
BuildPalette html
CVDistD html
CVDistD_HC html
CountPep html
GOAnalysisSave html
finding level-2 HTML links ... done
GetDetailedNbPeptides html
GetDetailedNbPeptidesUsed html
GetNbPeptidesUsed html
Get_AllComparisons html
GlobalQuantileAlignment html
GraphPepProt html
LH0 html
LH0.lm html
LH1 html
LH1.lm html
LOESS html
MeanCentering html
NumericalFiltering html
NumericalgetIndicesOfLinesToRemove html
QuantileCentering html
StringBasedFiltering html
StringBasedFiltering2 html
SumByColumns html
addOriginOfValue html
aggregateIter html
aggregateIterParallel html
aggregateMean html
aggregateSum html
aggregateTopn html
averageIntensities html
barplotEnrichGO_HC html
barplotGroupGO_HC html
boxPlotD_HC html
buildGraph html
check.conditions html
check.design html
checkClusterability html
classic1wayAnova html
compareNormalizationD_HC html
compute_t_tests html
corrMatrixD_HC html
createMSnset html
dapar_hc_ExportMenu html
dapar_hc_chart html
deleteLinesFromIndices html
densityPlotD html
densityPlotD_HC html
diffAnaComputeFDR html
diffAnaGetSignificant html
diffAnaSave html
diffAnaVolcanoplot html
diffAnaVolcanoplot_rCharts html
display.CC.visNet html
enrich_GO html
finalizeAggregation html
findMECBlock html
formatLimmaResult html
formatPHResults html
fudge2LRT html
get.pep.prot.cc html
getIndicesConditions html
getIndicesOfLinesToRemove html
getListNbValuesInLines html
getNumberOf html
getNumberOfEmptyLines html
getPourcentageOfMV html
getProcessingInfo html
getProteinsStats html
getQuantile4Imp html
getTextForAggregation html
getTextForAnaDiff html
getTextForFiltering html
getTextForGOAnalysis html
getTextForHypothesisTest html
getTextForNewDataset html
getTextForNormalization html
getTextForpeptideImputation html
getTextForproteinImputation html
group_GO html
hc_logFC_DensityPlot html
hc_mvTypePlot2 html
heatmap.DAPAR html
heatmapD html
histPValue_HC html
impute.detQuant html
impute.pa2 html
inner.aggregate.iter html
inner.aggregate.topn html
inner.mean html
inner.sum html
is.MV html
is.OfType html
limmaCompleteTest html
listSheets html
make.contrast html
make.design.1 html
make.design.2 html
make.design.3 html
make.design html
mvFilter html
mvFilterFromIndices html
mvFilterGetIndices html
mvHisto_HC html
mvImage html
mvPerLinesHistoPerCondition_HC html
mvPerLinesHisto_HC html
my_hc_ExportMenu html
my_hc_chart html
nonzero html
normalizeMethods.dapar html
pepa.test html
plotJitter html
plotJitter_rCharts html
plotPCA_Eigen html
plotPCA_Eigen_hc html
plotPCA_Ind html
plotPCA_Var html
postHocTest html
proportionConRev_HC html
rbindMSnset html
reIntroduceMEC html
readExcel html
removeLines html
samLRT html
saveParameters html
scatterplotEnrichGO_HC html
setMEC html
splitAdjacencyMat html
test.design html
translatedRandomBeta html
univ_AnnotDbPkg html
violinPlotD html
visualizeClusters html
vsn html
wrapper.CVDistD html
wrapper.CVDistD_HC html
wrapper.compareNormalizationD_HC html
wrapper.corrMatrixD_HC html
wrapper.dapar.impute.mi html
wrapper.hc_mvTypePlot2 html
wrapper.heatmapD html
wrapper.impute.KNN html
wrapper.impute.detQuant html
wrapper.impute.fixedValue html
wrapper.impute.mle html
wrapper.impute.pa html
wrapper.impute.pa2 html
wrapper.impute.slsa html
wrapper.mvHisto_HC html
wrapper.mvImage html
wrapper.mvPerLinesHistoPerCondition_HC
html
wrapper.mvPerLinesHisto_HC html
wrapper.normalizeD html
wrapper.pca html
wrapperCalibrationPlot html
wrapperClassic1wayAnova html
wrapperRunClustering html
writeMSnsetToCSV html
writeMSnsetToExcel html
** 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
install for x64
* installing *source* package 'DAPAR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DAPAR' as DAPAR_1.22.9.zip
* DONE (DAPAR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'DAPAR' successfully unpacked and MD5 sums checked
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DAPAR.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
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)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'DynDoc'
The following object is masked from 'package:BiocGenerics':
path
>
> test_check("DAPAR")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 0 ]
>
> proc.time()
user system elapsed
12.29 1.06 13.89
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DAPAR.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'DynDoc'
The following object is masked from 'package:BiocGenerics':
path
>
> test_check("DAPAR")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 0 ]
>
> proc.time()
user system elapsed
13.20 0.54 13.82
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DAPAR.Rcheck/examples_i386/DAPAR-Ex.timings
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DAPAR.Rcheck/examples_x64/DAPAR-Ex.timings
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