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This page was generated on 2021-07-24 12:05:23 -0400 (Sat, 24 Jul 2021).

CHECK results for DAPAR on nebbiolo2

To the developers/maintainers of the DAPAR package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 431/2008HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.25.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2021-07-23 14:50:08 -0400 (Fri, 23 Jul 2021)
URL: https://git.bioconductor.org/packages/DAPAR
Branch: master
Last Commit: 4c21b18
Last Changed Date: 2021-05-20 22:41:10 -0400 (Thu, 20 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: DAPAR
Version: 1.25.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DAPAR_1.25.0.tar.gz
StartedAt: 2021-07-23 19:21:28 -0400 (Fri, 23 Jul 2021)
EndedAt: 2021-07-23 19:25:23 -0400 (Fri, 23 Jul 2021)
EllapsedTime: 234.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: DAPAR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DAPAR_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/DAPAR.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.25.0’
* 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 ‘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 ... NOTE
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘DAPARdata’ ‘clusterProfiler’ ‘igraph’ ‘knitr’ ‘lattice’
  ‘norm’ ‘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
heatmapForMissingValues: 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'
heatmapForMissingValues: warning in axis(1, 1:nc, label = rep("", nc),
  las = 2, tick = 0): partial argument match of 'label' to 'labels'
heatmapForMissingValues: 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'
heatmapForMissingValues: warning in axis(4, iy, label = rep("", nr),
  las = 2, line = -0.5, tick = 0): partial argument match of 'label' to
  'labels'
GetIndices_MetacellFiltering: no visible global function definition for
  ‘tsop’
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:
  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 tsop 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 ... ERROR
Running examples in ‘DAPAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: createMSnset
> ### Title: Creates an object of class 'MSnSet' from text file
> ### Aliases: createMSnset
> 
> ### ** Examples
> 
> require(Matrix)
Loading required package: Matrix
> exprsFile <- system.file("extdata", "Exp1_R25_pept.txt", package="DAPARdata")
> metadataFile <- system.file("extdata", "samples_Exp1_R25.txt", 
+ package="DAPARdata")
> metadata = read.table(metadataFile, header=TRUE, sep="\t", as.is=TRUE)
> indExpData <- c(56:61)
> indFData <- c(1:55,62:71)
> colnameForID <- 'id'
> obj <- createMSnset(exprsFile, metadata,indExpData,  indFData, colnameForID, 
+ indexForMetacell = c(43:48), pep_prot_data = "peptide", software = 'maxquant')
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
DAPAR
 --- call from context --- 
createMSnset(exprsFile, metadata, indExpData, indFData, colnameForID, 
    indexForMetacell = c(43:48), pep_prot_data = "peptide", software = "maxquant")
 --- call from argument --- 
if (colnameForID == "AutoID") {
    fd <- data.frame(data, AutoID = rep(paste(pep_prot_data, 
        "_", 1:nrow(data), sep = "")), stringsAsFactors = FALSE)
    rownames(fd) <- paste(pep_prot_data, "_", 1:nrow(fd), sep = "")
    rownames(Intensity) <- paste(pep_prot_data, "_", 1:nrow(Intensity), 
        sep = "")
} else {
    fd <- data
    rownames(fd) <- data[, colnameForID]
    rownames(Intensity) <- data[, colnameForID]
}
 --- R stacktrace ---
where 1: createMSnset(exprsFile, metadata, indExpData, indFData, colnameForID, 
    indexForMetacell = c(43:48), pep_prot_data = "peptide", software = "maxquant")

 --- value of length: 65 type: logical ---
 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[61] FALSE FALSE FALSE FALSE FALSE
 --- function from context --- 
function (file, metadata = NULL, indExpData, colnameForID = NULL, 
    indexForMetacell = NULL, logData = FALSE, replaceZeros = FALSE, 
    pep_prot_data = NULL, proteinId = NULL, software = NULL) 
{
    if (!is.data.frame(file)) {
        data <- read.table(file, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
    }
    else {
        data <- file
    }
    Intensity <- matrix(as.numeric(gsub(",", ".", as.matrix(data[, 
        indExpData]))), ncol = length(indExpData), byrow = FALSE)
    colnames(Intensity) <- gsub(".", "_", colnames(data)[indExpData], 
        fixed = TRUE)
    rownames(Intensity) <- rownames(data)
    metacell <- NULL
    if (!is.null(indexForMetacell)) {
        metacell <- data[, indexForMetacell]
        metacell <- apply(metacell, 2, tolower)
        metacell <- as.data.frame(apply(metacell, 2, function(x) gsub(" ", 
            "", x)), stringsAsFactors = FALSE)
    }
    if (is.null(colnameForID)) 
        colnameForID <- "AutoID"
    if (colnameForID == "AutoID") {
        fd <- data.frame(data, AutoID = rep(paste(pep_prot_data, 
            "_", 1:nrow(data), sep = "")), stringsAsFactors = FALSE)
        rownames(fd) <- paste(pep_prot_data, "_", 1:nrow(fd), 
            sep = "")
        rownames(Intensity) <- paste(pep_prot_data, "_", 1:nrow(Intensity), 
            sep = "")
    }
    else {
        fd <- data
        rownames(fd) <- data[, colnameForID]
        rownames(Intensity) <- data[, colnameForID]
    }
    colnames(fd) <- gsub(".", "_", colnames(fd), fixed = TRUE)
    pd <- as.data.frame(metadata, stringsAsFactors = FALSE)
    rownames(pd) <- gsub(".", "_", pd$Sample.name, fixed = TRUE)
    pd$Sample.name <- gsub(".", "_", pd$Sample.name, fixed = TRUE)
    if (identical(rownames(Intensity), rownames(fd)) == FALSE) 
        stop("Problem consistency between\n             row names expression data and featureData")
    if (identical(colnames(Intensity), rownames(pd)) == FALSE) 
        stop("Problem consistency between column names \n             in expression data and row names in phenoData")
    obj <- MSnSet(exprs = Intensity, fData = fd, pData = pd)
    if (replaceZeros) {
        Biobase::exprs(obj)[Biobase::exprs(obj) == 0] <- NA
        Biobase::exprs(obj)[is.nan(Biobase::exprs(obj))] <- NA
        Biobase::exprs(obj)[is.infinite(Biobase::exprs(obj))] <- NA
        obj@processingData@processing <- c(obj@processingData@processing, 
            "All zeros were replaced by NA")
    }
    if (logData) {
        Biobase::exprs(obj) <- log2(Biobase::exprs(obj))
        obj@processingData@processing <- c(obj@processingData@processing, 
            "Data has been Log2 tranformed")
    }
    if (!is.null(pep_prot_data)) {
        obj@experimentData@other$typeOfData <- pep_prot_data
    }
    obj@experimentData@other$Prostar_Version <- NA
    tryCatch({
        find.package("Prostar")
        obj@experimentData@other$Prostar_Version <- Biobase::package.version("Prostar")
    }, error = function(e) obj.prot@experimentData@other$Prostar_Version <- NA)
    obj@experimentData@other$DAPAR_Version <- NA
    tryCatch({
        find.package("DAPAR")
        obj@experimentData@other$Prostar_Version <- Biobase::package.version("DAPAR")
    }, error = function(e) obj@experimentData@other$DAPAR_Version <- NA)
    obj@experimentData@other$proteinId <- proteinId
    obj@experimentData@other$keyId <- colnameForID
    obj@experimentData@other$RawPValues <- FALSE
    metacell <- BuildMetaCell(from = software, level = pep_prot_data, 
        qdata = Biobase::exprs(obj), conds = Biobase::pData(obj)$Condition, 
        df = metacell)
    Biobase::fData(obj) <- cbind(Biobase::fData(obj), metacell, 
        deparse.level = 0)
    obj@experimentData@other$names_metacell <- colnames(metacell)
    return(obj)
}
<bytecode: 0x5626b59ee108>
<environment: namespace:DAPAR>
 --- function search by body ---
Function createMSnset in namespace DAPAR has this body.
Function createMSnset in namespace DAPAR has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (colnameForID == "AutoID") { : the condition has length > 1
Calls: createMSnset
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/DAPAR.Rcheck/00check.log’
for details.


Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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
** 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
* DONE (DAPAR)

Tests output

DAPAR.Rcheck/tests/testthat.Rout


R version 4.1.0 beta (2021-05-03 r80259) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
> 
> test_check("DAPAR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 10.378   0.602  10.950 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell2.4540.3122.719
BuildAdjacencyMatrix0.2520.0040.255
BuildColumnToProteinDataset0.4340.0720.500
BuildColumnToProteinDataset_par000
BuildMetaCell0.6170.0390.651
CVDistD_HC3.1941.5314.258
CountPep0.2810.0070.287
ExtendPalette0.0200.0120.031
GetColorsForConditions0.7470.0580.805
GetDetailedNbPeptides0.2000.0070.207
GetIndices_MetacellFiltering0.2090.0000.208
GetIndices_WholeLine0.2100.0000.209
GetIndices_WholeMatrix0.2090.0000.209
Get_AllComparisons0.2030.0010.202
GlobalQuantileAlignment0.2500.0070.256
GraphPepProt0.2240.0000.223
LOESS0.9330.0040.936
MeanCentering0.2050.0000.205
MetaCellFiltering0.2590.0070.266
Metacell_generic0.3800.0150.391
Metacell_maxquant0.4010.0240.420
Metacell_proline000
NumericalFiltering0.2390.0110.248
NumericalgetIndicesOfLinesToRemove0.2180.0030.220
QuantileCentering0.2260.0000.225
Set_POV_MEC_tags0.2130.0030.215
StringBasedFiltering0.2470.0080.253
StringBasedFiltering20.2610.0070.268
SumByColumns1.0660.1211.169
aggregateIter0.5130.0370.539
aggregateIterParallel000
aggregateMean0.4060.0320.431
aggregateSum0.4280.0120.437
aggregateTopn000
averageIntensities0.2160.0080.222
boxPlotD_HC0.3570.0300.379
buildGraph1.6440.0491.692
check.conditions0.1950.0000.195
check.design0.1920.0030.195
checkClusterability2.2190.6782.662
classic1wayAnova1.0230.1191.109
compareNormalizationD_HC2.3220.5162.680
compute_t_tests0.9010.1290.993
corrMatrixD_HC0.3100.0110.317