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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RcisTarget.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RcisTarget_1.28.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RcisTarget.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RcisTarget/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RcisTarget’ version ‘1.28.1’
* 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 ‘RcisTarget’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
* 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 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 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) dbRegionsLoc.Rd:11-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbRegionsLoc.Rd:16-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importAnnotations.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importAnnotations.Rd:27-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importAnnotations.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importAnnotations.Rd:33-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) motifAnnotations.Rd:18-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:58-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:63-66: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RcisTarget.Rd: GeneSet, GeneSetCollection
  calcAUC.Rd: GeneSet, GeneSetCollection
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘RcisTarget-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addSignificantGenes
> ### Title: Add significant genes
> ### Aliases: addSignificantGenes addSignificantGenes,list-method
> ###   addSignificantGenes,character-method
> ###   addSignificantGenes,GeneSet-method
> ###   addSignificantGenes,GeneSetCollection-method getSignificantGenes
> ###   getSignificantGenes,list-method getSignificantGenes,character-method
> ###   getSignificantGenes,factor-method getSignificantGenes,GeneSet-method
> ###   getSignificantGenes,GeneSetCollection-method
> 
> ### ** Examples
> 
> 
> ##################################################
> # Setup & previous steps in the workflow:
> 
> #### Gene sets
> # As example, the package includes an Hypoxia gene set:
> txtFile <- paste(file.path(system.file('examples', package='RcisTarget')),
+                  "hypoxiaGeneSet.txt", sep="/")
> geneLists <- list(hypoxia=read.table(txtFile, stringsAsFactors=FALSE)[,1])
> 
> #### Databases
> ## Motif rankings: Select according to organism and distance around TSS
> ## (See the vignette for URLs to download)
> # motifRankings <- importRankings("hg19-500bp-upstream-7species.mc9nr.feather")
> 
> ## For this example we will use a SUBSET of the ranking/motif databases:
> library(RcisTarget.hg19.motifDBs.cisbpOnly.500bp)
> data(hg19_500bpUpstream_motifRanking_cispbOnly)
> motifRankings <- hg19_500bpUpstream_motifRanking_cispbOnly
> 
> ## Motif - TF annotation:
> data(motifAnnotations_hgnc_v9) # human TFs (for motif collection 9)
> motifAnnotation <- motifAnnotations_hgnc_v9
> 
> ### Run RcisTarget
> # Step 1. Calculate AUC
> motifs_AUC <- calcAUC(geneLists, motifRankings)
> # Step 2. Select significant motifs, add TF annotation & format as table
> motifEnrichmentTable <- addMotifAnnotation(motifs_AUC,
+            motifAnnot=motifAnnotation)
> 
> ##################################################
> 
> ##################################################
> # (This step: Step 3)
> # Identify the genes that have the motif significantly enriched
> # (i.e. genes from the gene set in the top of the ranking)
> par(mfrow=c(1,2))
> motifEnrichmentTable_wGenes <- addSignificantGenes(motifEnrichmentTable,
+                                        genesFormat="geneList",
+                                        plotCurve=TRUE,
+                                        geneSets=geneLists,
+                                        rankings=motifRankings,
+                                        method="aprox")
> 
> #### Exploring the output:
> # The object returned is a data.table
> # Feel free to convert it to a data.frame:
> motifEnrichmentTable_wGenes <- as.data.frame(motifEnrichmentTable_wGenes)
> 
> # Enriched genes
> enrGenes <- motifEnrichmentTable_wGenes[1,"enrichedGenes"]
> enrGenes
[1] "AK4;BHLHE40;BNIP3L;C7orf68;CADM1;CAV1;CITED2;DDIT4;DTNA;GADD45B;INSIG2;KDM3A;KDM4B;MAFF;MET;MXI1;P4HA2;PGK1;RBPJ;RRAGD;SERPINE1;STC2;VLDLR;WSB1;ZNF292"
> strsplit(enrGenes, ";")
[[1]]
 [1] "AK4"      "BHLHE40"  "BNIP3L"   "C7orf68"  "CADM1"    "CAV1"    
 [7] "CITED2"   "DDIT4"    "DTNA"     "GADD45B"  "INSIG2"   "KDM3A"   
[13] "KDM4B"    "MAFF"     "MET"      "MXI1"     "P4HA2"    "PGK1"    
[19] "RBPJ"     "RRAGD"    "SERPINE1" "STC2"     "VLDLR"    "WSB1"    
[25] "ZNF292"  

> 
> # As incidence matrix
> motifEnr_wIncidMat <- addSignificantGenes(motifEnrichmentTable,
+                 geneSets=geneLists, rankings=motifRankings,
+                 method="aprox",
+                 genesFormat = "incidMatrix")
> 
> motifEnr_wIncidMat <- as.data.frame(motifEnr_wIncidMat)
> which(colnames(motifEnr_wIncidMat) == "rankAtMax")
[1] 8
> 
> incidMat <- motifEnr_wIncidMat[,8:ncol(motifEnr_wIncidMat)]
> rownames(incidMat) <- motifEnr_wIncidMat[,"motif"]
> incidMat <- incidMat[, colSums(incidMat)>0, drop=FALSE]
> 
> # Plot as network
> par(mfrow=c(1,1))
> library(igraph)

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

> plot(graph.incidence(incidMat))
Warning: `graph.incidence()` was deprecated in igraph 2.0.0.
ℹ Please use `graph_from_biadjacency_matrix()` instead.
Error in mde(x) : 'list' object cannot be coerced to type 'double'
Calls: plot ... graph_from_biadjacency_matrix -> graph_incidence_build -> mode<-
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
addMotifAnnotation 24.178  1.192  26.113
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/RcisTarget.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RcisTarget
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘RcisTarget’ ...
** this is package ‘RcisTarget’ version ‘1.28.1’
** using staged installation
** R
** data
** 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 (RcisTarget)

R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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(RcisTarget)
> 
> test_check("RcisTarget")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 58 ]
> 
> proc.time()
   user  system elapsed 
 71.107   6.370  76.196