* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/pcalg.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘pcalg/DESCRIPTION’ ... OK
* this is package ‘pcalg’ version ‘2.7-11’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pcalg’ can be installed ... [208s/279s] OK
* used C compiler: ‘gcc-13 (GCC) 13.2.0’
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
* 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [72s/92s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘pcalg-Ex.R’ failed
The error most likely occurred in:

> ### Name: ages
> ### Title: Estimate an APDAG within the Markov equivalence class of a DAG
> ###   using AGES
> ### Aliases: ages
> ### Keywords: models graphs
> 
> ### ** Examples
> 
> 
> ## Example 1: ages adds correct orientations: Bar --> V6 and Bar --> V8
> 
> set.seed(77)
> 
> p <- 8
> n <- 5000
> ## true DAG:
> vars <- c("Author", "Bar", "Ctrl", "Goal", paste0("V",5:8))
> gGtrue <- randomDAG(p, prob = 0.3, V = vars)
> data = rmvDAG(n, gGtrue)
> 
> 
> ## Estimate the aggregated PDAG with ages
> ages.fit <- ages(data = data)
> 
> 
> ## Estimate the essential graph with ges
> ## We specify the phases in order to have a fair comparison of the algorithms
> ## Without the phases specified it would be easy to find examples
> ## where each algorithm outperforms the other
> score <- new("GaussL0penObsScore", data)
> ges.fit <- ges(score, phase = c("forward","backward"), iterate = FALSE)
> 
> ## Plots
> par(mfrow=c(1,3))
> plot(ges.fit$essgraph, main="Estimated CPDAG with GES")
Error: package required but not installed: ‘Rgraphviz’
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_LINGAM.R’
  Running ‘test_addBgKnowledge.R’
  Running ‘test_adjustment.R’
  Running ‘test_ages.R’
  Running ‘test_amat2dag.R’
  Running ‘test_arges.R’
  Running ‘test_backdoor.R’ [13s/17s]
  Comparing ‘test_backdoor.Rout’ to ‘test_backdoor.Rout.save’ ... OK
  Running ‘test_bicscore.R’
  Running ‘test_causalEffect.R’
  Running ‘test_coercion.R’
  Running ‘test_compareGraphs.R’
  Running ‘test_dag2cpdag.R’
  Running ‘test_dag2essgraph.R’
  Running ‘test_displayAmat.R’
  Running ‘test_dsep.R’
  Running ‘test_dsepAM.R’
  Running ‘test_dsepAMTest.R’
  Running ‘test_fci.R’
  Running ‘test_fciPlus.R’
  Running ‘test_gSquareBin.R’
  Running ‘test_gSquareDis.R’
  Running ‘test_gac.R’ [8s/10s]
  Running ‘test_getNextSet.R’
  Running ‘test_gies.R’
  Running ‘test_ida.R’ [17s/21s]
  Running ‘test_idaFast.R’ [9s/12s]
  Running ‘test_isValidGraph.R’
  Running ‘test_jointIda.R’
  Running ‘test_mat2targets.R’
  Running ‘test_optAdjSet.R’
  Running ‘test_opttarget.R’
  Running ‘test_pag2anc.R’
  Running ‘test_pag2conf.R’
  Running ‘test_pag2edge.R’
  Running ‘test_pc.R’
  Running ‘test_pcSelect.R’
  Running ‘test_pcalg2dagitty.R’
  Running ‘test_pcorOrder.R’
  Running ‘test_pdag2allDags.R’
  Running ‘test_pdag2dag.R’
  Running ‘test_possDeAn.R’
  Running ‘test_randDAG.R’
  Running ‘test_randomDAG.R’
  Running ‘test_rfci.R’
  Running ‘test_rmvDAG.R’
  Running ‘test_searchAM.R’
  Running ‘test_shd.R’
  Running ‘test_skeleton.R’
  Running ‘test_udag2pag.R’
  Running ‘test_udag2pdag.R’ [11s/14s]
  Running ‘test_wgtMatrix.R’
 [240s/304s] ERROR
Running the tests in ‘tests/test_addBgKnowledge.R’ failed.
Complete output:
  > library(pcalg)
  > 
  > res <- rep(FALSE, 10)
  > set.seed(123)
  > g <- pcalg::randomDAG(n = 7, prob = 0.3)
  > plot(g)
  Error: package required but not installed: 'Rgraphviz'
  Execution halted
Running the tests in ‘tests/test_possDeAn.R’ failed.
Complete output:
  > library(pcalg)
  > 
  > ## possDe
  > ## a -> b -- c
  > amat <- matrix(c(0,1,0, 0,0,1, 0,1,0), 3,3)
  > colnames(amat) <- rownames(amat) <- letters[1:3]
  > ## plot(as(t(amat), "graphNEL"))
  > 
  > stopifnot(
  +   all(possDe(m = amat, x = 1, possible = TRUE, ds = FALSE, type = "pdag") == c(1,2,3)),
  +   all(possDe(m = amat, x = 1, possible = FALSE, ds = FALSE, type = "pdag") == c(1,2)),
  +   all(possDe(m = amat, x = 1, y = 2, possible = TRUE, ds = FALSE, type = "pdag") == 1) )
  > 
  > ## possAn
  > ## a -- b -> c
  > amat <- matrix(c(0,1,0, 1,0,1, 0,0,0), 3,3)
  > colnames(amat) <- rownames(amat) <- letters[1:3]
  > plot(as(t(amat), "graphNEL"))
  Error: package required but not installed: 'Rgraphviz'
  Execution halted
Running the tests in ‘tests/test_randDAG.R’ failed.
Complete output:
  > library(pcalg)
  > suppressWarnings(RNGversion("3.5.0"))
  > ## setwd("/sfs/u/kalischm/research/packages/unifDAGs/")
  > ## source("aux_general.R")
  > ## source("randDAG.R")
  > 
  > ### Check all methods: ----------------------------------------------
  > 
  > ## MM hack: extract them from the randDAG() function definition
  > body. <- body(randDAG)
  > is.switch <- function(P) !is.symbol(P) && identical(as.symbol("switch"), P[[1]])
  > switchCall <- body.[vapply(body., is.switch, NA)][[1]]
  > stopifnot(identical(as.symbol("switch"), switchCall[[1]]))
  > (rDAGmeths <- names(switchCall)[-c(1:2, length(switchCall))])
  [1] "er"        "regular"   "watts"     "bipartite" "barabasi"  "geometric"
  [7] "power"     "interEr"  
  > rDAGall <- function(n, d, ...)
  +   sapply(rDAGmeths, function(meth) randDAG(n,d, method=meth, ...),
  +          simplify=FALSE)
  > set.seed(37)
  > rD.10.4 <- rDAGall(10, 4) # 2024-02: no "low-level warning" anymore
  > ##     , warning = function(w) {
  > ##         rDAG.warn <<- conditionMessage(w); invokeRestart("muffleWarning") })
  > ## ## with a low-level warning:
  > ## ## IGNORE_RDIFF_BEGIN
  > ## rDAG.warn
  > ## ## IGNORE_RDIFF_END
  > ## stopifnot(grepl("graph_molloy_.*Cannot shuffle graph", rDAG.warn))
  > ##
  > rD.10.4 # looks ok
  $er
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 21 
  
  $regular
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 20 
  
  $watts
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 20 
  
  $bipartite
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 15 
  
  $barabasi
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 21 
  
  $geometric
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 13 
  
  $power
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 16 
  
  $interEr
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 19 
  
  > ## Show, but ignore the package startup messages:
  > ## IGNORE_RDIFF_BEGIN
  > stopifnot( require("graph") )
  Loading required package: graph
  Loading required package: BiocGenerics
  
  Attaching package: 'BiocGenerics'
  
  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, aperm, 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, table, tapply,
      union, unique, unsplit, which.max, which.min
  
  > ## IGNORE_RDIFF_END
  > 
  > stopifnot(vapply(rD.10.4, isDirected, NA),
  +           vapply(rD.10.4, inherits, NA, what="graph"))
  > ## nice plot of all 8 :
  > op <- par(mfrow=c(4,2))
  > invisible(lapply(names(rD.10.4), function(nm) plot(rD.10.4[[nm]], main=nm)))
  Error: package required but not installed: 'Rgraphviz'
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... NOTE
Note: skipping ‘vignette2018.Rnw’ due to unavailable dependencies:
  'Rgraphviz', 'huge', 'ggplot2'
* checking PDF version of manual ... [20s/25s] OK
* checking HTML version of manual ... [13s/20s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/pcalg.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 13:59.24, 608.77 + 45.66