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’
  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_fci.R’
  Running ‘test_fciPlus.R’
  Running ‘test_gSquareBin.R’
  Running ‘test_gSquareDis.R’
  Running ‘test_gac.R’
  Running ‘test_getNextSet.R’
  Running ‘test_gies.R’
  Running ‘test_ida.R’ [53s/54s]
  Running ‘test_idaFast.R’
  Running ‘test_isValidGraph.R’
  Running ‘test_jointIda.R’
  Running ‘test_mat2targets.R’
  Running ‘test_optAdjSet.R’
  Running ‘test_opttarget.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’
  Comparing ‘test_randDAG.Rout’ to ‘test_randDAG.Rout.save’ ... OK
  Running ‘test_randomDAG.R’
  Running ‘test_rfci.R’
  Running ‘test_rmvDAG.R’
  Running ‘test_shd.R’
  Running ‘test_skeleton.R’
  Running ‘test_udag2pag.R’
  Running ‘test_udag2pdag.R’
  Running ‘test_wgtMatrix.R’
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)
  
  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, which.max, which.min
  
  Error: package or namespace load failed for 'Rgraphviz':
   .onLoad failed in loadNamespace() for 'Rgraphviz', details:
    call: value[[3L]](cond)
    error: unable to load shared object '/data/gannet/ripley/R/test-clang/Rgraphviz/libs/Rgraphviz.so':
    /data/gannet/ripley/R/test-clang/Rgraphviz/libs/Rgraphviz.so: undefined symbol: __hypot_finite
  
    Rgraphviz is unable to be loaded.  This typically is a symptom of an
    installation problem.  From 2.x.x onwards, Graphviz ought to come
    bundled with Rgraphviz.
  
    If you are trying to use an external Graphviz, see additional
    instructions in the 'README' file of the Rgraphviz 'source'
    distribution, available at
  
    http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
  
    Ask further questions on the Bioconductor mailing list
  
    http://bioconductor.org/docs/mailList.html
  
  
    Rgraphviz is unable to be loaded.  This typically is a symptom of an
    installation problem.  From 2.x.x onwards, Graphviz ought to come
    bundled with Rgraphviz.
  
    If you are trying to use an external Graphviz, see additional
    instructions in the 'README' file of the Rgraphviz 'source'
    distribution, available at
  
    http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
  
    Ask further questions on the Bioconductor mailing list
  
    http://bioconductor.org/docs/mailList.html
  
  
  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"))
  
  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, which.max, which.min
  
  Error: package or namespace load failed for 'Rgraphviz':
   .onLoad failed in loadNamespace() for 'Rgraphviz', details:
    call: value[[3L]](cond)
    error: unable to load shared object '/data/gannet/ripley/R/test-clang/Rgraphviz/libs/Rgraphviz.so':
    /data/gannet/ripley/R/test-clang/Rgraphviz/libs/Rgraphviz.so: undefined symbol: __hypot_finite
  
    Rgraphviz is unable to be loaded.  This typically is a symptom of an
    installation problem.  From 2.x.x onwards, Graphviz ought to come
    bundled with Rgraphviz.
  
    If you are trying to use an external Graphviz, see additional
    instructions in the 'README' file of the Rgraphviz 'source'
    distribution, available at
  
    http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
  
    Ask further questions on the Bioconductor mailing list
  
    http://bioconductor.org/docs/mailList.html
  
  
    Rgraphviz is unable to be loaded.  This typically is a symptom of an
    installation problem.  From 2.x.x onwards, Graphviz ought to come
    bundled with Rgraphviz.
  
    If you are trying to use an external Graphviz, see additional
    instructions in the 'README' file of the Rgraphviz 'source'
    distribution, available at
  
    http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
  
    Ask further questions on the Bioconductor mailing list
  
    http://bioconductor.org/docs/mailList.html
  
  
  Error: package required but not installed: 'Rgraphviz'
  Execution halted