CRAN Package Check Results for Package NetRep

Last updated on 2019-10-13 01:46:20 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.1 153.18 142.18 295.36 OK
r-devel-linux-x86_64-debian-gcc 1.2.1 108.32 109.78 218.10 OK
r-devel-linux-x86_64-fedora-clang 1.2.1 372.69 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2.1 360.50 OK
r-devel-windows-ix86+x86_64 1.2.1 298.00 182.00 480.00 OK
r-patched-linux-x86_64 1.2.1 116.60 139.97 256.57 OK
r-patched-solaris-x86 1.2.1 253.70 ERROR
r-release-linux-x86_64 1.2.1 114.14 138.70 252.84 OK
r-release-windows-ix86+x86_64 1.2.1 361.00 244.00 605.00 OK
r-release-osx-x86_64 1.2.1 NOTE
r-oldrel-windows-ix86+x86_64 1.2.1 261.00 177.00 438.00 OK
r-oldrel-osx-x86_64 1.2.1 NOTE

Check Details

Version: 1.2.1
Check: installed package size
Result: NOTE
     installed size is 8.9Mb
     sub-directories of 1Mb or more:
     doc 1.8Mb
     libs 6.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.2.1
Check: examples
Result: ERROR
    Running examples in ‘NetRep-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: combineAnalyses
    > ### Title: Combine results of multiple permutation procedures
    > ### Aliases: combineAnalyses
    > ### Keywords: internal
    >
    > ### ** Examples
    >
    > data("NetRep")
    >
    > # Set up input lists for each input matrix type across datasets. The list
    > # elements can have any names, so long as they are consistent between the
    > # inputs.
    > network_list <- list(discovery=discovery_network, test=test_network)
    > data_list <- list(discovery=discovery_data, test=test_data)
    > correlation_list <- list(discovery=discovery_correlation, test=test_correlation)
    > labels_list <- list(discovery=module_labels)
    >
    > pres1 <- modulePreservation(
    + network=network_list, data=data_list, correlation=correlation_list,
    + moduleAssignments=labels_list, nPerm=1000, discovery="discovery",
    + test="test", nThreads=2
    + )
    [2019-09-21 19:46:48 BST] Validating user input...
    [2019-09-21 19:46:49 BST] Checking matrices for problems...
    [2019-09-21 19:46:49 BST] Input ok!
    [2019-09-21 19:46:49 BST] Calculating preservation of network subsets from
     dataset "discovery" in dataset "test".
    [2019-09-21 19:46:49 BST] Pre-computing network properties in dataset
     "discovery"...
    [2019-09-21 19:46:49 BST] Calculating observed test statistics...
    [2019-09-21 19:46:49 BST] Generating null distributions from 1000
     permutations using 2 threads...
    
    
     0% completed.Warning in value[[3L]](cond) :
     Failed with error:
    BLAS/LAPACK routine 'DORGQRNo transposeCo' gave error code -3
    Skipping to next comparison
    [2019-09-21 19:46:49 BST] Done!
    >
    > pres2 <- modulePreservation(
    + network=network_list, data=data_list, correlation=correlation_list,
    + moduleAssignments=labels_list, nPerm=1000, discovery="discovery",
    + test="test", nThreads=2
    + )
    [2019-09-21 19:46:49 BST] Validating user input...
    [2019-09-21 19:46:50 BST] Checking matrices for problems...
    [2019-09-21 19:46:50 BST] Input ok!
    [2019-09-21 19:46:50 BST] Calculating preservation of network subsets from
     dataset "discovery" in dataset "test".
    [2019-09-21 19:46:50 BST] Pre-computing network properties in dataset
     "discovery"...
    [2019-09-21 19:46:50 BST] Calculating observed test statistics...
    [2019-09-21 19:46:50 BST] Generating null distributions from 1000
     permutations using 2 threads...
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: PermutationProcedure(discProps, dataEnv$matrix, correlationEnv$matrix, networkEnv$matrix, moduleAssignments[[di]], modules[[di]], nPerm, nThreads, model, verbose, vCat)
     2: doTryCatch(return(expr), name, parentenv, handler)
     3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     4: tryCatchList(expr, classes, parentenv, handlers)
     5: tryCatch({ vCat(verbose, 0, sep = "", "Calculating preservation of network subsets from dataset ", "\"", datasetNames[di], "\"", " in dataset ", "\"", datasetNames[ti], "\"", ".") ct <- contingencyTable(moduleAssignments[c(di, ti)], modules[[di]], nodelist[[ti]]) contingency <- ct$contingency propVarsPres <- ct$propVarsPres overlapVars <- ct$overlapVars varsPres <- ct$varsPres overlapModules <- ct$overlapModules overlapAssignments <- ct$overlapAssignments nStatistics <- ifelse(!is.null(data[[di]]) && !is.null(data[[ti]]), 7, 4) nModules <- length(overlapModules) if (di != loadedIdx) { anyDM <- any.disk.matrix(data[[loadedIdx]], correlation[[loadedIdx]], network[[loadedIdx]]) vCat(verbose && anyDM, 1, "Unloading dataset from RAM...") dataEnv$matrix <- NULL correlationEnv$matrix <- NULL networkEnv$matrix <- NULL gc() anyDM <- any.disk.matrix(data[[di]], correlation[[di]], network[[di]]) vCat(verbose && anyDM, 1, "Loading matrices of dataset \"", datasetNames[di], "\" into RAM...", sep = "") if (!is.null(data[[di]])) { dataEnv$matrix <- Scale(loadIntoRAM(data[[di]])) gc() } else { dataEnv$matrix <- NULL } correlationEnv$matrix <- loadIntoRAM(correlation[[di]]) networkEnv$matrix <- loadIntoRAM(network[[di]]) loadedIdx <- di } vCat(verbose, 1, "Pre-computing network properties in dataset \"", datasetNames[di], "\"...", sep = "") if (is.null(data[[di]]) || is.null(data[[ti]])) { discProps <- IntermediatePropertiesNoData(correlationEnv$matrix, networkEnv$matrix, nodelist[[ti]], moduleAssignments[[di]], modules[[di]]) } else { discProps <- IntermediateProperties(dataEnv$matrix, correlationEnv$matrix, networkEnv$matrix, nodelist[[ti]], moduleAssignments[[di]], modules[[di]]) } if (ti != loadedIdx) { anyDM <- any.disk.matrix(data[[loadedIdx]], correlation[[loadedIdx]], network[[loadedIdx]]) vCat(verbose && anyDM, 1, "Unloading dataset from RAM...") dataEnv$matrix <- NULL correlationEnv$matrix <- NULL networkEnv$matrix <- NULL gc() anyDM <- any.disk.matrix(data[[ti]], correlation[[ti]], network[[ti]]) vCat(verbose && anyDM, 1, "Loading matrices of dataset \"", datasetNames[ti], "\" into RAM...", sep = "") if (!is.null(data[[ti]])) { dataEnv$matrix <- Scale(loadIntoRAM(data[[ti]])) gc() } else { dataEnv$matrix <- NULL } correlationEnv$matrix <- loadIntoRAM(correlation[[ti]]) networkEnv$matrix <- loadIntoRAM(network[[ti]]) loadedIdx <- ti } if (is.null(data[[di]]) || is.null(data[[ti]])) { perms <- PermutationProcedureNoData(discProps, correlationEnv$matrix, networkEnv$matrix, moduleAssignments[[di]], modules[[di]], nPerm, nThreads, model, verbose, vCat) } else { perms <- PermutationProcedure(discProps, dataEnv$matrix, correlationEnv$matrix, networkEnv$matrix, moduleAssignments[[di]], modules[[di]], nPerm, nThreads, model, verbose, vCat) } observed <- perms$observed if (nPerm > 0) { nulls <- perms$nulls } else { nulls <- NULL } if (nPerm > 0) { vCat(verbose, 1, "Calculating P-values...") if (model == "overlap") { totalSize <- length(overlapVars) } else { totalSize <- ncol(correlation[[ti]]) } p.values <- permutationTest(nulls, observed, varsPres, totalSize, alternative) } else { p.values <- NULL totalSize <- NULL } vCat(verbose, 1, "Collating results...") res[[di]][[ti]] <- list(nulls = nulls, observed = observed, p.values = p.values, nVarsPresent = varsPres, propVarsPresent = propVarsPres, totalSize = totalSize, alternative = alternative, contingency = contingency) res[[di]][[ti]] <- res[[di]][[ti]][!sapply(res[[di]][[ti]], is.null)] gc()}, error = function(e) { warning("Failed with error:\n", e$message, "\nSkipping to next comparison", immediate. = TRUE)})
     6: modulePreservation(network = network_list, data = data_list, correlation = correlation_list, moduleAssignments = labels_list, nPerm = 1000, discovery = "discovery", test = "test", nThreads = 2)
    An irrecoverable exception occurred. R is aborting now ...
    
    
     1% completed.
Flavor: r-patched-solaris-x86

Version: 1.2.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘NetRep.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
     *** caught segfault ***
    address ddccbab1, cause 'memory not mapped'
Flavor: r-patched-solaris-x86