HDF5Array
package seems to install correctly but I cannot load it, it gives me the following error:
library(HDF5Array)
Error : package or namespace load failed for ‘HDF5Array’:
.onLoad failed in loadNamespace() for 'HDF5Array', details :
call : H5Fcreate(file)
error : HDF5. File accessibilty. Unable to open file.
biocValid()
tells me my BiocParallel
version is out of date but I cannot install the latest from source because I get a "non zero exit status".
sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 16299) Matrix products: default locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C LC_TIME=French_France.1252 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] rhdf5_2.24.0 DelayedArray_0.6.0 BiocParallel_1.13.1 IRanges_2.14.1 S4Vectors_0.18.1 BiocGenerics_0.26.0 matrixStats_0.53.1 httr_1.3.1 [9] BiocInstaller_1.30.0 loaded via a namespace (and not attached): [1] digest_0.6.15 withr_2.1.2 R6_2.2.2 git2r_0.21.0 curl_3.2 devtools_1.13.5 Rhdf5lib_1.2.0 tools_3.5.0 compiler_3.5.0 memoise_1.1.0
EDIT 2018/05/22 : outputs of library(HDF5Array)
and traceback()
library(HDF5Array) Le chargement a nécessité le package : DelayedArray Le chargement a nécessité le package : stats4 Le chargement a nécessité le package : matrixStats Le chargement a nécessité le package : BiocGenerics Le chargement a nécessité le package : parallel Attachement du 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’: anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colnames, colSums, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Le chargement a nécessité le package : S4Vectors Attachement du package : ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Le chargement a nécessité le package : IRanges Attachement du package : ‘IRanges’ The following object is masked from ‘package:grDevices’: windows Le chargement a nécessité le package : BiocParallel Attachement du package : ‘DelayedArray’ The following objects are masked from ‘package:matrixStats’: colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from ‘package:base’: aperm, apply Le chargement a nécessité le package : rhdf5 Erreur : package or namespace load failed for ‘HDF5Array’: .onLoad a échoué dans loadNamespace() pour 'HDF5Array', détails : appel : H5Fcreate(file) erreur : HDF5. File accessibilty. Unable to open file. > traceback() 6: stop(msg, call. = FALSE, domain = NA) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(HDF5Array)
I just tried and it works perfectly :-)