Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-21 12:03 -0400 (Tue, 21 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 958/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HDF5Array 1.37.0 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the HDF5Array package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HDF5Array.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: HDF5Array |
Version: 1.37.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HDF5Array_1.37.0.tar.gz |
StartedAt: 2025-10-21 00:38:39 -0400 (Tue, 21 Oct 2025) |
EndedAt: 2025-10-21 00:53:47 -0400 (Tue, 21 Oct 2025) |
EllapsedTime: 907.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: HDF5Array.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HDF5Array_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/HDF5Array.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘HDF5Array/DESCRIPTION’ ... OK * this is package ‘HDF5Array’ version ‘1.37.0’ * 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 hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘HDF5Array’ can be installed ... OK * checking installed package size ... INFO installed size is 9.0Mb sub-directories of 1Mb or more: extdata 7.7Mb * 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 whether startup messages can be suppressed ... 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: H5SparseMatrix-class.Rd: h5ls H5SparseMatrixSeed-class.Rd: h5ls HDF5Array-class.Rd: H5File, h5ls HDF5ArraySeed-class.Rd: h5ls ReshapedHDF5Array-class.Rd: h5ls ReshapedHDF5ArraySeed-class.Rd: h5ls TENxMatrix-class.Rd: h5ls TENxMatrixSeed-class.Rd: h5ls dump-management.Rd: h5createDataset, h5ls writeHDF5Array.Rd: DelayedArray, h5writeDimnames, h5ls writeTENxMatrix.Rd: DelayedMatrix, h5ls 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘HDF5Array-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: HDF5Array-class > ### Title: HDF5 datasets as DelayedArray objects > ### Aliases: class:HDF5Array HDF5Array-class HDF5Array > ### DelayedArray,HDF5ArraySeed-method class:HDF5Matrix HDF5Matrix-class > ### HDF5Matrix is_sparse<-,HDF5Array-method matrixClass,HDF5Array-method > ### coerce,HDF5Array,HDF5Matrix-method coerce,HDF5Matrix,HDF5Array-method > ### coerce,ANY,HDF5Matrix-method > ### Keywords: classes methods > > ### ** Examples > > ## --------------------------------------------------------------------- > ## A. CONSTRUCTION > ## --------------------------------------------------------------------- > > ## With a local file: > toy_h5 <- system.file("extdata", "toy.h5", package="HDF5Array") > h5ls(toy_h5) group name otype dclass dim 0 / M1 H5I_DATASET FLOAT 10000 x 150 1 / M2 H5I_DATASET FLOAT 150 x 200 > > HDF5Array(toy_h5, "M2") <150 x 200> HDF5Matrix object of type "double": [,1] [,2] [,3] ... [,199] [,200] [1,] 9.0325451 -0.8372894 -3.0655634 . 4.202503 7.212745 [2,] 0.5603696 1.4590217 1.6268596 . 14.854123 3.481012 [3,] 8.1094489 2.9110584 12.7574103 . 0.520843 8.876323 [4,] 5.8518510 6.4912588 13.8403073 . 8.795605 12.342113 [5,] -0.8206218 10.1040618 10.6219819 . 8.756145 3.130079 ... . . . . . . [146,] 11.2827878 -3.7808660 5.4538427 . -0.762771429 6.070777178 [147,] -2.3159837 10.5172435 -2.9781124 . 0.824398901 -3.154179584 [148,] 0.9635204 13.8644578 11.6860867 . 5.761504602 1.688992344 [149,] 12.6951503 11.6835890 13.4213585 . 13.590451800 2.134752800 [150,] -1.8871983 9.9152485 8.6534266 . -0.007439521 7.164514768 > HDF5Array(toy_h5, "M2", type="integer") <150 x 200> HDF5Matrix object of type "integer": [,1] [,2] [,3] [,4] ... [,197] [,198] [,199] [,200] [1,] 9 0 -3 14 . -1 11 4 7 [2,] 0 1 1 14 . 12 6 14 3 [3,] 8 2 12 6 . 10 0 0 8 [4,] 5 6 13 12 . -1 6 8 12 [5,] 0 10 10 -4 . 9 14 8 3 ... . . . . . . . . . [146,] 11 -3 5 0 . 1 6 0 6 [147,] -2 10 -2 -1 . 3 9 0 -3 [148,] 0 13 11 -2 . 2 -4 5 1 [149,] 12 11 13 8 . 13 3 13 2 [150,] -1 9 8 9 . 10 -2 0 7 > HDF5Array(toy_h5, "M2", type="complex") <150 x 200> HDF5Matrix object of type "complex": [,1] [,2] [,3] ... [,199] [1,] 9.0325451+0i -0.8372894+0i -3.0655634+0i . 4.202503+0i [2,] 0.5603696+0i 1.4590217+0i 1.6268596+0i . 14.854123+0i [3,] 8.1094489+0i 2.9110584+0i 12.7574103+0i . 0.520843+0i [4,] 5.8518510+0i 6.4912588+0i 13.8403073+0i . 8.795605+0i [5,] -0.8206218+0i 10.1040618+0i 10.6219819+0i . 8.756145+0i ... . . . . . [146,] 11.2827878+0i -3.7808660+0i 5.4538427+0i . -0.762771429+0i [147,] -2.3159837+0i 10.5172435+0i -2.9781124+0i . 0.824398901+0i [148,] 0.9635204+0i 13.8644578+0i 11.6860867+0i . 5.761504602+0i [149,] 12.6951503+0i 11.6835890+0i 13.4213585+0i . 13.590451800+0i [150,] -1.8871983+0i 9.9152485+0i 8.6534266+0i . -0.007439521+0i [,200] [1,] 7.212745+0i [2,] 3.481012+0i [3,] 8.876323+0i [4,] 12.342113+0i [5,] 3.130079+0i ... . [146,] 6.070777178+0i [147,] -3.154179584+0i [148,] 1.688992344+0i [149,] 2.134752800+0i [150,] 7.164514768+0i > > ## With a file stored in an Amazon S3 bucket: > if (Sys.info()[["sysname"]] != "Darwin") { + public_S3_url <- + "https://rhdf5-public.s3.eu-central-1.amazonaws.com/rhdf5ex_t_float_3d.h5" + h5file <- H5File(public_S3_url, s3=TRUE) + h5ls(h5file) + + HDF5Array(h5file, "a1") + } <5 x 10 x 2> HDF5Array object of type "double": ,,1 [,1] [,2] [,3] ... [,9] [,10] [1,] 0.122377600 0.473829743 0.244448476 . 0.06294312 0.25262216 [2,] 0.257908699 0.009508783 0.387372283 . 0.52225184 0.94390880 [3,] 0.886223679 0.211665150 0.404533111 . 0.95703000 0.18594012 [4,] 0.549336179 0.071420332 0.617852765 . 0.20320586 0.48317974 [5,] 0.179772913 0.557769188 0.553050760 . 0.72190719 0.18467657 ,,2 [,1] [,2] [,3] ... [,9] [,10] [1,] 0.6848327 0.1282442 0.7906603 . 0.40603368 0.01085798 [2,] 0.6579706 0.4897645 0.3274960 . 0.47773518 0.38283946 [3,] 0.7180033 0.4929566 0.2159982 . 0.48220542 0.56122233 [4,] 0.8445332 0.8016226 0.8083879 . 0.26790274 0.17247477 [5,] 0.4086140 0.3476558 0.7067179 . 0.18221174 0.99788310 > > ## --------------------------------------------------------------------- > ## B. BASIC MANIPULATION > ## --------------------------------------------------------------------- > > library(h5vcData) > tally_file <- system.file("extdata", "example.tally.hfs5", + package="h5vcData") > h5ls(tally_file) group name otype dclass dim 0 / ExampleStudy H5I_GROUP 1 /ExampleStudy 16 H5I_GROUP 2 /ExampleStudy/16 Counts H5I_DATASET INTEGER 12 x 6 x 2 x 90354753 3 /ExampleStudy/16 Coverages H5I_DATASET INTEGER 6 x 2 x 90354753 4 /ExampleStudy/16 Deletions H5I_DATASET INTEGER 6 x 2 x 90354753 5 /ExampleStudy/16 Reference H5I_DATASET INTEGER 90354753 6 /ExampleStudy 22 H5I_GROUP 7 /ExampleStudy/22 Counts H5I_DATASET INTEGER 12 x 6 x 2 x 51304566 8 /ExampleStudy/22 Coverages H5I_DATASET INTEGER 6 x 2 x 51304566 9 /ExampleStudy/22 Deletions H5I_DATASET INTEGER 6 x 2 x 51304566 10 /ExampleStudy/22 Reference H5I_DATASET INTEGER 51304566 > > ## Pick up "Coverages" dataset for Human chromosome 16: > name <- "/ExampleStudy/16/Coverages" > cvg <- HDF5Array(tally_file, name) > cvg <6 x 2 x 90354753> HDF5Array object of type "integer": ,,1 [,1] [,2] [1,] 0 0 [2,] 0 0 ... . . [5,] 0 0 [6,] 0 0 ... ,,90354753 Error in .Call2("C_h5getdimscales", filepath, name, scalename, PACKAGE = "h5mread") : failed to open HDF5 file '/home/biocbuild/bbs-3.22-bioc/R/site-library/h5vcData/extdata/example.tally.hfs5' Calls: <Anonymous> ... h5readDimnames -> get_h5dimnames -> h5getdimscales -> .Call2 Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/HDF5Array.Rcheck/00check.log’ for details.
HDF5Array.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL HDF5Array ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘HDF5Array’ ... ** this is package ‘HDF5Array’ version ‘1.37.0’ ** using staged installation ** R ** 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 (HDF5Array)
HDF5Array.Rcheck/tests/run_unitTests.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. > require("HDF5Array") || stop("unable to load HDF5Array package") Loading required package: HDF5Array Loading required package: SparseArray Loading required package: Matrix Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:Matrix': expand, unname The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: h5mread Loading required package: rhdf5 Attaching package: 'h5mread' The following object is masked from 'package:rhdf5': h5ls [1] TRUE > HDF5Array:::.test() Loading required package: SummarizedExperiment Loading required package: GenomicRanges Loading required package: Seqinfo Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:SparseArray': rowMedians The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians automatic block size set to 77 bytes (was 1e+08) automatic block size set to 1e+08 bytes (was 77) automatic block size set to 77 bytes (was 1e+08) automatic block size set to 1e+08 bytes (was 77) RUNIT TEST PROTOCOL -- Tue Oct 21 00:41:08 2025 *********************************************** Number of test functions: 5 Number of errors: 0 Number of failures: 0 1 Test Suite : HDF5Array RUnit Tests - 5 test functions, 0 errors, 0 failures Number of test functions: 5 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 13.833 0.830 20.808
HDF5Array.Rcheck/HDF5Array-Ex.timings
name | user | system | elapsed | |
H5ADMatrix-class | 2.126 | 0.188 | 2.317 | |
H5ADMatrixSeed-class | 0.087 | 0.004 | 0.091 | |
H5SparseMatrix-class | 0.249 | 0.048 | 0.300 | |
H5SparseMatrixSeed-class | 0.001 | 0.000 | 0.001 | |