Bug in makeCappedVolumeBox() results in zero-column volumn box #34
Description
suppressPackageStartupMessages(library(DelayedArray))
# What triggered the error
makeCappedVolumeBox(maxvol = 1000000L, maxdim = c(24587696L, 18L), shape = "scale")
#> [1] 1168752 0
# Some exploring to see when you end up with boxes with zero columns
nc <- seq.int(1, 50)
names(nc) <- nc
sapply(nc, function(i) {
makeCappedVolumeBox(maxvol = 1000000L, maxdim = c(24587696L, i), shape = "scale")[2]
})
#> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
#> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
#> 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
#> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1Created on 2018-09-27 by the reprex package (v0.2.1)
Session info
devtools::session_info()
#> Session info -------------------------------------------------------------
#> setting value
#> version R version 3.5.1 (2018-07-02)
#> system x86_64, darwin15.6.0
#> ui X11
#> language (EN)
#> collate en_AU.UTF-8
#> tz Australia/Melbourne
#> date 2018-09-27
#> Packages -----------------------------------------------------------------
#> package * version date source
#> backports 1.1.2 2017-12-13 CRAN (R 3.5.0)
#> base * 3.5.1 2018-07-05 local
#> BiocGenerics * 0.27.1 2018-06-17 Bioconductor
#> BiocParallel * 1.15.12 2018-09-13 Bioconductor
#> compiler 3.5.1 2018-07-05 local
#> datasets * 3.5.1 2018-07-05 local
#> DelayedArray * 0.7.41 2018-09-14 Bioconductor
#> devtools 1.13.6 2018-06-27 CRAN (R 3.5.0)
#> digest 0.6.17 2018-09-12 CRAN (R 3.5.1)
#> evaluate 0.11 2018-07-17 CRAN (R 3.5.0)
#> graphics * 3.5.1 2018-07-05 local
#> grDevices * 3.5.1 2018-07-05 local
#> htmltools 0.3.6 2017-04-28 CRAN (R 3.5.0)
#> IRanges * 2.15.17 2018-08-24 Bioconductor
#> knitr 1.20 2018-02-20 CRAN (R 3.5.0)
#> magrittr 1.5 2014-11-22 CRAN (R 3.5.0)
#> matrixStats * 0.54.0 2018-07-23 CRAN (R 3.5.1)
#> memoise 1.1.0 2017-04-21 CRAN (R 3.5.0)
#> methods * 3.5.1 2018-07-05 local
#> parallel * 3.5.1 2018-07-05 local
#> Rcpp 0.12.18 2018-07-23 CRAN (R 3.5.1)
#> rmarkdown 1.10 2018-06-11 CRAN (R 3.5.0)
#> rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0)
#> S4Vectors * 0.19.19 2018-07-18 Bioconductor
#> stats * 3.5.1 2018-07-05 local
#> stats4 * 3.5.1 2018-07-05 local
#> stringi 1.2.4 2018-07-20 CRAN (R 3.5.1)
#> stringr 1.3.1 2018-05-10 CRAN (R 3.5.0)
#> tools 3.5.1 2018-07-05 local
#> utils * 3.5.1 2018-07-05 local
#> withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
#> yaml 2.2.0 2018-07-25 CRAN (R 3.5.1)I initially hit this when running the following:
dim(x)
#> [1] 24587696 18
saveHDF5SummarizedExperiment(x)
#> Start writing assay 1/3 to '/scratch/temp/5531374.1.cegs2.q/Rtmp0WGrOh/test/assays.h5':
#> Error in chunkdim(x) :
#> The "chunkdim" method for HDF5RealizationSink objects returned an
#> integer vector with illegal zeros. chunkdim() should always return an
#> integer vector with nonzero values unless the zero values correspond to
#> dimensions in 'x' that are also zero. Please contact the author of the
#> HDF5RealizationSink class (defined in the HDF5Array package) about this
#> and point him/her to the man page for extract_array() in the
#> DelayedArray package (?extract_array).