Empty strings fail?

[muschellij2]

Empty string gives bad value in a a list. This only started happening with new Bioc version.

library(rhdf5)
filepath = tempfile(fileext = ".h5")
name = "x"
hdr = list(descrip = "")
rhdf5::h5write(hdr, file = filepath, name = name)
#> Error in H5Tset_size(tid, size): HDF5. Invalid arguments to routine. Bad value.

^{Created on 2020-05-18 by the reprex package (v0.3.0)}

Session info

devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                                      
#>  version  R version 4.0.0 Patched (2020-05-13 r78451)
#>  os       CentOS Linux 7 (Core)                      
#>  system   x86_64, linux-gnu                          
#>  ui       X11                                        
#>  language (EN)                                       
#>  collate  en_US.UTF-8                                
#>  ctype    en_US.UTF-8                                
#>  tz       US/Eastern                                 
#>  date     2020-05-18                                 
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date       lib source                            
#>  assertthat    0.2.1   2019-03-21 [2] CRAN (R 4.0.0)                    
#>  backports     1.1.7   2020-05-13 [2] CRAN (R 4.0.0)                    
#>  callr         3.4.3   2020-03-28 [2] CRAN (R 4.0.0)                    
#>  cli           2.0.2   2020-02-28 [2] CRAN (R 4.0.0)                    
#>  colorout    * 1.2-2   2020-05-18 [1] Github (jalvesaq/colorout@726d681)
#>  crayon        1.3.4   2017-09-16 [2] CRAN (R 4.0.0)                    
#>  desc          1.2.0   2018-05-01 [2] CRAN (R 4.0.0)                    
#>  devtools      2.3.0   2020-04-10 [2] CRAN (R 4.0.0)                    
#>  digest        0.6.25  2020-02-23 [2] CRAN (R 4.0.0)                    
#>  ellipsis      0.3.1   2020-05-15 [2] CRAN (R 4.0.0)                    
#>  evaluate      0.14    2019-05-28 [2] CRAN (R 4.0.0)                    
#>  fansi         0.4.1   2020-01-08 [2] CRAN (R 4.0.0)                    
#>  fs            1.4.1   2020-04-04 [2] CRAN (R 4.0.0)                    
#>  glue          1.4.1   2020-05-13 [2] CRAN (R 4.0.0)                    
#>  highr         0.8     2019-03-20 [2] CRAN (R 4.0.0)                    
#>  htmltools     0.4.0   2019-10-04 [2] CRAN (R 4.0.0)                    
#>  knitr         1.28    2020-02-06 [2] CRAN (R 4.0.0)                    
#>  magrittr      1.5     2014-11-22 [2] CRAN (R 4.0.0)                    
#>  memoise       1.1.0   2017-04-21 [2] CRAN (R 4.0.0)                    
#>  pkgbuild      1.0.8   2020-05-07 [2] CRAN (R 4.0.0)                    
#>  pkgload       1.0.2   2018-10-29 [2] CRAN (R 4.0.0)                    
#>  prettyunits   1.1.1   2020-01-24 [2] CRAN (R 4.0.0)                    
#>  processx      3.4.2   2020-02-09 [2] CRAN (R 4.0.0)                    
#>  ps            1.3.3   2020-05-08 [2] CRAN (R 4.0.0)                    
#>  R6            2.4.1   2019-11-12 [2] CRAN (R 4.0.0)                    
#>  Rcpp          1.0.4.6 2020-04-09 [2] CRAN (R 4.0.0)                    
#>  remotes       2.1.1   2020-02-15 [2] CRAN (R 4.0.0)                    
#>  rhdf5       * 2.33.0  2020-04-27 [2] Bioconductor                      
#>  Rhdf5lib      1.11.0  2020-04-27 [2] Bioconductor                      
#>  rlang         0.4.6   2020-05-02 [2] CRAN (R 4.0.0)                    
#>  rmarkdown     2.1     2020-01-20 [1] CRAN (R 4.0.0)                    
#>  rprojroot     1.3-2   2018-01-03 [2] CRAN (R 4.0.0)                    
#>  sessioninfo   1.1.1   2018-11-05 [2] CRAN (R 4.0.0)                    
#>  stringi       1.4.6   2020-02-17 [2] CRAN (R 4.0.0)                    
#>  stringr       1.4.0   2019-02-10 [2] CRAN (R 4.0.0)                    
#>  testthat      2.3.2   2020-03-02 [2] CRAN (R 4.0.0)                    
#>  usethis       1.6.1   2020-04-29 [2] CRAN (R 4.0.0)                    
#>  withr         2.2.0   2020-04-20 [2] CRAN (R 4.0.0)                    
#>  xfun          0.13    2020-04-13 [2] CRAN (R 4.0.0)                    
#>  yaml          2.2.1   2020-02-01 [2] CRAN (R 4.0.0)                    
#> 
#> [1] /users/jmuschel/R/4.0.x
#> [2] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0.x/R/4.0.x/lib64/R/site-library
#> [3] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0.x/R/4.0.x/lib64/R/library

[grimbough]

Thanks for the report, I'll look into it.

[grimbough]

Thanks again, this should be patched in version 2.33.4. It didn't only affect writing lists, but any character vector where the contents were all the empty string. I'll also patch the release version on Bioconductor since this is a bug.

library(rhdf5)
filepath = tempfile(fileext = ".h5")
rhdf5::h5write("", file = filepath, name = "X")
h5read(filepath, "X")
#> [1] ""

rhdf5::h5write(list(empty_char = ""), file = filepath, name = "Y")
h5read(filepath, "Y")
#> $empty_char
#> [1] ""

Let me know if you run into more issues.

[muschellij2]

Was this patched on BioC release? Still seeing the same bug.

[grimbough]

Sorry, I should have left the issue open. Thank for reminding me, I wanted to wait a few day to make sure nothing downstream broke in devel before pushing this.

It is now in rhdf5 v 2.32.1, which should propagate in the next day.

Out of interest, what's the usecase for creating vectors with only empty strings?