Bug#1148854: hdf5: Uncalled test suite affected by libhdf5 2.2.0 legacy-chunk regression

[Gilles Filippini]

Control: tags -1 + moreinfo

Hi Andreas,

Andreas Tille a écrit le 24/09/2026 à 11:00 :

Source: hdf5
Severity: normal

Hi,

I had to skip a part of the test suite of the uncalled package.  You
can see the according commit with verbose documentation here:

    
https://salsa.debian.org/med-team/uncalled/-/commit/607d1ec0f8bbc3f2e9f755000705b1325c87c769

It would be great if we could run the full test suite[1] including the
command

    uncalled map index/example_ref fast5_filename.txt

If you think there is no chance to support this please tag the bug
wontfix and let me know.  Most probably this will affect more packages
than just uncalled.

Kind regards
    Andreas.

[1] 
https://salsa.debian.org/med-team/uncalled/-/blob/master/example/run_example.sh?ref_type=heads#L13

GROUP "/" {
   ATTRIBUTE "file_version" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 0.6
      }
   }
[snip]
         ATTRIBUTE "version" {
            DATATYPE  H5T_STRING {
               STRSIZE 7;
               STRPAD H5T_STR_NULLTERM;
               CSET H5T_CSET_ASCII;
               CTYPE H5T_C_S1;
            }
            DATASPACE  SCALAR
            DATA {
            (0): "1.13.5"
            }
         }
      }
   }
}
}

Best,
_g.

Please be more specific. A quick check using h5dump shows that the file is correctly read by HDF5 2.2.0. $ h5dump GXB01153_20180730_FAH86930_GA30000_mux_scan_Zymo_CS_LSK109_29137_read_101_ch_486_strand.fast5 DF5 "GXB01153_20180730_FAH86930_GA30000_mux_scan_Zymo_CS_LSK109_29137_read_101_ch_486_strand.fast5" {

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