[Bioc-devel] rhdf5 and left-justified output in h5ls - is this sensible?

[Aaron Lun]

Dear List, Bernd;

I've noticed that h5ls now left-justifies its output. For example, if I 
were to run example(h5ls) on my BioC-devel system, I would get:

>   group   name         ltype corder_valid corder cset       otype num_attrs
> 0  /    foo    H5L_TYPE_HARD        FALSE      0    0 H5I_GROUP           0
> 1  /foo B      H5L_TYPE_HARD        FALSE      0    0 H5I_DATASET         0
> 2  /foo foobaa H5L_TYPE_HARD        FALSE      0    0 H5I_GROUP           0
>   dclass          dtype  stype rank       dim    maxdim
> 0                                 0
> 1  FLOAT H5T_IEEE_F64LE SIMPLE    3 5 x 2 x 2 5 x 2 x 2
> 2                                 0

... whereas if I run it on release, I would get:

>   group   name         ltype corder_valid corder cset       otype num_attrs
> 0     /    foo H5L_TYPE_HARD        FALSE      0    0   H5I_GROUP         0
> 1  /foo      B H5L_TYPE_HARD        FALSE      0    0 H5I_DATASET         0
> 2  /foo foobaa H5L_TYPE_HARD        FALSE      0    0   H5I_GROUP         0
>   dclass          dtype  stype rank       dim    maxdim
> 0                                 0
> 1  FLOAT H5T_IEEE_F64LE SIMPLE    3 5 x 2 x 2 5 x 2 x 2
> 2                                 0

Now, my problem is that I use h5ls to determine what data substructures 
are available in a particular *.h5 file, and how I should load them with 
h5read. I can do this on release:

 > x <- h5ls("ex_ls_dump.h5",all=TRUE)
 > h5read("ex_ls_dump.h5", file.path(x$group[2], x$name[2]))
# gives me the data under /foo/B

... but not on BioC-devel:

 > Error in h5read("ex_ls_dump.h5", file.path(x$group[2], x$name[2])) :
 >   Object /foo/B      does not exist in this HDF5 file.

... due to the extra spaces. Suffice to say that it was a rather 
unpleasant surprise to get at 2am in the morning!

I can't see any purpose of the left-justification except for aesthetics. 
Is it sensible to compromise the expected behaviour of the function just 
to make its output look pretty?

Here's the session information for my devel build:

> R Under development (unstable) (2016-02-24 r70217)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.04.4 LTS
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rhdf5_2.15.6
>
> loaded via a namespace (and not attached):
> [1] zlibbioc_1.17.1 tools_3.3.0

... and again, for release:

> R version 3.2.2 (2015-08-14)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.04.4 LTS
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rhdf5_2.14.0
>
> loaded via a namespace (and not attached):
> [1] zlibbioc_1.16.0 tools_3.2.2

Cheers,

Aaron