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