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
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