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

[Fischer, Bernd]

Dear Aaron,

Sorry for any inconvenience. I just wanted to change ‘aesthetics’, but
not ‘expected behaviour of the function’.
I moved the format call from h5ls to the show method.

Will be effective in version 2.15.7 from tomorrow on.

Best,

Bernd


On 08.04.2016, at 10:15, Aaron Lun <alun at wehi.edu.au<mailto:alun at wehi.edu.au>> wrote:

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

_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

—

Bernd Fischer
Computational Genome Biology / B210
group leader

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-1280
fax:      +49 6221 42-1289
b.fischer at dkfz.de<mailto:b.fischer at dkfz.de>
http://www.dkfz.de/en/computational-genome-biology
Management Board: Prof. Dr. Michael Boutros (interim), Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537