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.
Ah, aesthetics. My old arch-nemesis...
Will be effective in version 2.15.7 from tomorrow on.
The function works great now, thanks. - Aaron
On 08.04.2016, at 10:15, Aaron Lun <a...@wehi.edu.au<mailto:a...@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@r-project.org<mailto:Bioc-devel@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.fisc...@dkfz.de<mailto:b.fisc...@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
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