[Bioc-devel] A handful of check to follow up on R CMD BiocCheck

[Kevin RUE]

Thanks for the feedback!

I also tend to prefer *all* the lines being reported (or to be honest, that
was really true when I had lots of them; a problem that I largely mitigated
by fixing all of them once and subsequently paying more attention while
developing).

Printing the content of the offending line somewhat helps me spot the line
faster (more so for tab issues). But I must admit that showing the whole
line is somewhat "overkill". I just started thinking of a compromise being
to only show the first N characters of the line, with N being 80 minus the
number of characters necessary to print the filename and line number.

Thanks Martin for pointing out the lines in BiocCheck. (Now I feel bad for
not having checked sooner.. hehe!)
I think the idea of BiocCheck showing the first 6 offenders in BiocCheck
quite nice, as I rarely have more since I use using the RStudio "Tools >
Global Options > Code > Display > Show Margin > Margin column: 80" feature.

I'll give a go at both approaches (developing BiocCheck and my own scripts)

Cheers,
Kevin


On Wed, Nov 2, 2016 at 7:41 PM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:

> I would prefer all line numbers reported, but on the other hand I am
> indifferent wrt. the content of the line, unless (say) TABs are marked up
> somehow.
>
> Kasper
>
> On Wed, Nov 2, 2016 at 3:17 PM, Martin Morgan <
> martin.morgan at roswellpark.org> wrote:
>
>> On 11/02/2016 02:49 PM, Kevin RUE wrote:
>>
>>> Dear all,
>>>
>>> Just thought I'd share a handful of scripts that I wrote to follow up on
>>> certain NOTE messages thrown by R CMD BiocCheck.
>>>
>>> https://github.com/kevinrue/BiocCheckTools
>>>
>>> They're very simple, but I occasionally find them quite convenient.
>>> Apologies if something similar already exists somewhere :)
>>>
>>
>> Maybe consider creating a diff against the source code that, e.g.,
>> reported the first 6 offenders? The relevant lines are near
>>
>> https://github.com/Bioconductor-mirror/BiocCheck/blob/master
>> /R/checks.R#L1081
>>
>> Martin
>>
>>
>>> All the best,
>>> Kevin
>>>
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>>>
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>>>
>>>
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>

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