[Bioc-devel] Question about sumbition process and biocviews

Ioannis Vardaxis ioannis.vardaxis at math.ntnu.no
Mon Nov 7 00:10:17 CET 2016


For the references I just used @references \insertRef{key}{pkg}, and
although it shows up in the ??pkg::function help, I get an error in

For the vignettes, my vignette is generated without any errors. What I get
as en error in Rcheck is that: “From R version >=3.2 vignettes is required
to be placed in /inst/doc”
But if I do that the bioCheck gives an error, if I don’t then Rcheck gives
an error. If I place vignettes in /inst/doc then Rcheck checks it without
any error.

Ioannis Vardaxis

Stipendiat IMF

On 06/11/16 23:59, "Martin Morgan" <martin.morgan at roswellpark.org> wrote:

>On 11/06/2016 04:54 PM, Ioannis Vardaxis wrote:
>> Thanks for the answer,
>> I have some other questions about BiocCheck.
>> First I get the following warning:
>> * This is a software package, checking vignette directories...
>>     * ERROR: 'vignettes' directory!
>> I have my vignettes directory in the inst/doc/vignettes. If I change the
>> directory and place the vignettes in the top directory I don¹t get an
>> error from biocCheck, but I get a fatal error from Rcheck.
>The vignettes directory should be in the top-level directory
>YourPacakge/vignettes/ and not in YourPackage/inst/doc. If you get a
>fatal error, then there is something about your vignette (or indirectly
>in your package code) that is very incorrect. You should be able to
>'tangle' your vignette to get the pure R code, and then to run it, e.g.,
>I can
>     $ cd Rsamtools/vignettes
>     $ R CMD Stangle Rsamtools-Overview.Rnw
>     Output file:  Rsamtools-Overview.R
>     $ R -f Rsamtools-Overview.R
>> Secondly:
>> Checking unit tests...
>>     * NOTE: Consider adding unit tests. We strongly encourage them. See
>>       http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
>> I read about unit tests, however the package is done and it works fine,
>> and at the same time I don¹t see how unit tests would benefit me based
>> the functions in my package. Are them necessary?
>They are strongly encouraged but not required. Many would argue that
>they are necessary to ensure that your package behaves as expected, and
>continues to do so as underlying dependencies change. Here's a silly
>     f = function(n) {
>         x = integer(n)
>         for (i in 1:n)
>             x[i] = i
>         x
>     }
>and a unit test that reveals an error.
>     test_that("f works as expected for common cases", {
>         expect_equal(f(2), c(1L, 2L))
>         expect_equal(f(1), 1L)
>         expect_equal(f(0), integer(0))
>         expect_error(f("two"))
>     })
>Which leads to
>Error: Test failed: 'f works as expected for common cases'
>* f(0) not equal to integer(0).
>Lengths differ: 1 vs 0
>The fix in this case might be
>     f = function(n) {
>         seq_len(n)
>     }
>though now its clear that my four lines of code were not necessary at all.
>Interestingly, in writing that example I made a mistake in my original
>f(), writing x[i] = n rather than my intended x[i] = i. The first
>expectation failed, helping to show me what I was doing wrong. I also
>wrote the last expectation as f("2"), which a little surprisingly also
>failed (to create an error) -- R coerced 1:"2" to 1:2; maybe I'd want to
>think about whether this behavior would be appropriate in my actual
>code, and if not write some checks on the inputs. It's surprising how
>easy bugs creep into code, and how unit tests help to see those bugs. See
>   http://bioconductor.org/developers/how-to/unitTesting-guidelines/
>for some further motivation.
>> Thirdly, I used the Rdpack for adding references to the roxynen files,
>> I get an error from biocCheck that the macro is unknown. Is there
>> way of using references in roxygen?
>this isn't formulated in a clear enough way (e.g., with a short example
>and with the exact error message) to be able to provide an answer.
>> Finally, a question about coding: My longest function is 326 lines long,
>> and cannot be smaller, is that ok? I get a note in biocCheck. Moreover I
>> get the following note:
>> * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
>>   and vignette source...
>>     * NOTE: Consider shorter lines; 4 lines (0%) are > 80 characters
>>       long.
>>     * NOTE: Consider indenting lines with a multiple of 4 spaces; 462
>>       lines (6%) are not.
>> None of my code cross the 80 character line though and the spaces are
>> using the double tab that you need.
>These are style recommendations and generally 'at your discretion'. Of
>course your 326 line function can be smaller -- identify the logical
>steps of your computation ('check inputs', 'initialize', 'iterate to
>convergence', 'validate result', 'format result for user') and implement
>each as a (non-exported) function called by the the function exposed to
>the user. This way you can think carefully about the logic of each
>function, write extensive unit tests that validate the inputs and
>expected outputs of the function, and hopefully re-use code in several
>different places.
>The second NOTE above suggests indentation with spaces rather than tabs
>(4 spaces per tab) simply because tab width (and hence visual
>indentation) is at the discretion of the editor in use.
>> Best,
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