[Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck

[Jurat Shayidin]

Dear Lori:

Thanks for your respond on my question. I fixed the error from unit test. I
tried to edit the tag on bibliography.bib file, but Rstudio still did not
print that out. Why is that?

R CMD check report only one Notes when I tried to generate stack bar plot
for my output set by using ggplot2 packages, this note also appeared in R
CMD BiocCheck. I really don't know how to get rid of this note. Any idea
please ? How to remove this note ? Should I suppress this? Here is note
that raised by R CMD check :

Undefined global functions or variables:
  . Replicate cn mcols<- n original_list output p.value peakStringency

plus, I've used tidyr package to categorize my intermediate output in order
to get desired result, but when I execute .Rmd files, it gaves warning,
that didn't appeared in R CMD check, R CMD BiocCheck. Because R CMD check,
R CMD BiocCheck never report this as a warning. Should I keep aside this ?
R markdown report this warning :

Warning messages:
1: Too many values at 158 locations: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, ...


What possible changes I might to do on my package before issuing package
submission? Thank you very much.

Best regards :

Jurat



On Thu, Dec 15, 2016 at 2:36 PM, Shepherd, Lori <
Lori.Shepherd at roswellpark.org> wrote:

> $error
> [1] "At least 80% of man pages documenting exported objects must have
> runnable examples. The following pages do not:"
>
> This ERROR occurs when man pages are included without runnable examples.
> You have examples in it looks like 5/12 of your man pages (~42%). We
> encourage 80%
>
> $warning
> [1] "Add non-empty \\value sections to the following man pages:
> man/filterBycombStringency.Rd"
>
> Most man pages encourage a \value{} section describing the output of the
> function or what would be returned.  This is asking that you add this
> section to this specific man page with information about what the function
> returns.
>
>
> On quick glance I think you would cite the references in the bibliography
> with the tag
> Vahid_Jalili_MSPC_2015  not the title "Using combined evidence from
> replicates to evaluate ChIP-seq peaks"
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Jurat
> Shayidin <juratbupt at gmail.com>
> *Sent:* Thursday, December 15, 2016 7:17:42 AM
> *To:* bioc-devel at r-project.org
> *Subject:* [Bioc-devel] Quick question about result of R CMD check and R
> CMD BiocCheck
>
> Dear BiocDevel :
>
> I got confused about the message from R CMD BiocCheck, and R CMD check on
> my packages. Precisely speaking, R CMD check throws an error that my unit
> test is failed, zero warning, 2 notes; instead R CMD BiocCheck complain
> with one error that no runnable example found, one warning (I don't
> undersand this warning, becuase R CMD check doesn't report this), 4 notes.
> I don't understand the result of R CMD BiocCheck, can't figure out the
> exact issue . However, result of R CMD check is more clear and
> self-explanatory. I did add example for each of my function, R CMD check
> okay with it, but R CMD BiocCheck complain about this, Why ? How to address
> the issues raised by R CMD BiocCheck ?  R CMD BiocCheck gave me following
> message :
>
> $error
> [1] "At least 80% of man pages documenting exported objects must have
> runnable examples. The following pages do not:"
>
> $warning
> [1] "Add non-empty \\value sections to the following man pages:
> man/filterBycombStringency.Rd"
>
>
>
> Plus, I tried to attach bibliography.bib files on my package's vignette,
> but Rstudio didn't print out the bibliography information at the end of
> .Rmd file. How can I make this happen ? I did push all recent changes to
> github <https://github.com/julaiti/MSPC>, so everything is synchronized.
> Is
> that possible to kindly ask Bioconductor team to briefly review my packages
> and getting valuable opinion to improve my work? I am grad students and
> very few experiences in Bioinformatics field (not in this major), so my
> very first R package might have a lot of issues, getting possible
> contribution would be highly appreciated. Many thanks to Bioconductor team.
>
> Best regards :
>
> --
> Jurat Shahidin
>
> Dipartimento di Elettronica, Informazione e Bioingegneria
> Politecnico di Milano
> Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
> Mobile : +39 3279366608 <+39%20327%20936%206608> <+39%20327%20936%206608>
>
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-- 
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608 <+39%20327%20936%206608>

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