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

[Jurat Shayidin]

Dear Lori :

Thanks again for your prompt respond. I corrected my mistake, now Reference
can be printed out. However, R CMD check raised one NOTE, how can I fix
this ? I've searched related question in stackoverflow and tried given
solution, but it cause error instead. How can I possibly get rid of this
NOTE ? Could you give me idea to address this problem please?

Plus, R markdown report warnings but that doesn't effect output of package
vignette, even R CMD check, and R CMD BiocCheck didn't report this as a
warning . Should I ignore this ? Thank you very much

Best regards :
Jurat

On Fri, Dec 16, 2016 at 2:09 PM, Shepherd, Lori <
Lori.Shepherd at roswellpark.org> wrote:

>
> You should change the references in your vignette MSPC-User-Guide.Rmd not
> in the bibliography.bib file.  In your vignette, use the tag not the title;
> so as an example:
>
>  [@ Using combined evidence from replicates to evaluate ChIP-seq peaks.]
>
> would become [@Vahid_Jalili_MSPC_2015]
>
>
>
> Once you submit your package to Bioconductor, a reviewer will be assigned
> to formally review your package and advise on additional changes.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* Jurat Shayidin <juratbupt at gmail.com>
> *Sent:* Friday, December 16, 2016 6:06:41 AM
> *To:* Shepherd, Lori; bioc-devel at r-project.org
> *Subject:* Re: [Bioc-devel] Quick question about result of R CMD check
> and R CMD BiocCheck
>
> 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>
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> This email message may contain legally privileged and/or confidential
>> information. If you are not the intended recipient(s), or the employee or
>> agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
>> distribution, or use of this email message is prohibited. If you have
>> received this message in error, please notify the sender immediately by
>> e-mail and delete this email message from your computer. Thank you.
>
>
>
>
> --
> 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>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>



-- 
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>

	[[alternative HTML version deleted]]