[Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck
Jurat Shayidin
juratbupt at gmail.com
Sat Dec 17 05:12:23 CET 2016
Dear Lori :
Thanks for this useful link. I tried dplyr underscore command separate_,
mutate_ in my implementation,but I got vignette error as follows :
vignette.Rmd' failed with diagnostics: object 'cn' not found. Execution
halted
So I tried another approach that suggested in stackoverflow, I used
utils::globalVariables() at the end of my function :
utils::globalVariables (c ("cn", "p.value", ".", "peakStringency",
"original_list", "n", "Replicate","output"))
but now I got building error as follows:
Error: processing vignette 'MSPC-User-Guide.Rmd' failed with diagnostics:
The namespace for package "MSPC" is locked; no changes in the global
variables list may be made.
Execution halted
I don't know what to do on this R CMD check NOTE. Could you give me
possible solution on this problem ? How can I avoid this issue ? Any
further solution please ? Thank you very much.
Best regards :
Jurat
On Fri, Dec 16, 2016 at 3:15 PM, Shepherd, Lori <
Lori.Shepherd at roswellpark.org> wrote:
> This might be a helpful link
>
> https://cran.r-project.org/web/packages/dplyr/vignettes/nse.html
> Standard Evaluation vs. Non-Standard Evaluation
> <https://cran.r-project.org/web/packages/dplyr/vignettes/nse.html>
> cran.r-project.org
> Standard evaluation basics. Every function in dplyr that uses NSE also has
> a version that uses SE. The name of the SE version is always the NSE name
> with an _ on the end.
>
> and also see the help page in R: ?globalVariables
>
>
>
> I would ignore the Rmarkdown warning for now if your output is getting
> created correctly and it does not appear in the other checks.
>
>
> 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 8:51:43 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 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>
>>>
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>>>
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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>
>>
>> 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
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