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

Fri Dec 16 15:15:53 CET 2016

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<mailto: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<mailto:juratbupt at gmail.com>>
Sent: Friday, December 16, 2016 6:06:41 AM
To: Shepherd, Lori; bioc-devel at r-project.org<mailto: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<mailto: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<mailto:bioc-devel-bounces at r-project.org>> on behalf of Jurat Shayidin <juratbupt at gmail.com<mailto:juratbupt at gmail.com>>
Sent: Thursday, December 15, 2016 7:17:42 AM
To: bioc-devel at r-project.org<mailto: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<tel:+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<tel:+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<tel:+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.
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