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

[Shepherd, Lori]

$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>

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