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 <juratb...@gmail.com> Sent: Friday, December 16, 2016 6:06:41 AM To: Shepherd, Lori; bioc-devel@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.sheph...@roswellpark.org<mailto:lori.sheph...@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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on behalf of Jurat Shayidin <juratb...@gmail.com<mailto:juratb...@gmail.com>> Sent: Thursday, December 15, 2016 7:17:42 AM To: bioc-devel@r-project.org<mailto:bioc-devel@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> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@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<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. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
