[Bioc-devel] WARNING on tokay1 for SIAMCAT package

[Shepherd, Lori]

Similarly answered here:

https://stat.ethz.ch/pipermail/bioc-devel/2018-October/014139.html




I think there is a reference here

https://stackoverflow.com/questions/48430093/how-do-i-resolve-rd-warning-missing-file-link-when-building-packages-in-rstudio

So for example:
Where the actual name of the man file that has otu_table is otu_table-methods and otu_table is an alias.

I believe if you change the link to be

\code{\link[pyloseq:otu_table-methods]{otu_table}}  It should remedy the issue.




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 using r-project.org> on behalf of Konrad Zych <konrad.zych using embl.de>
Sent: Tuesday, November 6, 2018 9:34:45 AM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] WARNING on tokay1 for SIAMCAT package

Hi all,

our package got a check warning on tokay1 and I cannot figure out where it
is coming from. The Warning:

* checking whether package 'SIAMCAT' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpw5jgK9/R.INSTALL9f82974290/SIAMCAT/man/siamcat.Rd:43:
file link 'otu_table' in package 'phyloseq' does not exist and so has
been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpw5jgK9/R.INSTALL9f82974290/SIAMCAT/man/siamcat.Rd:50:
file link 'sample_data' in package 'phyloseq' does not exist and so
has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SIAMCAT.Rcheck/00install.out'
for details.

Does anybody know how to solve that?

Best

Konrad Zych
Postdoctoral Fellow
Zeller Team, Structural and Computational Biology Unit
EMBL Heidelberg, Meyerhofstra�e 1, 69117 Heidelberg, Germany

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using 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.
	[[alternative HTML version deleted]]