[Bioc-devel] WARNING on tokay1 for SIAMCAT package

Shepherd, Lori Lori@Shepherd @ending from Ro@wellP@rk@org
Tue Nov 6 15:53:04 CET 2018

Similarly answered here:


I think there is a reference here


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?


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

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