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