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-boun...@r-project.org> on behalf of Konrad Zych <konrad.z...@embl.de> Sent: Tuesday, November 6, 2018 9:34:45 AM To: bioc-devel@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@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]]
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