Dear all, I am the creator of the hummingbird package ( https://bioconductor.org/packages/release/bioc/html/hummingbird.html ) and suddenly today I noticed that the build is failing, even though I did not make any change to the package, it was building fine the previous days. I am not sure why this has happened? The error message occurring states: Error: processing vignette 'hummingbird.Rmd' failed with diagnostics: The 'rmarkdown' package should be declared as a dependency of the 'hummingbird' package (e.g., in the 'Suggests' field of DESCRIPTION), because the latter contains vignette(s) built with the 'rmarkdown' package. Please see https://github.com/yihui/knitr/issues/1864 for more information. --- failed re-building ?hummingbird.Rmd? Could you please help me? Thank you, Eleni Adam *PhD Candidate in CS* *Old Dominion University* *Norfolk, VA, USA*
[Bioc-devel] Error building package
4 messages · ELENI ADAM, alan murphy, Shepherd, Lori
2 days later
Even though you did not make any changes to your package, a dependency you use has changed. This currently requires attention by you (and any other package / package maintainer affected) to make appropriate changes in your package code and to push up to bioconductor.org The changes comes from an update in CRAN package knitr version 1.33. See https://github.com/yihui/knitr/issues/1864 regarding the change. The ERROR is very informative and following its advice by updating the Suggest of the package DESCRIPTION should remedy. If your vignette is based on the vignette engine knitr::rmarkdown, you have to declare the dependency on rmarkdown, e.g., Suggests: rmarkdown VignetteBuilder: knitr If your vignette is based on the vignette engine knitr::markdown, you have to declare the dependency on markdown, e.g., Suggests: markdown VignetteBuilder: knitr For quick reference, here is a useful help page on fixing bugs in release and devel for Bioconductor. bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ We are exploring other options for fixing this issue since it affects hundreds of Bioconductor package but currently if you would like to follow the above instructions it is greatly appreciated. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of alan murphy <alanmurph94 at hotmail.com>
Sent: Saturday, April 17, 2021 4:52 AM
To: ELENI ADAM <eadam002 at odu.edu>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Error building package
Sent: Saturday, April 17, 2021 4:52 AM
To: ELENI ADAM <eadam002 at odu.edu>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Error building package
_______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/1wU9NHjSrv-PW4vXomr3nbTfLlNrpYcAdIXDKF9IJwD_30nfUqXWry9jLafvge770Btz8rqwoqcGM7vvaSr2phWVirmkMR_dDW4c9EA3ddTbEd7-sCu3xxR-_OFWI7jeYGomVtJk74L6CQbCQT2LNSSfboIU_Sxj7jvfmxbEeOTz-HRLJ3ZrBfzlRGSq8RooD1Pz3BkwnJXcQuPiMwg3s_O4B-Jvi6WO5rRjH5L_-ihzGePUJIZVZzOI8NAos9XPYOmHmvWjXJIZ3p_nCDcjnvtHOVJzHyE9jP7PV3b0VSz8WQMeRCs40fbaSM-3SPI86CcZRIzXyxjFgvbzMCUdSig/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-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.
Dear Lori, Thank you very much for explaining to me what exactly happened. I have made the appropriate changes and fixed the issue. Thank you, Eleni On Mon, Apr 19, 2021, 9:21 AM Kern, Lori <Lori.Shepherd at roswellpark.org> wrote:
Even though you did not make any changes to your package, a dependency you use has changed. This currently requires attention by you (and any other package / package maintainer affected) to make appropriate changes in your package code and to push up to bioconductor.org The changes comes from an update in CRAN package knitr version 1.33. See https://github.com/yihui/knitr/issues/1864 regarding the change. The ERROR is very informative and following its advice by updating the Suggest of the package DESCRIPTION should remedy. If your vignette is based on the vignette engine knitr::rmarkdown, you have to declare the dependency on rmarkdown, e.g., Suggests: rmarkdown VignetteBuilder: knitr If your vignette is based on the vignette engine knitr::markdown, you have to declare the dependency on markdown, e.g., Suggests: markdown VignetteBuilder: knitr For quick reference, here is a useful help page on fixing bugs in release and devel for Bioconductor. bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ We are exploring other options for fixing this issue since it affects hundreds of Bioconductor package but currently if you would like to follow the above instructions it is greatly appreciated. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ------------------------------ *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of alan murphy <alanmurph94 at hotmail.com> *Sent:* Saturday, April 17, 2021 4:52 AM *To:* ELENI ADAM <eadam002 at odu.edu> *Cc:* bioc-devel at r-project.org <bioc-devel at r-project.org> *Subject:* Re: [Bioc-devel] Error building package
_______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/1wU9NHjSrv-PW4vXomr3nbTfLlNrpYcAdIXDKF9IJwD_30nfUqXWry9jLafvge770Btz8rqwoqcGM7vvaSr2phWVirmkMR_dDW4c9EA3ddTbEd7-sCu3xxR-_OFWI7jeYGomVtJk74L6CQbCQT2LNSSfboIU_Sxj7jvfmxbEeOTz-HRLJ3ZrBfzlRGSq8RooD1Pz3BkwnJXcQuPiMwg3s_O4B-Jvi6WO5rRjH5L_-ihzGePUJIZVZzOI8NAos9XPYOmHmvWjXJIZ3p_nCDcjnvtHOVJzHyE9jP7PV3b0VSz8WQMeRCs40fbaSM-3SPI86CcZRIzXyxjFgvbzMCUdSig/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-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.