[Bioc-devel] SeqArray build failing due to missing VariantAnnotation

[Kern, Lori]

It looks like the ERROR is actually because of your call to requireNamespace where it actually does not have a verbose argument and causes unexpected failures because of this.  I think if you remove the verbose argument it should work as expected. For consistency I would also recommend keeping the open bracket on the if ...

> if (!requireNamespace("VariantAnnotation", quietly = TRUE, verbose=FALSE)) {
    stop("Please install VariantAnnotation to use this function")
}
Error: Please install VariantAnnotation to use this function

> if (!requireNamespace("VariantAnnotation", quietly = TRUE)) {
    stop("Please install VariantAnnotation to use this function")
}
>




Lori Kern

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 using r-project.org> on behalf of Stephanie Gogarten <sdmorris using uw.edu>
Sent: Monday, March 30, 2026 7:50 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Cc: Xiuwen Zheng <zhengxwen using gmail.com>
Subject: [Bioc-devel] SeqArray build failing due to missing VariantAnnotation

Hi,

SeqArray is failing to build on nebbiolo1, with the error

Quitting from SeqArray.Rmd:293-299 [unnamed-chunk-11]
Error in `seqAsVCF()`:
! Please install VariantAnnotation to use this function

It looks like VariantAnnotation is passing its own builds, so I don't
understand why this error is happening. Is it related to the ordering of
package builds? One potential fix could be to add VariantAnnotation to
VignetteDepends, but it's already in Suggests which implies that it should
be installed prior to building the vignette, right?

thanks,
Stephanie Gogarten

--

Stephanie M. Gogarten, PhD

Senior Research Scientist / Genetic Analysis Center
<https://secure-web.cisco.com/1OIcJAYMnZJUlIdHMbfUdY62Z16BbLUQMoOtsIRtyvjKTTIUe3fiKaOwXVlgZeVTPEYN1QOvGhm2BgMR4-TGJimlwX5_NM144Do1PiW2LUtejBKT-hkRlJMmiHQ1nbRwLfuRy7PxY93DL_7cXYXaBTYgXqgS_KOXkPm59mhsUDD8gAfODdINfK5EgaUXlmWj0ZrmDE9Vq-Tb03BBbKkiyP8bq8uR4yHfpnXzkYv2eDhh0o3xuLA0j0GZ8G5P9aGKdGykCNpqvsJXb_kTA_Rd2HlfCSje1lSNis5p8xQUGJ6bKXnFGWQrUox9HCzh3qDML/https%3A%2F%2Fwww.biostat.washington.edu%2Fresearch%2Fcenters%2Fgac>

Department of Biostatistics <https://secure-web.cisco.com/18J0owqfxmCTB7X8kQz9eLNDeYtu5yO6-5IwDbh1jKNPSsbYqF9CFTRVhsPLFH8vn1yfjBvVgHCuZsl53ewIrfJBKZ0wVLU5IioQSKa3Fuw30zy19l2yLHiUyCK-dOOkfqGXwZRu6zggxPfIgaLQMtG7GwATugxcImraJVWFyaFm5Bg4BHebQAvrwiT4elVylBNzlwGZcottc8OEhlEbhf7iqK4PB3OFTM1h-qHIyKohbTacoC2jl6uX0cAm9CjwihnxlWzkcmiwzkpVtfmC3uZ23uNz0hkq3mKTZ1P4lcrWsupOMtnM7XaD1uncMmfjx/https%3A%2F%2Fwww.biostat.washington.edu%2F>

UNIVERSITY OF WASHINGTON



UW Tower Box 359461

4333 Brooklyn Ave NE, Seattle, WA 98195

206.221.0757

sdmorris using uw.edu

she/her/hers

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://secure-web.cisco.com/1D0gBOkuN_3S0YRi6axUwg3frXGJ7ATqWrZLSTQ4knSRrKd8ponTCXekksJ0U07Fen-5Nk2hTUlHzuPCc7FHV2dYnf4wPlGapOCdaVrp83i4ZrwQaxvDRoaljsD4O9k3_5i2xcnik0ijwg_hnw09XktFTw8y0FYqJHR50R00YuwcoFIYkjiFWK5ART2YHZhCLSVQRHsKcdw_TbY58zLXP7u2ZVrA4dqfQebfvSS_wEsh--aWtCQpT9ugin7uO8x6HB1yaXwS201a4eKN0omhTlV7lmVOo9KKffKgPGvw6e_W9zO_L71PoGbpe7aa1Ou3Y/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.
	[[alternative HTML version deleted]]