Hi Pooja, In the code below, you install msa if it's missing. This is considered bad practice, as it installs a new package without explicitly asking for the user's permission. I'm surprised it wasn't flagged by the CRAN checks.
Make sure msa is in the "Imports" field of your DESCRIPTION file, and you should be fine. As Sebastian mentioned, it's possible the error you saw is transient, as Bioconductor packages are typically available for testing on CRAN machines. Best, Max Turgeon<https://www.name-coach.com/maxime-turgeon> Assistant Professor Department of Statistics Department of Computer Science University of Manitoba maxturgeon.ca<http://maxturgeon.ca> ________________________________ From: R-package-devel <r-package-devel-boun...@r-project.org> on behalf of Pooja Gangras via R-package-devel <r-package-devel@r-project.org> Sent: Monday, August 16, 2021 10:37 AM To: r-package-devel@r-project.org <r-package-devel@r-project.org> Subject: [R-pkg-devel] FW: [EXTERNAL] [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000 ******************************************************** Caution: This message was sent from outside the University of Manitoba. ******************************************************** Hi all, PFA the pre-check results for my package surfaltr from CRAN. I am having troubles with a package dependency on Debian that I am not able to fix. 2 functions in my package require a Bioconductor package msa (https://bioconductor.org/packages/release/bioc/html/msa.html). To deal with this error, I tried the following solution of adding a call to BiocManager and also including a code for msa installation but it did not help: #' @importFrom BiocManager install #' @import msa . . . Foo() { if (!requireNamespace("msa", quietly = TRUE)){ BiocManager::install("msa")} } How do I solve the problem so that I don't generate this error with Debian? Thank you, Pooja Pooja Gangras, Ph.D. Postdoctoral Research Scientist - RNA Therapeutics Eli Lilly and Company Lilly Corporate Center, Indianapolis IN 46285 U.S.A. Office phone number: (317) 651-0589 Cellphone number: (614) 906-0940 gangras_po...@lilly.com | www.lilly.com<http://www.lilly.com> CONFIDENTIALITY NOTICE: This email message (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. -----Original Message----- From: lig...@statistik.tu-dortmund.de <lig...@statistik.tu-dortmund.de> Sent: Monday, August 16, 2021 10:32 AM To: Pooja Gangras <gangras_po...@lilly.com> Cc: cran-submissi...@r-project.org Subject: [EXTERNAL] [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000 EXTERNAL EMAIL: Use caution before replying, clicking links, and opening attachments. Dear maintainer, package surfaltr_1.0.0.9000.tar.gz does not pass the incoming checks automatically, please see the following pre-tests: Windows: <https://win-builder.r-project.org/incoming_pretest/surfaltr_1.0.0.9000_20210816_162209/Windows/00check.log> Status: 1 NOTE Debian: <https://win-builder.r-project.org/incoming_pretest/surfaltr_1.0.0.9000_20210816_162209/Debian/00check.log> Status: 1 ERROR, 1 NOTE Please fix all problems and resubmit a fixed version via the webform. If you are not sure how to fix the problems shown, please ask for help on the R-package-devel mailing list: <https://stat.ethz.ch/mailman/listinfo/r-package-devel> If you are fairly certain the rejection is a false positive, please reply-all to this message and explain. More details are given in the directory: <https://win-builder.r-project.org/incoming_pretest/surfaltr_1.0.0.9000_20210816_162209/> The files will be removed after roughly 7 days. No strong reverse dependencies to be checked. Best regards, CRAN teams' auto-check service [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
