[R-pkg-devel] [EXTERNAL] [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000

[Max Turgeon]

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-bounces using r-project.org> on behalf of Pooja Gangras via R-package-devel <r-package-devel using r-project.org>
Sent: Monday, August 16, 2021 10:37 AM
To: r-package-devel using r-project.org <r-package-devel using r-project.org>
Subject: [R-pkg-devel] FW: [EXTERNAL] [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000

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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_pooja using lilly.com | www.lilly.com<http://www.lilly.com>


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-----Original Message-----
From: ligges using statistik.tu-dortmund.de <ligges using statistik.tu-dortmund.de>
Sent: Monday, August 16, 2021 10:32 AM
To: Pooja Gangras <gangras_pooja using lilly.com>
Cc: CRAN-submissions using R-project.org
Subject: [EXTERNAL] [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000

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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

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