[Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Tue Apr 7 13:55:23 CEST 2020

There are many changes to base R hence the switch from 3.6 to 4.0.   I would highly suggest using R 4.0.  There is a R-alpha version now available for all platforms with the R - 4.0 release schedule for later this month.  Please use the R-alpha version .

on CRAN.r-project.org you should see a section
Sources of R alpha and beta releases (daily snapshots, created only in time periods before a planned release) with links to R-alpha for linux.  There is a link here to R-alpha for mac  http://mac.r-project.org/   and one here for windows:  https://cran.rstudio.com/bin/windows/base/rpatched.html

This should allow you to download the most stable R-4.0 alpha before the release at the end of the month.
Hope this helps.

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 using r-project.org> on behalf of Christian Holland <cholland2408 using gmail.com>
Sent: Tuesday, April 7, 2020 7:22 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

Hi there,

the unit tests (implemented with testthat) of my package (https://github.com/saezlab/dorothea <https://github.com/saezlab/dorothea>) run smoothly on local machines (tested for Linux, Windows and macOS). However, on the Bioconductor machines (both Linux and Window) a particular test fails. The feature that distinguish this particular test from all other (that passed without any problems) is the use of the ExpressionSet class from the Biobase package. Locally I am using the Biobase version 2.46.0.

You can see the build output from Bioconductor here: http://bioconductor.org/spb_reports/dorothea_buildreport_20200407063358.html <http://bioconductor.org/spb_reports/dorothea_buildreport_20200407063358.html>

Is it possible that this error is somehow related to the used R Version? Locally I am still using 3.6.2 but if I understand correctly the package is build and checked on Bioconductor machines with R version 4.0. So far I refrained from installing the development version of R4.0 as it crashed RStudio for a colleague of mine.

Many thanks for your support.


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