[Bioc-devel] Unit tests pass locally but fail on Bioconductor machines
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 at r-project.org> on behalf of Christian Holland <cholland2408 at gmail.com>
Sent: Tuesday, April 7, 2020 7:22 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Unit tests pass locally but fail on Bioconductor machines
Sent: Tuesday, April 7, 2020 7:22 AM
To: bioc-devel at r-project.org <bioc-devel at 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. Christian [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-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.