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From: Bioc-devel <bioc-devel-bounces at r-project.org <mailto:bioc-devel-bounces at r-project.org>> on behalf of Christian Holland <cholland2408 at gmail.com <mailto:cholland2408 at gmail.com>>
Sent: Tuesday, April 7, 2020 7:22 AM
To: bioc-devel at r-project.org <mailto:bioc-devel at r-project.org> <bioc-devel at r-project.org <mailto: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> <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> <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
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