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

[Vincent Carey]

I will chime in because the error is a bit obscure.  You serialized
ExpressionSet instances for testing.  In the expected_res
in your tests we have


 ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1
slot

  .. .. ..@ .Data:List of 4

  .. .. .. ..$ : int [1:3] 3 6 1

  .. .. .. ..$ : int [1:3] 2 46 0

  .. .. .. ..$ : int [1:3] 1 3 0

  .. .. .. ..$ : int [1:3] 1 0 0


which formally encodes the version of R with which the ExpressionSet was

created.  The one created in the test on the

build system will have first list element c(4,0,0)


How to get around this for the long run?  One possibility is to create your

S4 instances from serializations of more basic objects as

part of the test process.

On Tue, Apr 7, 2020 at 7:55 AM Shepherd, Lori <Lori.Shepherd using roswellpark.org>
wrote:

> 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.
>
> Christian
>
>
>
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