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

[Christian Holland]

Dear Vincent,

you've hit the nail on the head! Indeed the error was raised by the fact that ExpressionSet objects store the R version. I followed your suggestion and create this object now every time I run the tests.

And also thanks @Lori, part of the solution was indeed to update to R4.0

Thanks,
Christian

> On 7. Apr 2020, at 14:17, Vincent Carey <stvjc using channing.harvard.edu> wrote:
> 
> 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 <mailto: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 <http://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/ <http://mac.r-project.org/>   and one here for windows:  https://cran.rstudio.com/bin/windows/base/rpatched.html <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 <mailto:bioc-devel-bounces using r-project.org>> on behalf of Christian Holland <cholland2408 using gmail.com <mailto:cholland2408 using gmail.com>>
> Sent: Tuesday, April 7, 2020 7:22 AM
> To: bioc-devel using r-project.org <mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org <mailto: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> <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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