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 <st...@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.sheph...@roswellpark.org > <mailto:lori.sheph...@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-boun...@r-project.org > <mailto:bioc-devel-boun...@r-project.org>> on behalf of Christian Holland > <cholland2...@gmail.com <mailto:cholland2...@gmail.com>> > Sent: Tuesday, April 7, 2020 7:22 AM > To: bioc-devel@r-project.org <mailto:bioc-devel@r-project.org> > <bioc-devel@r-project.org <mailto:bioc-devel@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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <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. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > The information in this e-mail is intended only for th...{{dropped:16}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
