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

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 ..

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

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

Re: [Bioc-devel] git.bioconductor identifies me as a different person

Hi, Please add another SSH key in BiocCredentials and it'll give you access. Feel free to remove any key in that list which you think is not needed. There cannot be keys which are concatenated, it will not work that way. Let me know if there is problem. Best, Nitesh > On Apr 7, 2020, at

Re: [Bioc-devel] HDF5Array failure on windows

Thanks for the two pointers. Herve: we are using a number of unexpected functions from HDF5Array: ‘HDF5Array:::.create_dir’, ‘HDF5Array:::.replace_dir’, ‘HDF5Array:::.shorten_assay2h5_links’ That might be relevant in light of that specific test error. On Mon, Apr 6, 2020 at 1:13 PM Hervé

Re: [Bioc-devel] git.bioconductor identifies me as a different person

Sorry the term concatenate was poorly chosen. I meant to say that my BiocCredential ssh key list consist of all the keys both from my public github and from koen's. Adding a new key did not fix the issue though and lead to the same error. Hector Roux de Bezieux UC Berkeley - PhD Student in

Re: [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

[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 ) run smoothly on local machines (tested for Linux, Windows and macOS). However, on the Bioconductor machines (both Linux and Window) a particular test

Re: [Bioc-devel] git.bioconductor identifies me as a different person

Do you have koenvandenberge's public key in your github repository? On 4/7/20, 3:51 AM, "Bioc-devel on behalf of Hector Roux de Bezieux" wrote: Hi, My github usernameis HectorRDB but this is what happens if I try to connect to git.bioconductor ssh

[Bioc-devel] git.bioconductor identifies me as a different person

Hi, My github usernameis HectorRDB but this is what happens if I try to connect to git.bioconductor ssh g...@git.bioconductor.org PTY allocation request failed on channel 0 hello koenvandenberge, this is ... However, I am not koenvandenberge. I am working with him on the tradeSeq package but the

Re: [Bioc-devel] git.bioconductor identifies me as a different person

Hi, There is no overlap between https://github.com/HectorRDB.keys and https://github.com/koenvandenberge.keys. However, the keys listed in my BiocCredential page (https://git.bioconductor.org/BiocCredentials/profile/) are a concatenation of koen's public github keys and mine. However, none of the