Can't run countRNAData - Githubissues

gagneurlab / FRASER

FRASER - Find RAre Splicing Events in RNA-seq

MIT License

36 stars 20 forks source link

Can't run countRNAData #67

Closed mmartinezj closed 3 months ago

mmartinezj commented 5 months ago

Hello, First of all, thank you for devoloping this tool. Secondly, after trying to run the countRNAData function, the following error appears: "Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.". After looking up the reason behind this, seems that the version 1.2 of the matrixStats package causes this error. If I could have some help on how should I proceed in order to be able to use countRNAData function with this happening, I would really appreciate it. (I have tried to downgrade the matrixStats version, but haven't been lucky with it either). Thank you in advance.

Best regards,

Miriam

laetitiarialland commented 4 months ago

Hello, I just install FRASER on R 4.1.2 and I am facing the same issue. Did you find any solution ? Thank you so much for your help !! Kind regards

Laëtitia

AtaJadidAhari commented 3 months ago

Hi, there is indeed a compatibility problem with MatrixGenerics and base R version. Using R version 4.3.0 solves this issue for me. Can you try to redo your analysis with this version? Running functions such as rowMaxs with useNames = TRUE is another way to solve the problem, but there are several usages of such functions and it's a bit tedious to change all of them.

Best,

Ata

laetitiarialland commented 3 months ago

Hello ! I try with R4.3.3, and it works, !! Thanks you so much @AtaJadidAhari

Kind regards,

Laëtitia