Gratia function deprecation

[teerjk]

I'm trying to test the installation using the "cov_example" file, and am getting the following error:

TCRA.test<-runTcellExTRECT(cov_example, TCRA_exons_hg19, tcra_seg_hg19, 'hg19')
Use of the newdata argument is deprecated.
Instead, use the data argument data.

Error: 'data', if supplied, must be a numeric vector or data frame.

It appears this is related to gratia. I am currently running R 4.1.2 on Ubuntu 22.04.2 LTS, with gratia 0.8.1.
Thanks!

[rbentham]

I have just pushed a new commit that fixes this issue. If you re-install the package everything should be now working.

Thank you for reporting this!

[teerjk]

Great, thanks for the quick fix! I can confirm the example and my own data are successfully completing.
In case it helps, I'm running this in a Docker container (then converted to Singularity) under Ubuntu 22.04. These are the dependencies I installed, which then allowed the R dependencies and TcellExTRECT to install successfully:
Packages: tzdata wget git make unzip gcc g++ r-base-dev samtools vim gzip ca-certificates locales libc6-dev
R install commands:
Rscript -e 'install.packages(c("dplyr", "readr", "zoo", "seqinr", "rlang", "ggplot2", "magrittr", "gratia"))'
Rscript -e 'install.packages("/usr/src/TcellExTRECT-main/", repos=NULL, type ="source")'

Took a while to compile, but runs successfully for me. Thanks again!