Duration: 2m 49s 0 errors ✓ | 0 warnings ✓ | 0 notes ✓
0 errors ✓ | 0 warnings ✓ | 2 notes x There were 0 ERRORs and 0 WARNINGS
Comments on the notes:
Note 1:
checking installed package size ... NOTE installed size is 80.2Mb sub-directories of 1Mb or more: data 80.0Mb
There was one note about the size of the files in the /data. I know there are (at times) exceptions that are made. I am hopeful that one can be made in this case as the data is single-cell gene expression data along with labels/ bulk data in order for the user to see a best real-world example.
Note 2:
checking R code for possible problems ... NOTE DEAnalysisMAST: no visible binding for global variable ‘Number.of.Cells’ Undefined global functions or variables: Number.of.Cells
There was one note about there not being visible binding for global variables 'Number.of.cells'. This come from this line of code in the DEAnalysisMAST.R file.
''' colnames(data_for_MIST) = c("Gene", "Subject.ID", "Et", "Population", "Number.of.Cells") vbeta = data_for_MIST vbeta.fa <-FromFlatDF(vbeta, idvars=c("Subject.ID"), primerid='Gene', measurement='Et', ncells='Number.of.Cells', geneid="Gene", cellvars=c('Number.of.Cells', 'Population'), phenovars=c('Population'), id='vbeta all') vbeta.1 <- subset(vbeta.fa,Number.of.Cells==1)
'''
Number.of.cells is not a global variable (rather it comes from the FromFlatDF -
https://rdrr.io/bioc/MAST/man/FromFlatDF.html within the MAST function)
therefore I believe this note to be spurious.
The notice ' * checking installed package size ... NOTE ', CRAN has a limit of 100 MB for a *.tar.gz file (Package is under size requirements)