Deprecated data.table functions

[rdmorin]

I have tried both bioconductor and github installations of GenVisR and have been getting the same errors. Is there some way around this?

cnSpec(mcl_seg, genome="hg38")
genome specified is preloaded, retrieving data...
Warning messages:
1: In data.table::dcast(x, chromosome + start + end ~ sample, value.var = "segmean") :
The dcast generic in data.table has been passed a data.frame and will attempt to redirect to the reshape2::dcast; please note that reshape2 is deprecated, and this redirection is now deprecated as well. Please do this redirection yourself like reshape2::dcast(x). In the next version, this warning will become an error.
2: In data.table::melt(CN_data, id.vars = c("chromosome", "start", :
The melt generic in data.table has been passed a data.frame and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(CN_data). In the next version, this warning will become an error.

[zlskidmore]

those look like warnings instead of errors, but still need to be fixed. I'm currently on holiday and will have to take a closer look when I get back around the end of Jan.

you should be able to convert your data.table to a data frame though

cnSpec(as.data.frame(mcl_seg), genome="hg38")

[2waybene]

Hi, zlskidmore

I posted same error recently without knowing someone has already posted. It is still there, any update on fixing it?

Thanks.

[2waybene]

with the sample code:

waterfall(brcaMAF, plotGenes=c("PIK3CA", "TP53", "USH2A", "MLL3", "BRCA1"))
Checking if input is properly formatted...
Calculating frequency of mutations...
Removing genes not in: PIK3CA, TP53, USH2A, MLL3, BRCA1
setting mutation hierarchy...
NULL
Warning messages:
1: In data.table::melt(mutation_counts) :
The melt generic in data.table has been passed a table and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(mutation_counts). In the next version, this warning will become an error.
2: In data.table::dcast(x, sample ~ gene, fun.aggregate = length, value.var = "trv_type") :
The dcast generic in data.table has been passed a data.frame and will attempt to redirect to the reshape2::dcast; please note that reshape2 is deprecated, and this redirection is now deprecated as well. Please do this redirection yourself like reshape2::dcast(x). In the next version, this warning will become an error.

[zlskidmore]

@2waybene let's move the conversation here from issue #351, do you see a plot? these should be benign warnings still but if they aren't fixing it becomes more critical

[zlskidmore]

re your comment from #351, if they do become errors this will become a top priority and will be fixed immediately. As it stands now, as long as they remain benign, I am thinking i'll tackle this sometime this month