Fixed "drop" argument errors preventing R check and build #61
Conversation
* change from homemade gha scripts to biocthis gha workflow * install tinytex v2 and packages * include bioc devel test
R/AllGenerics.R
Outdated
| #' fds[1:10,2:3] | ||
| #' fds[,samples(fds) %in% c("sample1", "sample2")] | ||
| #' fds[1:10,by="ss"] | ||
| #' fds[1:10,2:3,,drop=FALSE] |
There was a problem hiding this comment.
I see this as a problem. As we do not want to ask the user to always set the drop argument. So we have to make sure it works without that for the end user. Within the package I'm fine with this. But outside on the user facing side we should not rely on this. to work properly.
R/AllGenerics.R
Outdated
| @@ -672,7 +673,7 @@ FRASER.results <- function(object, sampleIDs, fdrCutoff, zscoreCutoff, | |||
| ans <- lapply(seq_along(sampleChunks), function(idx){ | |||
| message(date(), ": Process chunk: ", idx, " for: ", type) | |||
| sc <- sampleChunks[[idx]] | |||
| tmp_x <- object[,sc] | |||
| tmp_x <- object[,sc,,drop=FALSE] | |||
There was a problem hiding this comment.
Why do you have the extra ,? They are not positional arguments so it should work without the extra missing argument or? This looks to me as wrong coding or some potential problematic code in the future.
R/AllGenerics.R
Outdated
| @@ -864,7 +865,7 @@ mapSeqlevels <- function(fds, style="UCSC", ...){ | |||
| nonSplicedReads(fds) <- keepStandardChromosomes(nonSplicedReads(fds)) | |||
| validObject(fds) | |||
| } | |||
| fds <- fds[as.vector(seqnames(fds)) %in% names(mappings)] | |||
| fds <- fds[as.vector(seqnames(fds)) %in% names(mappings),,,drop=FALSE] | |||
There was a problem hiding this comment.
Same as above. Works for all the ,,, parts. can you please check this?
R/countRNAseqData.R
Outdated
| @@ -459,8 +459,8 @@ getSplitCountCacheFile <- function(sampleID, settings){ | |||
| #' @export | |||
| countSplitReads <- function(sampleID, fds, NcpuPerSample=1, genome=NULL, | |||
| recount=FALSE, keepNonStandardChromosomes=TRUE, | |||
| bamfile=bamFile(fds[,sampleID]), | |||
| pairedend=pairedEnd(fds[,sampleID]), | |||
| bamfile=bamFile(fds[,sampleID,,drop=FALSE]), | |||
There was a problem hiding this comment.
So this is kind of user facing code here. So not sure why we need it. I dont want to polute the code with things we do not need.
One Idea that could happen, is that fds is not a fraserdataset object but rather a summarizedexperiment object. Then the default with subsetting is drop=TRUE which could the underlying problem
| #' junctions or splice sites | ||
| #' @param drop Currently not used |
There was a problem hiding this comment.
did you run devtools::document() i think this did not populate into the documentation.
No description provided.