[Bioc-devel] Manually editing man/.Rd files to pass BiocCheck

[Michael Lawrence]

On Sun, Nov 18, 2018 at 9:16 PM L Rutter <lindsayannerutter using gmail.com> wrote:
>
> Hello all:
>
> I am preparing to submit a package to Bioconductor and have one note
> from R CMD BiocCheck that I have been unable to resolve. The note I
> receive is:
>
> NOTE: Consider multiples of 4 spaces for line indents, 40 lines(1%) are not.
>     First 6 lines:
>       man/plotClusters.Rd:8   threshVal = 0.05, outDir = getwd(), colList = r...
>       man/plotClusters.Rd:9   aggMethod = "ward.D", yAxisLabel = "Count", xAx...
>       man/plotClusters.Rd:10   lineSize = 0.1, lineAlpha = 0.5, clusterAllDat...
>       man/plotClusters.Rd:11   verbose = FALSE, saveFile = TRUE, vxAxis = FALSE,
>       man/plotClusters.Rd:12   geneList = NULL)
>       man/plotLitre.Rd:8   pointSize = 2, pointColor = "orange", xbins = 10,
>
> Lines 6-13 of man/plotClusters.Rd appear as follows:
>
> \usage{
> plotClusters(data, dataMetrics = NULL, nC = 4, threshVar = "FDR",
>   threshVal = 0.05, outDir = getwd(), colList = rainbow(nC),
>   aggMethod = "ward.D", yAxisLabel = "Count", xAxisLabel = "Sample",
>   lineSize = 0.1, lineAlpha = 0.5, clusterAllData = TRUE,
>   verbose = FALSE, saveFile = TRUE, vxAxis = FALSE,
>   geneList = NULL)
> }
>
> In case the formatting of my post causes misconceptions, I will state
> that Lines 8-12 above are indented two spaces (instead of the four
> spaces they evidently should be, which the note catches). At the top
> of man/plotClusters.Rd, I have the statement:
>
> % Generated by roxygen2: do not edit by hand
> % Please edit documentation in R/plotClusters.R
>
> So, I tried to edit what I believe are the corresponding lines in
> R/plotClusters.R, which appear as follows:
>
> plotClusters <- function(data, dataMetrics = NULL, nC = 4, threshVar="FDR",
>     threshVal=0.05, outDir=getwd(), colList = rainbow(nC),
>     aggMethod = "ward.D", yAxisLabel = "Count", xAxisLabel = "Sample",
>     lineSize = 0.1, lineAlpha = 0.5, clusterAllData = TRUE, verbose=FALSE,
>     saveFile = TRUE, vxAxis = FALSE, geneList = NULL){
>
> In case the formatting of my post causes misconceptions, I will state
> that the last four lines above are indented FOUR spaces. I tried
> deleting the man folder and rerunning devtools::document() on my
> package to recreate the man folder, but this note persists and the
> FOUR spaces in the .R file continue to be reduced to TWO spaces in the
> .Rd file.
>
> I did manually edit the man/plotClusters.Rd file and added two more
> spaces to the lines in question. After that, the note in BiocCheck was
> resolved. My question is: Is it acceptable for me to manually edit the
> man/.Rd file by manually adding two more spaces?

Of course it's acceptable. Some developers write all of their Rd manually.

> If not, is there a
> way to solve this note?
>

There's probably a way to adjust how Roxygen formats its usage.

> The R/plotClusters.R file causing the issues is accessible at:
> https://raw.githubusercontent.com/lrutter/bigPint/master/R/plotClusters.R.
>
> Thank you for any input!...
> Lindsay
>
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