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

[L Rutter]

Thanks for the confirmation. I will post if I do find ways to resolve
this issue without manually editing the .Rd file.
On Mon, Nov 19, 2018 at 12:31 AM Michael Lawrence
<lawrence.michael using gene.com> wrote:
>
> 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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