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

[L Rutter]

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

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