#'100を超える列がある場合は、ブロックの一部（#'（）で始まる行）を設定するときにコード行を破棄（追加）したいと思います。#\x27

私のソリューションは複数のブロックで動作しません。

サンプルファイル：

#' chunk line
#' big chunk line to split big chunk line to split big chunk line to split big chunk line to split big chunk line to split
#' ruler90123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
#'
not chunk line do nothing

big do nothing line big do nothing line big do nothing line big do nothing line big do nothing line big do nothing line big do nothing line

#' chunk line
#' big chunk line to split big chunk line to split big chunk line to split big chunk line to split big chunk line to split
#' ruler90123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
#'
not chunk line do nothing

big do nothing line big do nothing line big do nothing line big do nothing line big do nothing line big do nothing line big do nothing line

私の試み：（ブロックが1つだけ存在する場合は機能します）

perl -0777 -pe '
  s{#\x27.*#\x27}{                          q{ gets lines from #\x27 to #\x27 (chunk) };
    ($r = $&) =~ s/\n!\n#\x27//g;           q{ removes breaks except followed by #\x27 }; 
    $r =~ s/\G.{0,100}(\s|.$)\K/\n#\x27 /g; q{ before column 100 adds break + #\x27 };
    $r =~ s/#\x27 #\x27/#\x27/g;            q{ removes duplicated #\x27 };
    $r =~ s/\n\n/\n/g;                      q{ removes duplicated breaks };
    $r
  }gse' < chunks.txt

予想出力：（2回）

#' chunk line
#' big chunk line to split big chunk line to split big chunk line to split big chunk line to split
#' big chunk line to split
#' ruler90123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
#'
not chunk line do nothing

big do nothing line big do nothing line big do nothing line big do nothing line big do nothing line big do nothing line big do nothing line

Rのソリューション

psum <- function(...,na.rm=FALSE) {
  rowSums(do.call(cbind,list(...)),na.rm=na.rm)
}    

gblines<-readLines("chunks.txt")

newgblines<-character()
i<-1
j<-1
repeat {
  newgblines[j] <- gblines[i]
    if (grepl("^#\'",newgblines[j] ) & nchar( newgblines[j] ) > 100 ) { # select lines with more than 100 and beginning in #'
      repeat{
        greps<-gregexpr(pattern ="\\s",newgblines[j])[[1]] # get position of spaces
        lenG<-length(greps)
        sums<-psum(-greps , rep(100,lenG ) )               # calculate which space is closest to col. 100
        index <- which(sums>0)
        minSums<- min(sums[index])
        index2<-which(sums==minSums)                       # index of space in greps
        cutpoint<-greps[index2]
        nchar2<-nchar(newgblines[j])                       # number of chars. in line
        strFirst <-substr(newgblines[j],1,cutpoint)        # cut before col. 100
        strSecond<-substr(newgblines[j],cutpoint+1,nchar2) # segmente after col. 100
        newgblines[j]<-strFirst
        j<-j+1
        newgblines[j]<-paste0("#\' ",strSecond)
        if (nchar(strSecond)<=100 ){
          break
        }
      } # 
    } #  if
  i <- i+1
  j <- j+1
  if (i>length(gblines) ){
    break
  }
}
newgblines