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replace line 143 with: sdata<-icoads.utils::read_trackmonth(paste0(config$output_dir,"MFILES_TMP"),syr=iyear)

Next change alters nrow(nonship)==0 {next} to >0 and if, else
replace lines 332-346 with:

  # manual exclusions  
  man.ex<-c("ISW1","3FNX","C7M","C7C")  
  dck.excl<-c(667)  
  nonship<-subset(nonship,!(id %in% man.ex))  
  nonship<-subset(nonship,!(grepl("^[0-9]{4,5}$",nonship$id) & dck == 927) )  
  nonship<-subset(nonship,!(dck %in% dck.excl))  
  if ( length(uid.want) > 0 ) {  
    toadd<-subset(sdata,uid %in% uid.want)  
    cat('adding',nrow(toadd),'reports with generic ID',"\n")  
    if ( nrow(toadd) > 0 ) {  
      print(table(toadd$id,toadd$dck,useNA='ifany'))  
    }  
    nonship<-rbind(nonship,toadd)  
  }  

After line 383 add:

  # and write out ship-only subset  
  if(!is.null(nonship)) sdata <- subset(sdata,!(uid %in% nonship$uid))  
  sdata$nonship.flag<-NULL  
  cat("final ship subset",nrow(sdata),"reports","\n")  
  if (!dir.exists(paste0(config$output_dir,"MFILES_SHIP"))) dir.create(paste0(config$output_dir,"MFILES_SHIP"))  
  YRMO <- split(sdata, data.frame(sdata$yr, sdata$mo), drop=TRUE)  
  names_mo <- gsub("\\.","_", names(YRMO))  
  names_mo <- gsub("_R",".R", names_mo)  
  filenames <- paste(paste0(config$output_dir,"MFILES_SHIP/"), names_mo, ".Rda",sep="")  
  jj<-mapply(saveRDS, YRMO, file = filenames)  

  # and remove files from MFILES_TMP  
  flist<-list.files(paste0(config$output_dir,"MFILES_TMP"),pattern=as.character(iyear),full.names=T)  
  if(length(flist)>0) file.remove(flist)