R devel - Jul 2007 - (PR#9796) write.dcf/read.dcf cycle converts missing entry

BIll,

Thanks.

I am seeing some problems here, for example when all the fields are 
missing, or all the fields in a row are missing.  I've fixes for those, 
and will commit to R-devel shortly.

On Tue, 17 Jul 2007, bill at insightful.com wrote:
> Full_Name: Bill Dunlap
> Version: 2.5.0
> OS: Red Hat Enterprise Linux WS release 3 (Taroon Update 6)
> Submission from: (NULL) (24.17.60.30)
>
>
> If you read a dcf file with read.dcf(file,fields=c("Field",...))
> and the file does not contain the desired field "Field",
> read.dcf puts a character NA for that entry in its output
> matrix.  If you then call write.dcf, passing it the output
> of read.dcf(), it will write the entry "Field: NA".  A subsequent
> read.dcf() on write.dcf's output file will then have a "NA",
> not a character NA, in the entry for "Field".  I think that
> write.dcf() should not write lines in the output file where
> the input matrix contains a character NA.
>
> Here is a test function to demonstrate the problem.  It returns
> TRUE when a write.dcf/read.dcf cycle does not change the data.
>
>  test.write.dcf <- function () {
>     origFile <- tempfile()
>     copyFile <- tempfile()
>     on.exit(unlink(c(origFile, copyFile)))
>     writeLines(c("Package: testA", "Version: 0.1-1",
"Depends:", "",
>                  "Package: testB", "Version: 2.1"  ,
"Suggests: testA", "",
>                  "Package: testC", "Version: 1.3.1",
""),
>                origFile)
>     orig <- read.dcf(origFile,
>                     
fields=c("Package","Version","Depends","Suggests"))
>     write.dcf(orig, copyFile, width = 72)
>     copy <- read.dcf(copyFile,
>                     
fields=c("Package","Version","Depends","Suggests"))
>     value <- all.equal(orig, copy)
>     if (!identical(value, TRUE)) {
>        attr(value, "orig") <- orig
>        attr(value, "copy") <- copy
>     }
>     value
>  }
> Currently we get
>  > test.write.dcf()
>  [1] "'is.NA' value mismatch: 0 in current 4 in target"
>  attr(,"orig")
>       Package Version Depends Suggests
>  [1,] "testA" "0.1-1" ""      NA
>  [2,] "testB" "2.1"   NA      "testA"
>  [3,] "testC" "1.3.1" NA      NA
>  attr(,"copy")
>       Package Version Depends Suggests
>  [1,] "testA" "0.1-1" ""      "NA"
>  [2,] "testB" "2.1"   "NA"   
"testA"
>  [3,] "testC" "1.3.1" "NA"    "NA"
> With the attached write.dcf() it returns TRUE.
>
> The diff would be
> 19,22c19,24
> <     eor <- character(nr * nc)
> <     eor[seq.int(1, nr - 1) * nc] <- "\n"
> <     writeLines(paste(formatDL(rep.int(colnames(x), nr), c(t(x)),
> <         style = "list", width = width, indent = indent),
eor,
> ---
>>     tx <- t(x)
>>     not.na <- c(!is.na(tx))
>>     eor <- character(sum(not.na))
>>     eor[ c(diff(c(col(tx))[not.na]),0)==1 ] <- "\n"
>>     writeLines(paste(formatDL(rep.int(colnames(x), nr), c(tx),
>>         style = "list", width = width, indent =
indent)[not.na], eor,
>
> and the entire function would be
>
> `write.dcf` <-
> function (x, file = "", append = FALSE, indent = 0.1 *
getOption("width"),
>    width = 0.9 * getOption("width"))
> {
>    if (!is.data.frame(x))
>        x <- data.frame(x)
>    x <- as.matrix(x)
>    mode(x) <- "character"
>    if (file == "")
>        file <- stdout()
>    else if (is.character(file)) {
>        file <- file(file, ifelse(append, "a", "w"))
>        on.exit(close(file))
>    }
>    if (!inherits(file, "connection"))
>        stop("'file' must be a character string or
connection")
>    nr <- nrow(x)
>    nc <- ncol(x)
>    tx <- t(x)
>    not.na <- c(!is.na(tx))
>    eor <- character(sum(not.na))
>    eor[ c(diff(c(col(tx))[not.na]),0)==1 ] <- "\n"
>    writeLines(paste(formatDL(rep.int(colnames(x), nr), c(tx),
>        style = "list", width = width, indent = indent)[not.na],
eor,
>        sep = ""), file)
> }
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

On Wed, 18 Jul 2007 ripley at stats.ox.ac.uk wrote:
> I am seeing some problems here, for example when all the fields are
> missing, or all the fields in a row are missing.  I've fixes for those,
> and will commit to R-devel shortly.
write.dcf() is also used by print.packageDesription() so
this change affects how missing fields are printed there.
In 2.5 we got
   > packageDescription("base",
fields=c("Version","NoSuchField"))
   Version: 2.5.0
   NoSuchField: NA

   -- File: /dept/devel/sw/R/R.linux.2.5.0/lib/R/library/base/DESCRIPTION
   -- Fields read: Version, NoSuchField
and now it doesn't print anything about the non-existant field
   > packageDescription("base",
fields=c("Version","NoSuchField"))
   Version: 2.6.0
   -- File: /homes/bill/R-svn/r-devel/R/library/base/DESCRIPTION
   -- Fields read: Version, NoSuchField
If this isn't acceptable then write.dcf will need a new argument
to control the printing of missing lines.

The missing trailing blank line is an inadvertant change (although
it makes appending fields to a single record dcf file possible).
> > If you read a dcf file with
read.dcf(file,fields=c("Field",...))
> > and the file does not contain the desired field "Field",
> > read.dcf puts a character NA for that entry in its output
> > matrix.  If you then call write.dcf, passing it the output
> > of read.dcf(), it will write the entry "Field: NA".  A
subsequent
> > read.dcf() on write.dcf's output file will then have a
"NA",
> > not a character NA, in the entry for "Field".  I think that
> > write.dcf() should not write lines in the output file where
> > the input matrix contains a character NA.
> > ...
> > The diff would be
> > 19,22c19,24
> > <     eor <- character(nr * nc)
> > <     eor[seq.int(1, nr - 1) * nc] <- "\n"
> > <     writeLines(paste(formatDL(rep.int(colnames(x), nr), c(t(x)),
> > <         style = "list", width = width, indent =
indent), eor,
> > ---
> >>     tx <- t(x)
> >>     not.na <- c(!is.na(tx))
> >>     eor <- character(sum(not.na))
> >>     eor[ c(diff(c(col(tx))[not.na]),0)==1 ] <- "\n"
> >>     writeLines(paste(formatDL(rep.int(colnames(x), nr), c(tx),
> >>         style = "list", width = width, indent =
indent)[not.na], eor,
   [ The ==1 should be >=1 ]