I solved the mystery, but not the problem. The problem is that there's
an unclosed quote somewhere in those 5 additional records I'm trying to
access. So read.csv is reading million-character fields. It's slow at
that. That mystery solved.
However, the the problem persists: how to fix what is obvious to the
naked eye - a quote not adjacent to a comma - but that read.csv can't
handle. readLines followed by read.csv(text= ) works great because, in
that case, read.csv knows where the record terminates. Meaning, read.csv
throws an exception that I can catch and handle with a quick and clean
regex expression.
Thanks, I'll take a look at vroom.
-dave
On 4/8/24 09:18, Stevie Pederson wrote:
> Hi Dave,
>
> That's rather frustrating. I've found vroom (from the package vroom)
> to be helpful with large files like this.
>
> Does the following give you any better luck?
>
> vroom(file_name, delim = ",", skip = 2459465, n_max = 5)
>
> Of course, when you know you've got errors & the files are big like
> that it can take a bit of work resolving things. The command line
> tools awk & sed might even be a good plan for finding lines that have
> errors & figuring out a fix, but I certainly don't envy you.
>
> All the best
>
> Stevie
>
> On Tue, 9 Apr 2024 at 00:36, Dave Dixon <ddi...@swcp.com> wrote:
>
> Greetings,
>
> I have a csv file of 76 fields and about 4 million records. I know
> that
> some of the records have errors - unmatched quotes, specifically.
> Reading the file with readLines and parsing the lines with
> read.csv(text
> = ...) is really slow. I know that the first 2459465 records are
> good.
> So I try this:
>
> > startTime <- Sys.time()
> > first_records <- read.csv(file_name, nrows = 2459465)
> > endTime <- Sys.time()
> > cat("elapsed time = ", endTime - startTime, "\n")
>
> elapsed time = 24.12598
>
> > startTime <- Sys.time()
> > second_records <- read.csv(file_name, skip = 2459465, nrows = 5)
> > endTime <- Sys.time()
> > cat("elapsed time = ", endTime - startTime, "\n")
>
> This appears to never finish. I have been waiting over 20 minutes.
>
> So why would (skip = 2459465, nrows = 5) take orders of magnitude
> longer
> than (nrows = 2459465) ?
>
> Thanks!
>
> -dave
>
> PS: readLines(n=2459470) takes 10.42731 seconds.
>
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