Displaying 3 results from an estimated 3 matches for "1k_annotation".
2018 May 10
2
readLines() behaves differently for gzfile connection
When I read a .gz file with readLines() in 3.4.3, it returns text (and a
warning). In 3.5.0, it gives a warning, but no text. Is this expected
behavior or a bug?
3.4.3:
> source_file = "1k_annotation.gz"
> readfile_con <- gzfile(source_file, "r")
> readLines(readfile_con, n = 5)
[1] "#chr\tpos\tref\talt\t
<truncated output here>
Warning message:
In readLines(readfile_con, n = 5) :
seek on a gzfile connection returned an internal error
> close(readfile_...
2018 May 10
1
readLines() behaves differently for gzfile connection
You bet - it's available on github at
https://github.com/UW-GAC/wgsaparsr/blob/master/tests/testthat/1k_annotation.gz
-Ben
On Thu, May 10, 2018 at 4:17 PM, Michael Lawrence <lawrence.michael at gene.com
> wrote:
> Would it be possible to get that file or a representative subset of it
> somewhere so that I can reproduce this?
>
> Thanks,
> Michael
>
> On Thu, May 10, 2018 at 3:31 PM...
2018 May 10
0
readLines() behaves differently for gzfile connection
...u, May 10, 2018 at 3:31 PM, Ben Heavner <bheavner at gmail.com> wrote:
> When I read a .gz file with readLines() in 3.4.3, it returns text (and a
> warning). In 3.5.0, it gives a warning, but no text. Is this expected
> behavior or a bug?
>
> 3.4.3:
>> source_file = "1k_annotation.gz"
>> readfile_con <- gzfile(source_file, "r")
>> readLines(readfile_con, n = 5)
> [1] "#chr\tpos\tref\talt\t
>
> <truncated output here>
>
> Warning message:
> In readLines(readfile_con, n = 5) :
> seek on a gzfile connection returne...