From l@wrence@mich@el @ending from gene@com  Fri May 11 01:17:48 2018
From: l@wrence@mich@el @ending from gene@com (Michael Lawrence)
Date: Thu, 10 May 2018 16:17:48 -0700
Subject: [Rd] readLines() behaves differently for gzfile connection
In-Reply-To: <CAFsUf91sPtYv9QNcx5mbnFL_XD8_b46E8hPNGn6KY755ea8mYQ@mail.gmail.com>
References: <CAFsUf91sPtYv9QNcx5mbnFL_XD8_b46E8hPNGn6KY755ea8mYQ@mail.gmail.com>
Message-ID: <CAOQ5Nyf_FcvsbEhoQj=hf5BxzUdW0o8wRunzAhFbJ2-yMijp8g@mail.gmail.com>

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, 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 returned an internal error
>
>> close(readfile_con)
>
>> sessionInfo()
> R version 3.4.3 (2017-11-30)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Sierra 10.12.6
>
> Matrix products: default
> BLAS:
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
> LAPACK:
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.3
>
> ---------------------------------------------
>
> 3.5.0:
>> source_file = "1k_annotation.gz"
>> readfile_con <- gzfile(source_file, "r")
>> readLines(readfile_con, n = 5)
> [1] "" "" "" "" ""
> Warning message:
> In readLines(readfile_con, n = 5) :
>   seek on a gzfile connection returned an internal error
>> close(readfile_con)
>> sessionInfo()
> R version 3.5.0 (2018-04-23)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Debian GNU/Linux 9 (stretch)
>
> Matrix products: default
> BLAS: /usr/lib/openblas-base/libblas.so.3
> LAPACK: /usr/lib/libopenblasp-r0.2.19.so
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] compiler_3.5.0
>
> ----------------------------------------
> (note: I'm running 3.5.0 via the docker rocker/tidyverse:3.5 container, and
> 3.4.3 on my mac desktop machine)
>
> Thanks!
> Ben Heavner
>
>         [[alternative HTML version deleted]]
>
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>



[Rd] readLines() behaves differently for gzfile connection
Michael Lawrence