From bhe@vner @ending from gm@il@com  Fri May 11 00:31:56 2018
From: bhe@vner @ending from gm@il@com (Ben Heavner)
Date: Thu, 10 May 2018 15:31:56 -0700
Subject: [Rd] readLines() behaves differently for gzfile connection
Message-ID: <CAFsUf91sPtYv9QNcx5mbnFL_XD8_b46E8hPNGn6KY755ea8mYQ@mail.gmail.com>

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

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[Rd] readLines() behaves differently for gzfile connection
Ben Heavner