From bhe@vner @ending from gm@il@com  Fri May 11 01:21:19 2018
From: bhe@vner @ending from gm@il@com (Ben Heavner)
Date: Thu, 10 May 2018 16:21:19 -0700
Subject: [Rd] readLines() behaves differently for gzfile connection
In-Reply-To: <CAOQ5Nyf_FcvsbEhoQj=hf5BxzUdW0o8wRunzAhFbJ2-yMijp8g@mail.gmail.com>
References: <CAFsUf91sPtYv9QNcx5mbnFL_XD8_b46E8hPNGn6KY755ea8mYQ@mail.gmail.com>
 <CAOQ5Nyf_FcvsbEhoQj=hf5BxzUdW0o8wRunzAhFbJ2-yMijp8g@mail.gmail.com>
Message-ID: <CAFsUf91RTyY_AKBw_s5omZATfs4kKm6HUmgnp+9fu7FW5GWhuQ@mail.gmail.com>

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, 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]]
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>

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