I haven't been able to reproduce the empty lines issue on my Mac or Linux laptop, but I have yet to try that container.
The warning is because of a SEEK_SET to -1, which apparently is unsupported by zlib. Maybe the zlib version in that container is getting confused. I'm not sure why readLines() wants to seek to -1 instead of 0, but it only does that on non-blocking connections. The compressed file connections are effectively blocking but are marked as non-blocking. Marking them as blocking removes the warning. I will get that into devel and release soon. Hopefully that fixes the empty lines issue also. Michael On Thu, May 10, 2018 at 4:21 PM, Ben Heavner <bheav...@gmail.com> wrote: > 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.mich...@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 <bheav...@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@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/r-devel >> > > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
