hi, thank you for attempting this. it looks like your unix machine unzipped the txt file without corruption -- if you copied over the same txt file to windows 7, i don't think that would reproduce the problem? i think it needs to be the corrupted text file where R.utils::countLines( txtfile ) gives 809367. i am able to reproduce on two distinct windows machines but no guarantee i'm not doing something dumb
On Sat, Jul 15, 2017 at 6:29 PM, Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote: > I am not able to reproduce your segfault on a Windows 7 platform either: > > ########################## > fn1 <- "d:/DADOS_ENEM_2009.txt" > sessionInfo() > ## R version 3.4.1 (2017-06-30) > ## Platform: x86_64-w64-mingw32/x64 (64-bit) > ## Running under: Windows 7 x64 (build 7601) Service Pack 1 > ## > ## Matrix products: default > ## > ## locale: > ## [1] LC_COLLATE=English_United States.1252 > ## [2] LC_CTYPE=English_United States.1252 > ## [3] LC_MONETARY=English_United States.1252 > ## [4] LC_NUMERIC=C > ## [5] LC_TIME=English_United States.1252 > ## > ## attached base packages: > ## [1] stats graphics grDevices utils datasets methods base > ## > ## loaded via a namespace (and not attached): > ## [1] compiler_3.4.1 > tools::md5sum( fn1 ) > ## d:/DADOS_ENEM_2009.txt > ## "83e61c96092285b60d7bf6b0dbc7072e" > dat <- readLines( fn1 ) > length( dat ) > ## [1] 4148721 > > > On Sat, 15 Jul 2017, Jeff Newmiller wrote: > > I am not able to reproduce this on a Linux platform: >> >> #######################3 >> fn1 <- "/home/jdnewmil/Downloads/Microdados ENEM 2009/Dados Enem >> 2009/DADOS_ENEM_2009.txt" >> sessionInfo() >> ## R version 3.4.1 (2017-06-30) >> ## Platform: x86_64-pc-linux-gnu (64-bit) >> ## Running under: Ubuntu 14.04.5 LTS >> ## >> ## Matrix products: default >> ## BLAS: /usr/lib/libblas/libblas.so.3.0 >> ## LAPACK: /usr/lib/lapack/liblapack.so.3.0 >> ## >> ## 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=en_US.UTF-8 >> ## [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_3.4.1 >> tools::md5sum( fn1 ) >> ## /home/jdnewmil/Downloads/Microdados ENEM 2009/Dados Enem >> 2009/DADOS_ENEM_2009.txt >> ## >> "83e61c96092285b60d7bf6b0dbc7072e" >> dat <- readLines( fn1 ) >> length( dat ) >> ## [1] 4148721 >> >> No segfault occurs. >> >> On Sat, 15 Jul 2017, Anthony Damico wrote: >> >> hi, i realized that the segfault happens on the text file in a new R >>> session. so, creating the segfault-generating text file requires a >>> contributed package, but prompting the actual segfault does not -- pretty >>> sure that means this is a base R bug? submitted here: >>> https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17311 hopefully i >>> am >>> not doing something remarkably stupid. the text file itself is 4GB so >>> cannot upload it to bugzilla, and from the R_AllocStringBugger error in >>> the >>> previous message, i think most or all of it needs to be there to trigger >>> the segfault. thanks! >>> >>> >>> On Sat, Jul 15, 2017 at 10:32 AM, Anthony Damico <ajdam...@gmail.com> >>> wrote: >>> >>> hi, thanks Dr. Murdoch >>>> >>>> >>>> i'd appreciate if anyone on r-help could help me narrow this down? i >>>> believe the segfault occurs because there's a single line with 4GB and >>>> also >>>> embedded nuls, but i am not sure how to artificially construct that? >>>> >>>> >>>> the lodown package can be removed from my example.. it is just for file >>>> download cacheing, so `lodown::cachaca` can be replaced with >>>> `download.file` my current example requires a huge download, so sort of >>>> painful to repeat but i'm pretty confident that's not the issue. >>>> >>>> >>>> the archive::archive_extract() function unzips a (probably corrupt) .RAR >>>> file and creates a text file with 80,937 lines. this file is 4GB: >>>> >>>> > file.size(infile) >>>> [1] 4078192743 <(407)%20819-2743> >>>> >>>> >>>> i am pretty sure that nearly all of that 4GB is contained on a single >>>> line >>>> in the file. here's what happens when i create a file connection and >>>> scan >>>> through.. >>>> >>>> > file_con <- file( infile , 'r' ) >>>> > >>>> > first_80936_lines <- readLines( file_con , n = 80936 ) >>>> > scan( w , n = 1 , what = character() ) >>>> Read 1 item >>>> [1] "1000023930632009" >>>> > scan( w , n = 1 , what = character() ) >>>> Read 1 item >>>> [1] "36F2924009PAULO" >>>> > scan( w , n = 1 , what = character() ) >>>> Read 1 item >>>> [1] "AFONSO" >>>> > scan( w , n = 1 , what = character() ) >>>> Read 1 item >>>> [1] "BA11" >>>> > scan( w , n = 1 , what = character() ) >>>> Read 1 item >>>> [1] "00000" >>>> > scan( w , n = 1 , what = character() ) >>>> Read 1 item >>>> [1] "00" >>>> > scan( w , n = 1 , what = character() ) >>>> Read 1 item >>>> [1] "2924009PAULO" >>>> > scan( w , n = 1 , what = character() ) >>>> Read 1 item >>>> [1] "AFONSO" >>>> > scan( w , n = 1 , what = character() ) >>>> Read 1 item >>>> [1] "BA1111" >>>> > scan( w , n = 1 , what = character() ) >>>> Read 1 item >>>> [1] "467.20" >>>> > scan( w , n = 1 , what = character() ) >>>> Read 1 item >>>> [1] "346.10" >>>> > scan( w , n = 1 , what = character() ) >>>> Read 1 item >>>> [1] "414.40" >>>> > scan( w , n = 1 , what = character() ) >>>> Error in scan(w, n = 1, what = character()) : >>>> could not allocate memory (2048 Mb) in C function >>>> 'R_AllocStringBuffer' >>>> >>>> >>>> >>>> making a huge single-line file does not reproduce the problem, i think >>>> the >>>> embedded nuls have something to do with it-- >>>> >>>> >>>> # WARNING do not run with less than 64GB RAM >>>> tf <- tempfile() >>>> a <- rep( "a" , 1000000000 ) >>>> b <- paste( a , collapse = '' ) >>>> writeLines( b , tf ) ; rm( b ) ; gc() >>>> d <- readLines( tf ) >>>> >>>> >>>> >>>> On Sat, Jul 15, 2017 at 9:17 AM, Duncan Murdoch < >>>> murdoch.dun...@gmail.com> >>>> wrote: >>>> >>>> On 15/07/2017 7:35 AM, Anthony Damico wrote: >>>>> >>>>> hello, the last line of the code below causes a segfault for me on >>>>>> 3.4.1. >>>>>> i think i should submit to https://bugs.r-project.org/ unless others >>>>>> have >>>>>> advice? thanks >>>>>> >>>>>> >>>>> Segfaults are usually worth reporting as bugs. Try to come up with a >>>>> self-contained example, not using the lodown and archive packages. I >>>>> imagine you can do this by uploading the file you downloaded, or >>>>> enough of >>>>> a subset of it to trigger the segfault. If you can't do that, then >>>>> likely >>>>> the bug is with one of those packages, not with R. >>>>> >>>>> Duncan Murdoch >>>>> >>>>> >>>>> >>>>>> >>>>>> >>>>>> >>>>>> install.packages( "devtools" ) >>>>>> devtools::install_github("ajdamico/lodown") >>>>>> devtools::install_github("jimhester/archive") >>>>>> >>>>>> >>>>>> file_folder <- file.path( tempdir() , "file_folder" ) >>>>>> >>>>>> tf <- tempfile() >>>>>> >>>>>> # large download! cachaca saves on your local disk if already >>>>>> downloaded >>>>>> lodown::cachaca( ' >>>>>> http://download.inep.gov.br/microdados/microdados_enem2009.rar' , tf >>>>>> , >>>>>> mode >>>>>> = 'wb' ) >>>>>> >>>>>> archive::archive_extract( tf , dir = normalizePath( file_folder ) ) >>>>>> >>>>>> unzipped_files <- list.files( file_folder , recursive = TRUE , >>>>>> full.names = >>>>>> TRUE ) >>>>>> >>>>>> infile <- grep( "DADOS(.*)\\.txt$" , unzipped_files , value = TRUE ) >>>>>> >>>>>> # works >>>>>> R.utils::countLines( infile ) >>>>>> >>>>>> # works with warning >>>>>> my_file <- readLines( infile , skipNul = TRUE ) >>>>>> >>>>>> # crash >>>>>> my_file <- readLines( infile ) >>>>>> >>>>>> >>>>>> # run just before crash >>>>>> sessionInfo() >>>>>> # R version 3.4.1 (2017-06-30) >>>>>> # Platform: x86_64-w64-mingw32/x64 (64-bit) >>>>>> # Running under: Windows 10 x64 (build 15063) >>>>>> >>>>>> # Matrix products: default >>>>>> >>>>>> # locale: >>>>>> # [1] LC_COLLATE=English_United States.1252 >>>>>> # [2] LC_CTYPE=English_United States.1252 >>>>>> # [3] LC_MONETARY=English_United States.1252 >>>>>> # [4] LC_NUMERIC=C >>>>>> # [5] LC_TIME=English_United States.1252 >>>>>> >>>>>> # attached base packages: >>>>>> # [1] stats graphics grDevices utils datasets methods base >>>>>> >>>>>> # loaded via a namespace (and not attached): >>>>>> # [1] httr_1.2.1 compiler_3.4.1 R6_2.2.1 >>>>>> withr_1.0.2 >>>>>> # [5] tibble_1.3.3 curl_2.6 Rcpp_0.12.11 >>>>>> memoise_1.1.0 >>>>>> # [9] R.methodsS3_1.7.1 git2r_0.18.0 digest_0.6.12 >>>>>> lodown_0.1.0 >>>>>> # [13] R.utils_2.5.0 rlang_0.1.1 devtools_1.13.2 >>>>>> R.oo_1.21.0 >>>>>> # [17] archive_0.0.0.9000 >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> ______________________________________________ >>>>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >>>>>> https://stat.ethz.ch/mailman/listinfo/r-help >>>>>> PLEASE do read the posting guide http://www.R-project.org/posti >>>>>> ng-guide.html >>>>>> and provide commented, minimal, self-contained, reproducible code. >>>>>> >>>>>> >>>>>> >>>>> >>>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide http://www.R-project.org/posti >>> ng-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >>> >> ------------------------------------------------------------ >> --------------- >> Jeff Newmiller The ..... ..... Go >> Live... >> DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live >> Go... >> Live: OO#.. Dead: OO#.. Playing >> Research Engineer (Solar/Batteries O.O#. #.O#. with >> /Software/Embedded Controllers) .OO#. .OO#. >> rocks...1k >> >> ______________________________________________ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posti >> ng-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >> > ------------------------------------------------------------ > --------------- > Jeff Newmiller The ..... ..... Go Live... > DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live > Go... > Live: OO#.. Dead: OO#.. Playing > Research Engineer (Solar/Batteries O.O#. #.O#. with > /Software/Embedded Controllers) .OO#. .OO#. rocks...1k > ------------------------------------------------------------ > --------------- > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
