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 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/posting-guide.html and provide commented, minimal, self-contained, reproducible code.