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
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