[R] readLines without skipNul=TRUE causes crash
Anthony Damico
ajdamico at gmail.com
Sun Jul 16 12:21:21 CEST 2017
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 <jdnewmil at 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 <ajdamico at 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.duncan at 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 at 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 at 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:<jdnewmil at 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 at 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:<jdnewmil at 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
> ------------------------------------------------------------
> ---------------
>
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