Hi: I have a 2.1GB JSON file. Typically I use readLines() and jsonlite:fromJSON() to extract data from a JSON file.
When I try and read in this file using readLines() R segfaults. I believe the two salient issues with this file are 1). Its size 2). It is a single line (no line breaks) I can reproduce this issue as follows #Generate a big file with no line breaks # In R > writeLines(paste0(c(letters, 0:9), collapse=""), "alpha.txt", sep="") # in unix shell cp alpha.txt file.txt for i in {1..26}; do cat file.txt file.txt > file2.txt && mv -f file2.txt file.txt; done This generates a 2.3GB file with no line breaks in R: > moo <- readLines("file.txt") *** caught segfault *** address 0x7cffffff, cause 'memory not mapped' Traceback: 1: readLines("file.txt") Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: 3 I conclude: I am potentially running up against a limit in R, which should give a reasonable error, but currently just segfaults. My question: Most of the content of the JSON is an approximately 100K x 6K JSON equivalent of a dataframe, and I know R can handle much bigger than this size. I am expecting these JSON files to get even larger. My R code lives in a bigger system, and the JSON comes in via stdin, so I have absolutely no control over the data format. I can imagine trying to incrementally parse the JSON so I don't bump up against the limit, but I am eager for suggestions of simpler solutions. Also, I apologize for the timing of this bug report, as I know folks are working to get out the next release of R, but like so many things I have no control over when bugs leap up. Thanks. Jen > 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: R-3.4.1/lib/libRblas.so LAPACK:R-3.4.1/lib/libRlapack.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=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 [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel