Hello, I did the same question on stackoverflow (http://stackoverflow.com/questions/15784373/process-substitution) but did not understand completely the issue so I'm reporting it here:
" I've given a look around about what puzzles me and I only found this: http://stackoverflow.com/questions/4274171/do-some-programs-not-accept-process-substitution-for-input-files which is partially helping, but I really would like to understand the full story. I noticed that some of my R scripts give different (ie. wrong) results when I use process substitution. I tried to pinpoint the problem with a test case: This script: #!/usr/bin/Rscript args <- commandArgs(TRUE) file <-args[1] cat(file) cat("\n") data <- read.table(file, header=F) cat(mean(data$V1)) cat("\n") with an input file generated in this way: $ for i in `seq 1 10`; do echo $i >> p; done $ for i in `seq 1 500`; do cat p >> test; done leads me to this: $ ./mean.R test test 5.5 $ ./mean.R <(cat test) /dev/fd/63 5.501476 Further tests reveal that some lines are lost...but I would like to understand why. Does read.table (scan gives the same results) uses seek? Ps. with a smaller test file (100) an error is reported: $./mean.R <(cat test3) /dev/fd/63 Error in read.table(file, header = F) : no lines available in input Execution halted " Other notes: with a modified script that uses scan the results are the same. Printing the whole data.frame results in 5001 lines in the first case (which is correct) and only 3050 with the process redirection. I checked read.table source code and I saw that it goes around in the file to check for column types and so on...I thought that this was an explanation for this problem but I would prefer an error message reported instead than a result gotten from partial data...then someone on stackoverflow pointed me to fifo() which solves the problem (i.e the mean is reported correctly even with the process redirection) and therefore I'm even more puzzled: does fifo() allows seeks and peeks around a named pipe? I'm willing to read the relevant code to understand what's really happening (and even help if someone thinks that this issue could represent a small bug) but I would really appreciate some pointers. Here the sessionInfo() and other possibly relevant things: > sessionInfo() R version 3.0.0 beta (2013-03-23 r62384) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base $ uname -a Linux femto 3.6-trunk-amd64 #1 SMP Debian 3.6.9-1~experimental.1 x86_64 GNU/Linux I use the debian R package: r-base-core, 3.0.0~20130324-1 Thanks, Elena Grassi ps. I started on R-help as long as this could be of general interest, sorry if that's a bad call. -- $ pom ______________________________________________ R-help@r-project.org mailing list 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.
