The .Internal(La_rs(x,FALSE)) call inside of the eigen function used within fields:::Krig.engine.default causes my R console[1] to crash after it gets triggered during a huge script.
I am sure that that's the line that's causing the detonation. however, the same line does not crash on a fresh session using:
x <- structure(c(0.00251355321405019, -0.000589785531216647, -0.000172411748626129, -0.000589785531217227, 0.000897505637785858, -0.000714600035538855, -0.000172411748626269, -0.000714600035538766, 0.00123946691634644), .Dim = c(3L, 3L))
.Internal(La_rs(x,FALSE))
you can reproduce this console crash with the following three lines (takes about ten minutes):
# install.packages( c("MonetDB.R", "MonetDBLite" , "survey" , "SAScii" , "descr" , "downloader" , "digest" , "sas7bdat" , "R.utils" ,"survey","ggplot2","scales","mapproj","sqldf","maptools","raster","rgeos","stringr","plyr","mgcv","spatstat","rgeos") , repos=c("http://dev.monetdb.org/Assets/R/", "http://cran.rstudio.com/"))
# path.to.7z <- "7za" # macintosh/unix users need to specify 7z
# setwd("C:/My Directory/")
# warning: some large downloads
downloader::source_url( "https://raw.githubusercontent.com/davidbrae/swmap/8eecde1683efab65a7e27eb7c92e7967a98dc639/how%20to%20map%20the%20american%20community%20survey.R" , prompt = FALSE )
sorry the example isn't more minimal, the crash disappeared when i removed different things..
february 22nd 2016 edit: even worse, when i try a script intended to trigger the crash on its own, it does not die!
downloader::source_url("https://gist.githubusercontent.com/ajdamico/0c256ed3a77d77eecfd6/raw/ce0570effd37c6384f2e27f1b38335078adcb49d/La_rs_bughunt.R",echo=T,prompt=F)
thanks!
[1] R version 3.2.3 (2015-12-10) Platform: x86_64-w64-mingw32/x64 (64-bit)
if i run the whole script at once, R crashes without any info in Rterm.exe. but if i break the script up into two parts, R gives me this error:
> x
[,1] [,2] [,3]
[1,] 0.0025135532 -0.0005897855 -0.0001724117
[2,] -0.0005897855 0.0008975056 -0.0007146000
[3,] -0.0001724117 -0.0007146000 0.0012394669
> .Internal(La_rs(x,TRUE))
Error: 'a' must be a complex matrix
a bit more debugging info: it looks like the .Internal() function La_rs has been destroyed somehow?
> debug::mtrace(.Internal(La_rs(x,TRUE)))
Error in debug::mtrace(.Internal(La_rs(x, TRUE))) :
Dunno wot to do with .Internal(La_rs(x, TRUE))
> x
[,1] [,2] [,3]
[1,] 0.0025135532 -0.0005897855 -0.0001724117
[2,] -0.0005897855 0.0008975056 -0.0007146000
[3,] -0.0001724117 -0.0007146000 0.0012394669
> class(x)
[1] "matrix"
> .Internal(La_rs(x,FALSE))
Error: 'a' must be a complex matrix
> .Internal(La_rs(x,TRUE))
Error: 'a' must be a complex matrix
> .Internal(La_rs(1,TRUE))
Error: 'a' must be a complex matrix
> .Internal(La_rs(matrix(1,2,3,4),TRUE))
Error: 'a' must be a complex matrix
february 21 2016 update: i was able to reproduce this error (without R dying) on a second windows script. here is the permanent link
# install.packages( c( 'fields' , 'maps' , 'ggplot2' , 'raster' , 'sqldf' , 'rgeos' , 'rgdal' , 'sp' , 'digest' , 'ff' , 'descr' , 'SAScii' , 'stringr' , 'R.utils' , 'R.oo' , 'RCurl' , 'MonetDBLite' , 'MonetDB.R' , 'survey' , 'downloader' ) , repos=c("http://dev.monetdb.org/Assets/R/", "http://cran.rstudio.com/"))
# setwd( "S:/temp/PNAD" )
# warning: some large downloads
downloader::source_url( "https://raw.githubusercontent.com/davidbrae/swmap/4501e2c8927faaffa02c92d3e40d16beb44bca92/how%20to%20map%20the%20pesquisa%20nacional%20por%20amostra%20de%20domicilios.R" , echo = TRUE , prompt = FALSE )
and here is what happens at the point of the error. again La_rs appears corrupted.
> for ( i in 1:4 ){
+
+ this.krig.fit <-
+ Krig(
+ cbind( x$x , x$y ) ,
+ x[ , paste0( 'occcat' , i ) ] ,
+ weights = x[ , paste0( 'weigh .... [TRUNCATED]
Error in eigen(tempM, symmetric = TRUE) : 'a' must be a complex matrix
In addition: There were 50 or more warnings (use warnings() to see the first 50)
> traceback()
8: eigen(tempM, symmetric = TRUE)
7: Krig.engine.default(out, verbose = verbose)
6: Krig(cbind(x$x, x$y), x[, paste0("occcat", i)], weights = x[,
paste0("weight", i)]) at filee101515cee#676
5: eval(expr, envir, enclos)
4: eval(ei, envir)
3: withVisible(eval(ei, envir))
2: source(temp_file, ...)
1: downloader::source_url("https://raw.githubusercontent.com/davidbrae/swmap/master/how%20to%20map%20the%20pesquisa%20nacional%20por%20amostra%20de%20domicilios.R",
echo = T, prompt = F)
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 R2 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] tcltk grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] fields_8.3-6 maps_3.1.0 spam_1.3-0 ggplot2_2.0.0 raster_2.5-2
[6] sqldf_0.4-10 RSQLite_1.0.0 gsubfn_0.6-6 proto_0.3-10 rgeos_0.3-17
[11] rgdal_1.1-3 sp_1.2-2 digest_0.6.9 ff_2.2-13 bit_1.1-12
[16] descr_1.1.2 SAScii_1.0 stringr_1.0.0 R.utils_2.2.0 R.oo_1.19.0
[21] R.methodsS3_1.7.0 RCurl_1.95-4.6 bitops_1.0-6 MonetDBLite_0.2.0 MonetDB.R_1.0.1
[26] DBI_0.3.1 survey_3.30-3 downloader_0.4
loaded via a namespace (and not attached):
[1] Rcpp_0.12.3 plyr_1.8.3 tools_3.2.3 gtable_0.1.2 lattice_0.20-33
[6] magrittr_1.5 scales_0.3.0 codetools_0.2-14 xtable_1.8-0 colorspace_1.2-6
[11] stringi_1.0-1 munsell_0.4.2 chron_2.3-47
>
february 27th, 2016 edit: very similar bug, adding gc() in the middle of this script prevents the crash
# account creation page
# http://www.icpsr.umich.edu/rpxlogin?path=NACJD&request_uri=https%3a%2f%2fwww.icpsr.umich.edu%2ficpsrweb%2fNACJD%2f
your.username <- 'email@address.com'
your.password <- 'some_password'
setwd( "C:/My Directory/NCVS_BUG/" )
library(downloader)
source_url( "https://gist.githubusercontent.com/ajdamico/4cd5f76aebbdaae5bc88/raw/1ae140e84aa82f1c12af297badad6d8c2c50f5a1/ncvs_bughunt.R" , echo = TRUE , prompt = FALSE )
