I am trying to plot the following variables:
> df1$var1
[1] "2012Q1" "2012Q2" "2012Q3" "2012Q4" "2013Q1" "2013Q2" "2013Q3" "2013Q4" "2014Q1" "2014Q2"
[11] "2014Q3" "2014Q4" "2015Q1" "2015Q2" "2015Q3" "2015Q4" "2016Q1" "2016Q2" "2016Q3" "2016Q4"
[21] "2017Q1" "2017Q2" "2017Q3" "2017Q4" "2018Q1" "2018Q2" "2018Q3" "2018Q4" "2019Q1" "2019Q2"
> df1$var2
[1] NA NA NA NA 444618.3 1556125.2 744145.1 844862.2 773188.2
[10] 1204732.2 1832308.2 1732186.6 1475089.7 1238791.2 772359.0 927111.5 982978.9 581415.1
[19] 489457.8 446419.0 403841.0 654630.9 753729.4 513755.0 587031.5 465808.7 462710.4
[28] 537923.9 409037.8 785118.7
using the following code:
plot(df1$var1,df1$var2,type="l",col="red")
which gives me the following error:
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
how can I make it work?
User #zx8754 marked this question as a duplicate of this question and of this question.
The problem here is that var1 is of class "character", like in the questions believed to be duplicates, but it is obvious from its contents that what is needed is a year/quarter object.
Package zoo has a function ideal for this, as.yearqtr.
yq <- zoo::as.yearqtr(df1$var1)
plot(yq, df1$var2, type = "l", col = "red")
Data in dput format.
df1 <-
structure(list(var1 = c("2012Q1", "2012Q2", "2012Q3", "2012Q4",
"2013Q1", "2013Q2", "2013Q3", "2013Q4", "2014Q1", "2014Q2", "2014Q3",
"2014Q4", "2015Q1", "2015Q2", "2015Q3", "2015Q4", "2016Q1", "2016Q2",
"2016Q3", "2016Q4", "2017Q1", "2017Q2", "2017Q3", "2017Q4", "2018Q1",
"2018Q2", "2018Q3", "2018Q4", "2019Q1", "2019Q2"), var2 = c(NA,
NA, NA, NA, 444618.3, 1556125.2, 744145.1, 844862.2, 773188.2,
1204732.2, 1832308.2, 1732186.6, 1475089.7, 1238791.2, 772359,
927111.5, 982978.9, 581415.1, 489457.8, 446419, 403841, 654630.9,
753729.4, 513755, 587031.5, 465808.7, 462710.4, 537923.9, 409037.8,
785118.7)), class = "data.frame", row.names = c(NA, -30L))
I've been having an issue in a Shiny R application where I am getting intermittent errors when the application is supposed to render a ggplot2 plot.
The errors I've been seeing include:
Error in eval(expr, envir, enclos) :
arguments imply differing number of rows: 136, 129
and
Error in eval(expr, envir, enclos) :
Results must be all atomic, or all data frames
I'm seeing the same errors in my Shiny app.
After lots of searching, I found a recent post here that seems to reproduce the same set of errors:
http://cowboyjob.com/post/6523856/Reupping-my-question-from-a-few-hours-ago-I-have-word-from-another-channel-that
I also found this question, which may be related: Tracing root cause for R segfault
The code in that first link is as follows:
library(ggplot2)
set.seed(12345678)
sessionInfo()
littledata = data.frame(x=1:128, y=rlnorm(128))
bigdata = data.frame(x=1:129, y=rlnorm(129))
# plots as expected
lp = ggplot(littledata, aes(x, y))+geom_histogram(stat="identity", binwidth=1)
for (i in 1:20){
print(i)
try(print(lp+ggtitle(paste("128 points", i))))
}
# always warns "position_stack requires constant width",
# intermittently throws error, hangs, or segfaults.
# See below for details.
bp = ggplot(bigdata, aes(x, y))+geom_histogram(stat="identity", binwidth=1)
for(i in 1:20){
print(i)
try(print(bp+ggtitle(paste("129 points", i))))
}
## End demo code
For the machine I'm working on, here is the output from that code block:
> source('~/R/testing/segfault_test.R')
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
[1] 11
[1] 12
[1] 13
[1] 14
[1] 15
[1] 16
[1] 17
[1] 18
[1] 19
[1] 20
[1] 1
Error in eval(expr, envir, enclos) : replacement has length zero
In addition: Warning messages:
1: package ‘ggplot2’ was built under R version 3.1.2
2: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
[1] 2
[1] 3
[1] 4
[1] 5
Error in eval(expr, envir, enclos) :
Results must be all atomic, or all data frames
In addition: Warning messages:
1: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
2: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
3: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
4: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
[1] 6
[1] 7
Error in eval(expr, envir, enclos) :
arguments imply differing number of rows: 136, 129
In addition: Warning messages:
1: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
2: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
[1] 8
Error in eval(expr, envir, enclos) :
Results must be all atomic, or all data frames
In addition: Warning message:
In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
[1] 9
[1] 10
[1] 11
Error in eval(expr, envir, enclos) :
arguments imply differing number of rows: 136, 129
In addition: Warning messages:
1: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
2: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
3: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
[1] 12
[1] 13
Error in eval(expr, envir, enclos) :
Results must be all atomic, or all data frames
In addition: Warning messages:
1: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
2: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
[1] 14
[1] 15
Error in eval(expr, envir, enclos) :
arguments imply differing number of rows: 136, 129
In addition: Warning messages:
1: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
2: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
[1] 16
[1] 17
[1] 18
Error in eval(expr, envir, enclos) :
arguments imply differing number of rows: 136, 129
In addition: Warning messages:
1: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
2: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
3: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
[1] 19
[1] 20
Warning messages:
1: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
2: In loop_apply(n, do.ply) :
position_stack requires constant width: output may be incorrect
>
From this output, we can see that the first loop runs without any issues; however, the second loop with 129 points gives errors on some of the plots.
When I embed several ggplot plots into my shiny app, I'm seeing these errors show-up, often resulting in a segmentation fault.
Here's what I see in the javascript console when running the app on the shiny-server:
Error in eval(substitute(expr), envir, enclos) :
Results must be all atomic, or all data frames
*** caught segfault ***
address 0x2, cause 'memory not mapped'
Traceback:
1: dim(x)
2: FUN(X[[211L]], ...)
3: lapply(res, NROW)
4: unlist(lapply(res, NROW))
5: list_to_dataframe(res, attr(.data, "split_labels"), .id, id_as_factor)
6: ldply(.data = pieces, .fun = .fun, ..., .progress = .progress, .inform = .inform, .parallel = .parallel, .paropts = .paropts)
7: ddply(munched, .(group), function(df) { data.frame(solid = identical(unique(df$linetype), 1), constant = nrow(unique(df[, c("alpha", "colour", "size", "linetype")])) == 1)})
8: get(x, envir = this, inherits = inh)(this, ...)
9: GeomPath$draw(data, scales, coordinates, arrow, ...)
10: get(x, envir = this, inherits = inh)(this, ...)
11: .$draw(...)
12: get(x, envir = this, inherits = inh)(this, ...)
13: (function (...) get(x, envir = this, inherits = inh)(this, ...))(data = data, scales = scales, coordinates = cs)
14: do.call(.$geom$draw_groups, c(data = list(as.name("data")), scales = list(as.name("scales")), coordinates = list(as.name("cs")), .$geom_params))
15: get(x, envir = this, inherits = inh)(this, ...)
16: layer$make_grob(df, scales = panel$ranges[[panel_i]], cs = plot$coord)
17: .fun(piece, ...)
18: (function (i) { piece <- pieces[[i]] if (.inform) { res <- try(.fun(piece, ...)) if (inherits(res, "try-error")) { piece <- paste(capture.output(print(piece)), collapse = "\n") stop("with piece ", i, ": \n", piece, call. = FALSE) } } else { res <- .fun(piece, ...) } progress$step() res})(1L)
19: eval(substitute(expr), envir, enclos)
20: evalq((function (i) { piece <- pieces[[i]] if (.inform) { res <- try(.fun(piece, ...)) if (inherits(res, "try-error")) { piece <- paste(capture.output(print(piece)), collapse = "\n") stop("with piece ", i, ": \n", piece, call. = FALSE) } } else { res <- .fun(piece, ...) } progress$step() res})(1L), <environment>)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(evalq((function (i) { piece <- pieces[[i]] if (.inform) { res <- try(.fun(piece, ...)) if (inherits(res, "try-error")) { piece <- paste(capture.output(print(piece)), collapse = "\n") stop("with piece ", i, ": \n", piece, call. = FALSE) } } else { res <- .fun(piece, ...) } progress$step() res})(1L), <environment>), error = .rcpp_error_recorder)
25: withCallingHandlers(tryCatch(evalq((function (i) { piece <- pieces[[i]] if (.inform) { res <- try(.fun(piece, ...)) if (inherits(res, "try-error")) { piece <- paste(capture.output(print(piece)), collapse = "\n") stop("with piece ", i, ": \n", piece, call. = FALSE) } } else { res <- .fun(piece, ...) } progress$step() res})(1L), <environment>), error = .rcpp_error_recorder), warning = .rcpp_warning_recorder)
aborting ...
Segmentation fault (core dumped)
The output of my sessionInfo() command is as follows:
R version 3.1.1 (2014-07-10)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_1.0.1
loaded via a namespace (and not attached):
[1] colorspace_1.2-6 digest_0.6.8 grid_3.1.2 gtable_0.1.2 labeling_0.3 MASS_7.3-35
[7] munsell_0.4.2 plyr_1.8.2 proto_0.3-10 Rcpp_0.11.6 reshape2_1.4.1 scales_0.2.4
[13] stringr_0.6.2 tools_3.1.2
Has anyone else run into this? It's been driving me nuts (intermittently!) over the last few days. I've tried this with different versions of R (3.1.1 - 3.2.0), Rcpp (0.11.6, 0.11.5), plyr (1.8.1 - 1.8.2) as well as two different (Red Hat) Linux machines, and can reproduce the error on both.
Any help or suggestions are much appreciated.
EDIT:
I've done clean-installs of R and all packages on the machines I'm working on (based on an older suggestion found in issue #1006 of hadley/ggplot2)
I'm using version tracking and have the identical code base for the Shiny application on an OSX laptop as well as two different RedHat Linux machines.
I have had no problems running on OSX; so I used packrat to replicate the package library to the two RedHat machines and all three are running R-3.1.2, but this does not resolve the problem.
The Shiny application still crashes with the following output in the JS console:
Warning in run(timeoutMs) :
Removed 1 rows containing missing values (geom_path).
Error: Results must be all atomic, or all data frames
Execution halted
Here are results from the Javascript Console:
67: try(handler(binary, message))
68: (function (handle, binary, message) { for (handler in .wsconns[[as.character(handle)]]$.messageCallbacks) { result <- try(handler(binary, message)) if (inherits(result, "try-error")) { .wsconns[[as.character(handle)]]$close() return() } }})("266303168", FALSE, "{\"method\":\"update\",\"data\":{\".clientdata_output_out035b13d236a68453_width\":386,\".clientdata_output_out035b13d236a68453_height\":400,\".clientdata_output_out45a459f761c2bcff_width\":386,\".clientdata_output_out45a459f761c2bcff_height\":400,\".clientdata_output_out0b680f21f3d73958_width\":386,\".clientdata_output_out0b680f21f3d73958_height\":400,\".clientdata_output_out785a5b0a4a8d2872_width\":386,\".clientdata_output_out785a5b0a4a8d2872_height\":400,\".clientdata_output_out4d4c261305d448a2_width\":386,\".clientdata_output_out4d4c261305d448a2_height\":400,\".clientdata_output_outae8b99c9ab2044d8_width\":386,\".clientdata_output_outae8b99c9ab2044d8_height\":400,\".clientdata_output_oute11f4c69b81158cc_width\":386,\".clientdata_output_oute11f4c69b81158cc_height\":400,\".clientdata_output_out1beb34c46b1bdebd_width\":386,\".clientdata_output_out1beb34c46b1bdebd_height\":400,\".clientdata_output_out9b9abdc2e1b58daa_width\":386,\".clientdata_output_out9b9abdc2e1b58daa_height\":400,\".clientdata_output_out035b13d236a68453_hidden\":false,\".clientdata_output_out45a459f761c2bcff_hidden\":false,\".clientdata_output_out0b680f21f3d73958_hidden\":false,\".clientdata_output_out785a5b0a4a8d2872_hidden\":false,\".clientdata_output_out4d4c261305d448a2_hidden\":false,\".clientdata_output_outae8b99c9ab2044d8_hidden\":false,\".clientdata_output_oute11f4c69b81158cc_hidden\":false,\".clientdata_output_out1beb34c46b1bdebd_hidden\":false,\".clientdata_output_out9b9abdc2e1b58daa_hidden\":false}}")
69: eval(substitute(expr), envir, enclos)
70: evalq((function (handle, binary, message) { for (handler in .wsconns[[as.character(handle)]]$.messageCallbacks) { result <- try(handler(binary, message)) if (inherits(result, "try-error")) { .wsconns[[as.character(handle)]]$close() return() } }})("266303168", FALSE, "{\"method\":\"update\",\"data\":{\".clientdata_output_out035b13d236a68453_width\":386,\".clientdata_output_out035b13d236a68453_height\":400,\".clientdata_output_out45a459f761c2bcff_width\":386,\".clientdata_output_out45a459f761c2bcff_height\":400,\".clientdata_output_out0b680f21f3d73958_width\":386,\".clientdata_output_out0b680f21f3d73958_height\":400,\".clientdata_output_out785a5b0a4a8d2872_width\":386,\".clientdata_output_out785a5b0a4a8d2872_height\":400,\".clientdata_output_out4d4c261305d448a2_width\":386,\".clientdata_output_out4d4c261305d448a2_height\":400,\".clientdata_output_outae8b99c9ab2044d8_width\":386,\".clientdata_output_outae8b99c9ab2044d8_height\":400,\".clientdata_output_oute11f4c69b81158cc_width\":386,\".clientdata_output_oute11f4c69b81158cc_height\":400,\".clientdata_output_out1beb34c46b1bdebd_width\":386,\".clientdata_output_out1beb34c46b1bdebd_height\":400,\".clientdata_output_out9b9abdc2e1b58daa_width\":386,\".clientdata_output_out9b9abdc2e1b58daa_height\":400,\".clientdata_output_out035b13d236a68453_hidden\":false,\".clientdata_output_out45a459f761c2bcff_hidden\":false,\".clientdata_output_out0b680f21f3d73958_hidden\":false,\".clientdata_output_out785a5b0a4a8d2872_hidden\":false,\".clientdata_output_out4d4c261305d448a2_hidden\":false,\".clientdata_output_outae8b99c9ab2044d8_hidden\":false,\".clientdata_output_oute11f4c69b81158cc_hidden\":false,\".clientdata_output_out1beb34c46b1bdebd_hidden\":false,\".clientdata_output_out9b9abdc2e1b58daa_hidden\":false}}"), <environment>)
71: doTryCatch(return(expr), name, parentenv, handler)
72: tryCatchOne(expr, names, parentenv, handlers[[1L]])
73: tryCatchList(expr, classes, parentenv, handlers)
74: tryCatch(evalq((function (handle, binary, message) { for (handler in .wsconns[[as.character(handle)]]$.messageCallbacks) { result <- try(handler(binary, message)) if (inherits(result, "try-error")) { .wsconns[[as.character(handle)]]$close() return() } }})("266303168", FALSE, "{\"method\":\"update\",\"data\":{\".clientdata_output_out035b13d236a68453_width\":386,\".clientdata_output_out035b13d236a68453_height\":400,\".clientdata_output_out45a459f761c2bcff_width\":386,\".clientdata_output_out45a459f761c2bcff_height\":400,\".clientdata_output_out0b680f21f3d73958_width\":386,\".clientdata_output_out0b680f21f3d73958_height\":400,\".clientdata_output_out785a5b0a4a8d2872_width\":386,\".clientdata_output_out785a5b0a4a8d2872_height\":400,\".clientdata_output_out4d4c261305d448a2_width\":386,\".clientdata_output_out4d4c261305d448a2_height\":400,\".clientdata_output_outae8b99c9ab2044d8_width\":386,\".clientdata_output_outae8b99c9ab2044d8_height\":400,\".clientdata_output_oute11f4c69b81158cc_width\":386,\".clientdata_output_oute11f4c69b81158cc_height\":400,\".clientdata_output_out1beb34c46b1bdebd_width\":386,\".clientdata_output_out1beb34c46b1bdebd_height\":400,\".clientdata_output_out9b9abdc2e1b58daa_width\":386,\".clientdata_output_out9b9abdc2e1b58daa_height\":400,\".clientdata_output_out035b13d236a68453_hidden\":false,\".clientdata_output_out45a459f761c2bcff_hidden\":false,\".clientdata_output_out0b680f21f3d73958_hidden\":false,\".clientdata_output_out785a5b0a4a8d2872_hidden\":false,\".clientdata_output_out4d4c261305d448a2_hidden\":false,\".clientdata_output_outae8b99c9ab2044d8_hidden\":false,\".clientdata_output_oute11f4c69b81158cc_hidden\":false,\".clientdata_output_out1beb34c46b1bdebd_hidden\":false,\".clientdata_output_out9b9abdc2e1b58daa_hidden\":false}}"), <environment>), error = .rcpp_error_recorder)
75: withCallingHandlers(tryCatch(evalq((function (handle, binary, message) { for (handler in .wsconns[[as.character(handle)]]$.messageCallbacks) { result <- try(handler(binary, message)) if (inherits(result, "try-error")) { .wsconns[[as.character(handle)]]$close() return() } }})("266303168", FALSE, "{\"method\":\"update\",\"data\":{\".clientdata_output_out035b13d236a68453_width\":386,\".clientdata_output_out035b13d236a68453_height\":400,\".clientdata_output_out45a459f761c2bcff_width\":386,\".clientdata_output_out45a459f761c2bcff_height\":400,\".clientdata_output_out0b680f21f3d73958_width\":386,\".clientdata_output_out0b680f21f3d73958_height\":400,\".clientdata_output_out785a5b0a4a8d2872_width\":386,\".clientdata_output_out785a5b0a4a8d2872_height\":400,\".clientdata_output_out4d4c261305d448a2_width\":386,\".clientdata_output_out4d4c261305d448a2_height\":400,\".clientdata_output_outae8b99c9ab2044d8_width\":386,\".clientdata_output_outae8b99c9ab2044d8_height\":400,\".clientdata_output_oute11f4c69b81158cc_width\":386,\".clientdata_output_oute11f4c69b81158cc_height\":400,\".clientdata_output_out1beb34c46b1bdebd_width\":386,\".clientdata_output_out1beb34c46b1bdebd_height\":400,\".clientdata_output_out9b9abdc2e1b58daa_width\":386,\".clientdata_output_out9b9abdc2e1b58daa_height\":400,\".clientdata_output_out035b13d236a68453_hidden\":false,\".clientdata_output_out45a459f761c2bcff_hidden\":false,\".clientdata_output_out0b680f21f3d73958_hidden\":false,\".clientdata_output_out785a5b0a4a8d2872_hidden\":false,\".clientdata_output_out4d4c261305d448a2_hidden\":false,\".clientdata_output_outae8b99c9ab2044d8_hidden\":false,\".clientdata_output_oute11f4c69b81158cc_hidden\":false,\".clientdata_output_out1beb34c46b1bdebd_hidden\":false,\".clientdata_output_out9b9abdc2e1b58daa_hidden\":false}}"), <environment>), error = .rcpp_error_recorder), warning = .rcpp_warning_recorder)
aborting ...
One additional item I've noticed; the shiny app I'm running is like a monte-carlo simulation - and the more runs I pass through, the greater the chance that the application crashes. Fewer runs tend to be successful all the way through; it appears as though it may be related to memory allocation.
EDIT 2:
Reverting to older versions of Rcpp, plyr, and ggplot seems to resolve it on all three machines (OSX & Red Hat); I haven't tested to see if it's possible to upgrade one of the three from this point.
Rcpp 0.11.3
plyr 1.8.1
ggplot2 0.9.3
I can't post the code, because SO won't let me post more than two links, but I've installed using the following for all 3 packages:
install.packages(<<url to source tarball>>,repos = NULL,type="source")`
This error was caused by a bug, which was affecting the plyr package used by ggplot2. Hadley has fixed this in the latest development version by reverting to an older version of loop_apply.
The current fix is to install the development version of plyr:
devtools::install_github("hadley/plyr")
Fixed in commit: https://github.com/hadley/plyr/commit/3256bb524dbe04982ad54300057dd1e1bf852906