Error address (nil), cause 'memory not mapped'
nmolanog opened this issue · comments
this error was presented while runing this code:
library(animation)
library(tidyverse)
mu_seq<-c(seq(0,15,by = .5),seq(15,0,by = -.5),seq(0,-15,by = -.5),rev(seq(0,-15,by = -.5)))
sig_seq<-c(rev(seq(0.001,225,length.out = 20)),seq(0.001,225,length.out = 15))
dfp<-data.frame(mu=c(mu_seq,
rep(0,length(sig_seq))),
sig=c(rep(225,length(mu_seq)),sig_seq))
saveGIF({
ani.options(interval = 0.2, nmax = nrow(dfp))
## use a loop to create images one by one
for (i in 1:ani.options('nmax')) {
m1<-dfp[i,1]
sd1<-sqrt(dfp[i,2])
weight_lim<-c(-40, 40)
pdnorm1<-ggplot(data = data.frame(weight = weight_lim), aes(weight)) +
stat_function(fun = dnorm, n = 101, args = list(mean = m1, sd = sd1),aes(color="black")) +
ylab(expression(paste("f(x|",mu,",",sigma^2,")"))) +xlab("x") +
scale_color_identity(name = "",
breaks = c("black", "red", "blue","green"),
labels = c(substitute(paste(mu,"= ",m1,", ",sigma^2,"= ",sd1),list(m1=round(m1,1),sd1=round(sd1,3)))),
guide = "legend")+
ylim(0,.25)+
theme_bw()
print(pdnorm1)
ani.pause() ## pause for a while ('interval')
}
}, interval = 0.05, movie.name = 'dnorm.gif', ani.width = 680, ani.height = 500)
The Error output is this
Traceback:
1: magick_image_write(image, format, quality, depth, density, comment)
2: magick::image_write(anim, path = output)
3: magick.convert(files = files, output = output, loop = loop, interval = interval, dispose = dispose)
4: im.convert(img.files, output = path.expand(movie.name), convert = convert, cmd.fun = cmd.fun, clean = clean, extra.opts = extra.opts)
5: saveGIF({ ani.options(interval = 0.2, nmax = nrow(dfp)) for (i in 1:ani.options("nmax")) { m1 <- dfp[i, 1] sd1 <- sqrt(dfp[i, 2]) weight_lim <- c(-40, 40) pdnorm1 <- ggplot(data = data.frame(weight = weight_lim), aes(weight)) + stat_function(fun = dnorm, n = 101, args = list(mean = m1, sd = sd1), aes(color = "black")) + ylab(expression(paste("f(x|", mu, ",", sigma^2, ")"))) + xlab("x") + scale_color_identity(name = "", breaks = c("black", "red", "blue", "green"), labels = c(substitute(paste(mu, "= ", m1, ", ", sigma^2, "= ", sd1), list(m1 = round(m1, 1), sd1 = round(sd1, 3)))), guide = "legend") + ylim(0, 0.25) + theme_bw() print(pdnorm1) ani.pause() }}, interval = 0.05, movie.name = "dnorm.gif", ani.width = 680, ani.height = 500)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
my session info
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.0.2 (2020-06-22)
os Ubuntu 18.04.4 LTS
system x86_64, linux-gnu
ui X11
language en
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Bogota
date 2020-07-27
─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
animation * 2.6 2018-12-11 [1] CRAN (R 4.0.2)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
backports 1.1.8 2020-06-17 [1] CRAN (R 4.0.2)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.2)
broom 0.7.0 2020-07-09 [1] CRAN (R 4.0.2)
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.2)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.2)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.2)
dbplyr 1.4.4 2020-05-27 [1] CRAN (R 4.0.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2)
devtools 2.3.0 2020-04-10 [1] CRAN (R 4.0.2)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2)
dplyr * 1.0.0 2020-05-29 [1] CRAN (R 4.0.2)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
forcats * 0.5.0 2020-03-01 [1] CRAN (R 4.0.2)
fs 1.4.2 2020-06-30 [1] CRAN (R 4.0.2)
generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.2)
ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
haven 2.3.1 2020-06-01 [1] CRAN (R 4.0.2)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.2)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2)
jsonlite 1.7.0 2020-06-25 [1] CRAN (R 4.0.2)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2)
lubridate 1.7.9 2020-06-08 [1] CRAN (R 4.0.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2)
modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
processx 3.4.3 2020-07-05 [1] CRAN (R 4.0.2)
ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.2)
purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2)
Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
readr * 1.3.1 2018-12-21 [1] CRAN (R 4.0.2)
readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.2)
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.2)
reprex 0.3.0 2019-05-16 [1] CRAN (R 4.0.2)
rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2)
rvest 0.3.5 2019-11-08 [1] CRAN (R 4.0.2)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.2)
stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2)
tibble * 3.0.3 2020-07-10 [1] CRAN (R 4.0.2)
tidyr * 1.1.0 2020-05-20 [1] CRAN (R 4.0.2)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2)
tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.2)
usethis 1.6.1 2020-04-29 [1] CRAN (R 4.0.2)
vctrs 0.3.2 2020-07-15 [1] CRAN (R 4.0.2)
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.2)
The error is not present if number of iterations is reduced
rm(list=ls())
library(animation)
library(tidyverse)
mu_seq<-c(seq(0,15,by = 1.5),seq(15,0,by = -1.5),seq(0,-15,by = -1.5),rev(seq(0,-15,by = -1.5)))
sig_seq<-c(rev(seq(0.001,225,length.out = 20)),seq(0.001,225,length.out = 15))
dfp<-data.frame(mu=c(mu_seq,
rep(0,length(sig_seq))),
sig=c(rep(225,length(mu_seq)),sig_seq))
saveGIF({
ani.options(interval = 0.2, nmax = nrow(dfp))
## use a loop to create images one by one
for (i in 1:ani.options('nmax')) {
m1<-dfp[i,1]
sd1<-sqrt(dfp[i,2])
weight_lim<-c(-40, 40)
pdnorm1<-ggplot(data = data.frame(weight = weight_lim), aes(weight)) +
stat_function(fun = dnorm, n = 101, args = list(mean = m1, sd = sd1),aes(color="black")) +
ylab(expression(paste("f(x|",mu,",",sigma^2,")"))) +xlab("x") +
scale_color_identity(name = "",
breaks = c("black", "red", "blue","green"),
labels = c(substitute(paste(mu,"= ",m1,", ",sigma^2,"= ",sd1),list(m1=round(m1,3),sd1=round(sd1,3)))),
guide = "legend")+
ylim(0,.125)+
theme_bw()
print(pdnorm1)
ani.pause() ## pause for a while ('interval')
}
}, interval = 0.05, movie.name = 'dnorm.gif', ani.width = 680, ani.height = 500)
#> Output at: dnorm.gif
#> [1] TRUECreated on 2020-07-27 by the reprex package (v0.3.0)
I couldn't reproduce the bug, both scripts are running well on my CentOS server.
Maybe the memory of your machine is too limited to run the first script.
Here is my session info.
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines parallel stats4 stats graphics grDevices utils datasets
[9] methods base
other attached packages:
[1] animation_2.6 scClassify_1.0.0 monocle_2.16.0
[4] DDRTree_0.1.5 irlba_2.3.3 VGAM_1.1-3
[7] Matrix_1.2-18 plyr_1.8.6 ggpubr_0.4.0
[10] viridis_0.5.1 viridisLite_0.3.0 MAST_1.14.0
[13] ggplot2_3.3.2 cluster_2.1.0 Rtsne_0.15
[16] mclust_5.4.6 edgeR_3.30.3 limma_3.44.3
[19] dplyr_1.0.0 SingleCellExperiment_1.10.1 SummarizedExperiment_1.18.2
[22] DelayedArray_0.14.1 matrixStats_0.56.0 Biobase_2.48.0
[25] GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 IRanges_2.22.2
[28] S4Vectors_0.26.1 BiocGenerics_0.34.0
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 ggsignif_0.6.0 ellipsis_0.3.1
[4] rio_0.5.16 XVector_0.28.0 proxy_0.4-24
[7] rstudioapi_0.11 farver_2.0.3 graphlayouts_0.7.0
[10] ggrepel_0.8.2 docopt_0.7.1 polyclip_1.10-0
[13] hopach_2.48.0 broom_0.7.0 kernlab_0.9-29
[16] pheatmap_1.0.12 ggforce_0.3.2 compiler_4.0.2
[19] backports_1.1.8 tweenr_1.0.1 tools_4.0.2
[22] igraph_1.2.5 gtable_0.3.0 glue_1.4.1
[25] GenomeInfoDbData_1.2.3 RANN_2.6.1 reshape2_1.4.4
[28] Rcpp_1.0.5 carData_3.0-4 slam_0.1-47
[31] cellranger_1.1.0 vctrs_0.3.2 nlme_3.1-148
[34] ggraph_2.0.3 stringr_1.4.0 openxlsx_4.1.5
[37] lifecycle_0.2.0 statmod_1.4.34 rstatix_0.6.0
[40] zlibbioc_1.34.0 MASS_7.3-51.6 scales_1.1.1
[43] tidygraph_1.2.0 hms_0.5.3 RColorBrewer_1.1-2
[46] curl_4.3 gridExtra_2.3 segmented_1.2-0
[49] fastICA_1.2-2 stringi_1.4.6 densityClust_0.3
[52] zip_2.0.4 BiocParallel_1.22.0 rlang_0.4.7
[55] pkgconfig_2.0.3 bitops_1.0-6 qlcMatrix_0.9.7
[58] lattice_0.20-41 purrr_0.3.4 labeling_0.3
[61] tidyselect_1.1.0 magrittr_1.5 R6_2.4.1
[64] magick_2.4.0 generics_0.0.2 combinat_0.0-8
[67] pillar_1.4.6 haven_2.3.1 foreign_0.8-80
[70] withr_2.2.0 mgcv_1.8-31 proxyC_0.1.5
[73] mixtools_1.2.0 survival_3.2-3 abind_1.4-5
[76] RCurl_1.98-1.2 tibble_3.0.3 crayon_1.3.4
[79] car_3.0-8 locfit_1.5-9.4 grid_4.0.2
[82] readxl_1.3.1 minpack.lm_1.2-1 data.table_1.12.8
[85] FNN_1.1.3 forcats_0.5.0 HSMMSingleCell_1.8.0
[88] sparsesvd_0.2 digest_0.6.25 tidyr_1.1.0
[91] RcppParallel_5.0.2 munsell_0.5.0