Hello Everyone!
I'm using R studio server on an Arch Linux server.
My R base updated from 4.05 to 4.11 automatically by mistake, and now Rstudio server is having a lot of crashes (sometimes I can't debugg where it happened).
But I got one line of code which causes it to crash, but not on R base.
The code is:
wiki pathways
library(magrittr)
library(clusterProfiler)
wpgmtfile <- system.file("extdata/wikipathways-20180810-gmt-Homo_sapiens.gmt", package="clusterProfiler")
wp2gene <- read.gmt(wpgmtfile)
wp2gene <- wp2gene %>% tidyr::separate(term, c("name","version","wpid","org"), "%")
wpid2gene <- wp2gene %>% dplyr::select(wpid, gene) #TERM2GENE
wpid2name <- wp2gene %>% dplyr::select(wpid, name) #TERM2NAME#wikipathway
ewp <- enricher(resultados_deseq2, TERM2GENE = wpid2gene, TERM2NAME = wpid2name, pvalueCutoff = 0.3)
head(ewp)p1 <- dotplot(ewp, showCategory=10, orderBy="GeneRatio") + ggtitle("Anytitle")
Where resultados_deseq2 is a named ordered vector, for example:
124404 285613 64978 4161 56245 124857 7547 440387 3848 3589 64446 121599
8.481298 8.407554 8.238106 8.055501 7.963225 7.931862 7.863321 7.805318 7.787185 7.696609 7.471376 7.352266
Graphing p1 gets on forever, when I click "stop", it crashes immediately
Update:
I've observed that dev.off() consistently gives an error on R studio but not on R base. Leaving the plot processing also crashes R:
dev.off()
Error in dev.off() : cannot shut down device 1 (the null device)
sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux
Matrix products: default
BLAS: /usr/lib/libblas.so.3.10.0
LAPACK: /usr/lib/liblapack.so.3.10.0
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] tidyr_1.1.3 fansi_0.4.2 assertthat_0.2.1
[4] utf8_1.2.1 crayon_1.4.1 dplyr_1.0.5
[7] R6_2.5.0 DBI_1.1.1 lifecycle_1.0.0
[10] magrittr_2.0.1 pillar_1.5.1 rlang_0.4.11
[13] vctrs_0.3.6 generics_0.1.0 ellipsis_0.3.1
[16] tools_4.1.1 glue_1.4.2 purrr_0.3.4
[19] compiler_4.1.1 pkgconfig_2.0.3 BiocManager_1.30.10
[22] tidyselect_1.1.0 tibble_3.1.0
RStudio.Version()
$citation
To cite RStudio in publications use:
RStudio Team (2021). RStudio: Integrated Development Environment for
R. RStudio, PBC, Boston, MA URL http://www.rstudio.com/.
A BibTeX entry for LaTeX users is
@Manual{,
title = {RStudio: Integrated Development Environment for R},
author = {{RStudio Team}},
organization = {RStudio, PBC},
address = {Boston, MA},
year = {2021},
url = {http://www.rstudio.com/},
}
$mode
[1] "server"
$version
[1] ‘1.4.1106’
$release_name
[1] "Tiger Daylily"