I have a r-markdown chunk with this command line:
renv::activate(file.path(proj_root, "my_folder"))
When I run this line alone in the console or with ctrl+enter, it works perfectly.
But when I try the Run current chunk or Run all chunks above buttons, R session fails (I do not have more precise error message).
Here are my R specifs:
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.0.3 tools_4.0.3
Last time, I changed Ubuntu's system language from French to English, can it have something to do ?
Thanks for your ideas.
Related
Almost the time the app works find but the error occurs randomly, and I cannot find the error trace in the apps log(/var/log/shiny-server):
An error has occurred
The application exited unexpectedly.
read ECONNRESET
The sessionInfo() is as below:
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux buster/sid
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
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] compiler_3.4.3
And there's not much info about this issue with R shiny app, maybe it's about node.js?
Thanks for any advise in advance.
Finally I solved it by adding below code in server.r
onStop(function() {
odbcClose(conn)
})
I query data from database frequently but I did not close it.
After adding the code to close connection the error seldom occurs.
And I also adjust the app_idle_timeout to 0 in the /etc/shiny-server/shiny-server.conf
I am trying to install some packages (quite basic ones actually) for R 3.6, but I'm getting a fairly strange error message from BiocManager::install():
BiocManager::install("XML", destdir = "/my/dir/R/x86_64-pc-linux-gnu-library/3.6/")
error: could not load shared object '/my/dir/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-XML/00new/XML/libs/XML.so':
libicui18n.so.58: Could not open shared object file: No such file or directory
(Translated from french - could be approximate)
Does this mean that R can't write in /my/dir/R/x86_64-pc-linux-gnu-library/3.6/? That would be my first idea but I really don't know.
EDIT:
Here is my session info:
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=C
[4] LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=C LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.10
loaded via a namespace (and not attached):
[1] compiler_3.6.2 tools_3.6.2
This is a configuration problem, there is a fix available at github.com/r-lib/xml2/issues/219.
I have a memory issue with R.
I'm running a big and complex analysis on R installed via anaconda in my home on a cluster from my institution. I created my environment so that I can install packages without problems. While running the following error occurs:
Error: cannot allocate vector of size 26.7 Gb
I checked the memory limit by typing memory.limit() but it appears to be Inf.
This is the output of my sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /home/user/miniconda3/envs/py37/lib/libopenblasp-r0.3.7.so
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] compiler_3.6.1 tools_3.6.1
While running the tool responsible for the problem I performed ssh to a single node with 24 cores to allow the pipeline to run.
Can anyone help me to solve this problem? Thank you in advance!
Consider the following code block:
library(data.table)
library(parallel)
random_function<-function(i){
n<-1000000
big_list<-list("vector")
for (k in 1:100){
big_list[[k]]<-data.table(rnorm(n),rnorm(n))
}
rbindlist(big_list,use.names = TRUE,fill=TRUE)
}
cl<-makeCluster(8)
clusterExport(cl,"random_function")
clusterCall(cl,function()library(data.table))
parLapply(cl,1:1000,random_function)
stopCluster(cl)
When I run it on my machine, which has 36 threads suddenly all the threads are being activated (i.e., the 8 ones which I specified when creating cluster exceed 100% load).
This only happens with data.table 1.12.0. Everything works perfectly with data.table_1.11.8. Is this a bug or I am just doing something wrongly? It seems that the problem is within rbindlist, i.e., if I do not put within a function rbindlist there is no more than 100% load on my 8 threads.
Here is my session info:
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
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] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.12.0
loaded via a namespace (and not attached):
[1] compiler_3.5.2 tools_3.5.2
I try running:
install.packages("MonetDBLite")
in R. However, I get the following error:
cc1: error: -Wformat-security ignored without -Wformat [-Werror=format-security]
cc1: some warnings being treated as errors
Makevars:194: recipe for target 'build/objects/monetdblite/common/stream.o' failed
make: *** [build/objects/monetdblite/common/stream.o] Error 1
ERROR: compilation failed for package ‘MonetDBLite’
Does anyone know why this isn't working?
Output from sessionInfo() below:
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.10
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
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
LC_TELEPHONE=C 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] compiler_3.4.2 tools_3.4.2 yaml_2.1.15
This should be resolved with the latest version of MonetDBLite on CRAN, 0.5.1.