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.
Related
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.
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 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!
I try installing some required packages in R, which I just installed on a Linux machine. I am unable to install any package and get the below warning:
> install.packages("mongolite", repos="https://cran.r-project.org", lib="/opt/app/workload/deployments/installables/R-3.5.0/Rpackages")
^C
^CWarning: unable to access index for repository https://cran.r-project.org/src/contrib:
'wget' call had nonzero exit status
Warning message:
package ‘mongolite’ is not available (for R version 3.5.0)
I had to press ^+c after waiting for about 30 mins.
The same is the case with 'curl', but without the wait of 30 mins.
The following is the output of sessionInfo():
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.4 (Maipo)
Matrix products: default
BLAS: /.../R-3.5.0/lib/libRblas.so
LAPACK: /.../R-3.5.0/lib/libRlapack.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_3.5.0 tools_3.5.0
>
I am unable to understand what is blocking the packages to be installed. Please help.
Thank you
I'd like to install this Package from bitbucket: https://bitbucket.org/mkuhn/parallelrandomforest/
But this is what happends if i run install_bitbucket
> devtools::install_bitbucket("mkuhn/parallelrandomforest")
Downloading bitbucket repo mkuhn/parallelrandomforest#master
Error in download(dest, src, auth) : client error: (404) Not Found
If i run the command from ?install_bitbucket namely install_bitbucket("dannavarro/lsr-package") it works perfectly.
Any ideas
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] RCurl_1.95-4.5 bitops_1.0-6 devtools_1.7.0 httr_0.6.1 stringr_0.6.2 tools_3.1.2
Usually the master branch should be called master, but they managed to call it default.
devtools::install_bitbucket("mkuhn/parallelrandomforest#default")