I am getting the following error every time I run a Cox model using the survival package in R. This error arose within the last few days. To illustrate the error, I am using a standard example command which is given at https://stat.ethz.ch/R-manual/R-devel/library/survival/html/coxph.html:
# Fit a stratified model, clustered on patients
library(survival)
bladder1 <- bladder[bladder$enum < 5, ]
coxph(Surv(stop, event) ~ (rx + size + number) * strata(enum) +
cluster(id), bladder1)
The error I get is as follows:
Error in fitter(X, Y, strats, offset, init, control, weights = weights, :
object 'Ccoxmart' not found
I am using latest version of R [3.4.0 (2017-04-21) -- "You Stupid Darkness"].
I have tried to consult the survival package manual for R and researched on the internet. I am grateful for any resource or solution you may recommend.
I can confirm this error. It's definitely something to do with the update from R 3.3.3 (Another Canoe) -> R 3.4.0 (You Stupid Darkness). All unit tests in my system working correctly on Friday, broken Monday.
In addition, I'm also having an issue with "Ccoxph_wtest" not being found. Must be a similar issue.
I'll start debugging later today and let you know what I find, but for now if you have to get back up and running, I'd suggest reverting to R v3.3.3 (Another Canoe). I have rerun all my unit tests using v3.3.3 and all is fine.
Here is the sessionInfo():
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
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 base
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
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 base
loaded via a namespace (and not attached):
[1] compiler_3.4.0
My solution was to re-install the survival package. Just install it right on top of the original. install.packages("survival").
You have to re-install packages that use C or Fortran in R 3.4.0:
update.packages(checkBuild=TRUE)
See this post
Packages which register native routines for .C or .Fortran need
to be re-installed for this version (unless installed with
R-devel SVN revision r72375 or later)
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 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 recently installed rSymPy to perform some symbolic calculations in R. This step also installed some dependencies (“rJava”, “rjson” and “rJython”). After the installation was complete, I loaded the library and ran a very simple command which gave me an error:
> library("rSymPy")
Loading required package: rJython
Loading required package: rJava
Loading required package: rjson
> x <- Var("x")
Error in .jcheck() : No running JVM detected. Maybe .jinit() would help.
Here is my sessionInfo(), just in case you need it:
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)
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
other attached packages:
[1] rSymPy_0.2-1.1 rJython_0.0-4 rjson_0.2.15 rJava_0.9-8
loaded via a namespace (and not attached):
[1] tools_3.2.2 tcltk_3.2.2
I have tried to install different versions of required packages, but I always get this error. I would really appreciate any help.
Thanks,
Aashish
Thanks to Gabor Grothendieck (developer of rSymPy) for pointing out that sometimes one needs to manually initialize JVM. One can simply use "sympyStart()" at the beginning of the code, and that fixes the error.
I am updating a package qdap that had a single note on CRAN in its previous build, which was resolved.
In the qdap development version, under R 2.15.3, using --as-cran and --resave-data=best, I get the following note:
* checking R code for possible problems ... NOTE
Segmentation fault
Why is this segfault occurring (I'm somewhat new to Linux)? How can I find it? I googled this for sometime but I couldn't figure out what the problem is. I gather there's some sort of problem in my code but...
On Windows I get no notes.
I can provide more info if needed (though the GitHub repo is available).
Session Info:
R version 2.15.3 (2013-03-01)
Platform: i686-pc-linux-gnu (32-bit)
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=C LC_NAME=C LC_ADDRESS=C
[10] 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] pacman_0.2.0 XML_3.9-4
loaded via a namespace (and not attached):
[1] tools_2.15.3