A few days ago, I was having an error running models in R using 'brms', which said that my posterior samples didn't exist. Upon reading further, these links (1, 2, 3, 4) led me to think it was an rstan problem playing with my macOS (Catalina 10.15.6).
I followed their instructions, namely:
-updated packages Rcpp, rstan, arm, and brms
-followed these workaround instructions to alter the 'parallel' settings for stan: https://github.com/rstudio/rstudio/issues/6692
-updated R and RStudio, since this problem was supposedly fixed a few months ago with R 4.0
-updated XCode 11, Quartz 11, GNU Fortran 8.2
-updated latest macOS Catalina bug fixes
-ran sudo rm -rf [path to R] to uninstall R
-tried to do a thorough uninstall of all R and RStudio files, including deleting files in my Library/Frameworks folder, any .plist files in Library/Preferences, and any .Rprofile, .Rscript, .Rapp, .Rhistory, or .Renvirons files
-reinstalled R and RStudio after restart
Now, instead of having a "blank slate" to start from, I am experiencing some super weird behaviors. First, RStudio opens on a completely white blank screen and never loads. Second, when I try to open R directly either via terminal or with R Console, I get stuck in a loop for nearly 20 min that says:
Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, :
file descriptor is too large for select()
Calls: <Anonymous> ... makePSOCKcluster -> newPSOCKnode -> socketConnection
Execution halted
Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, :
cannot open the connection
Calls: <Anonymous> ... makePSOCKcluster -> newPSOCKnode -> socketConnection
In addition: Warning message:
In socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, :
port 11537 cannot be opened
Execution halted
At the very end, when it finally stops looping forever, it says:
/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R: cannot make pipe for command substitution: Too many open files
ERROR: option '-e' requires a non-empty argument
rm: /var/folders/54/km__8z8x78x8_ct1pw8w8bbh0000gn/T//RtmpVORdTy: Too many open files
I can't access a console or enter anything in R to try to troubleshoot. Moreover, it causes a massive slowdown to my computer and Activity Monitor shows more than 150 'R' processes running, which don't go away after quitting R, only after using 'killall R' in Terminal.
However, someone in IT helped me determine that it's something in my Mac user library or preferences, because we created a brand new user on my machine, installed R and RStudio, and had no problems loading them.
I am just a psychology grad student, so I really don't understand the back end that makes R work and I am totally baffled by these symptoms.
I suspect that these links (5, 6, 7) might help, but I don't know how to execute the solutions because right now I can't enter or run anything in R without triggering that endless loop of 'Execution halted.'
I could really use a hand, thanks!
Related
I am running Red Hat Enterprise Linux (RHEL) 8.5 with Linux kernel 4.18 and Gnome 3.32.2. In this system, I've got R 4.1.2 compiled with the tool asdf with shared libraries enabled. On top of that, I installed RStudio 2021.09.01-372 from an RPM from the official RStudio website.
When I start Rstudio, the first line of output after the usual R startup is an error:
Error in tools::startDynamicHelp() : internet routines cannot be loaded
I am unable to figure out what's causing this error, and with it I can't run things like refresh CRAN or update packages. But if I start a pure R session from the terminal (instead of Rstudio) this error does not occur.
Some things I tried:
Install the krb5 and libssh2 packages on my host system: Didn't help.
Starting a "pure" R session (both with and without the --vanilla argument) from the Terminal tab within Rstudio also gives this error. If I try to run update.packages() from this session, it pops up a window to select a CRAN mirror then fails with the following:
Warning: failed to download mirrors file (internet routines cannot be loaded); using local file '/home/[my username]/.asdf/installs/R/4.1.2/lib64/R/doc/CRAN_mirrors.csv'
Warning: unable to access index for repository https://cloud.r-project.org/src/contrib:
internet routines cannot be loaded
Warning message:
In download.file(url, destfile = f, quiet = TRUE) :
unable to load shared object '/home/penyuan/.asdf/installs/R/4.1.2/lib64/R/modules//internet.so':
/lib64/libssh.so.4: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b
But like I said, the strange thing is if I start an R session outside of Rstudio, these errors don't happen.
Within RStudio, the only workaround I can find is to run this command upon startup (suggested in this thread):
options(download.file.method="wget")
Once this is done, everything else seems to work, such as package updates.
However, I don't want to manually do this every time I start RStudio. So I tried to put it into ~/.Rprofile including a test print() as follows:
print("This is `~/.Rprofile`")
options(download.file.method="wget")
When I open RStudio, I can see the output from the print() call, but the options() command is not run because the original error shows up again. I still have to manually enter options(download.file.method="wget") every time.
I also tried to fold everything into a .First function in ~/.Rprofile as follows:
.First <- function() {
options(download.file.method="wget")
print("This is the `.First` function in `~/.Rprofile`")
}
Unfortunately, same result as before: print()'s output is seen, but options() is not run.
I also made sure that my ~/.Rprofile includes a trailing newline as discussed here. But this didn't help.
The above are the steps I've tried so far.
Why does this error only occur when running RStudio or a terminal within Rstudio? Why doesn't it happen if I start R from a terminal outside of Rstudio?
Is there a way to solve the problem so that the error doesn't happen in the first place? If it can't be solved, how do I set up my ~/.Rprofile so that options(download.file.method="wget") will be run?
Thank you.
I have recently installed R ver. 2.11.1 and RStudio ver. 1.0.143 and tcl/tk ver. 8.5.9 on my Mac (Mac OS 10.7).
When RStudio is launched I get the following "warning" message (in RED font):
"WARNING: You are configured to use the CRAN mirror at https://cran.rstudio.com/. This mirror supports secure (HTTPS) downloads however your system is unable to communicate securely with the server (possibly due to out of date certificate files on your system). Falling back to using insecure URL for this mirror."
When I try to install a package using the GUI Install -> Package , I get the following Error message:
a. Error in read.dcf(file = tmpf) :
Line starting '
When I try to use the Console (by double-clicking on the previous command executed (in the "History" pane) and hitting Enter [the Console shows the command "install.packages("")], the following error message is received:
a. Error in install.packages : Line starting '
If the same command is manually entered (i.e. install.packages(""), I get an error as follows:
a. R code execution error
b. Error in normalizePath(dir, winslash = "/", mustWork = TRUE) :
unused argument(s) (winslash = "/", mustWork = TRUE)
As suggested in the opening "warning" message (No. 1 above), I have tried the following (after each action rebooted system and tried RStudio):
A. Check if the date and time is set properly. Found correct. Also check box "Set date time automatically" is checked TRUE.
B. Checked firewall setting. Deleted (actually renamed) file "com.apple.alf.plist". On rebooting and starting internet, found that a new file with the same name is created by the system (which I assume is the correct behavior).
C. Created / rebuilt network connections (with a new location name).
D.Cleared certificate management database caches with command (sudo rm /var/db/crls/*cache.db).
E. Turned off OCSP and CRL services in keychain access utility preferences.
F. Checked root certificates in system roots keychain and everything was found ok (apparently so as I did not find any item withthe Blue Plus sign).
Even after the above mentioned steps the situation remains the same as at step 1.
Kindly suggest a way around or possible reason so that I may explore further.
Thanks
Kavi
I've tried to run command in R 2.15.2
rsaga.geoprocessor(lib="ta_channels", module=0, param=list(ELEVATION="DEMflt.sgrd", CHNLNTWRK=paste("channels", i, ".sgrd", sep=""), CHNLROUTE="channel_route.sgrd", SHAPES="channels.shp", INIT_GRID="DEMflt.sgrd", DIV_CELLS=3, MINLEN=40), show.output.on.console=FALSE)
and I'm constantly getting this warning:
Warning message:
running command '"C:/Users/Nenad/Documents/R/win-library/2.15/RSAGA/SAGA-GIS/saga_cmd.exe" ta_preprocessor 2 -DEM "DEM1.sgrd" -RESULT "DEMflt.sgrd" -MINSLOPE "0.05"' had status 1
I use windows 8 and also tried to ran R as admin.
Any idea what is the problem? Thanks!
Idk how actual it is, but I've been struggling with "had status 1" warning a lot. Especially it got really annoying when I tried to use seasonal package to conduct the X13-ARIMA-SEATS seasonal decomposition of time series. The seasonal::seas command just didn't work, because in the code of this command there is a stop condition when running a certain stuff with cmd.exe returns non-zero status. While, as it was mentioned before, 'status 1' doesn't prevent command execution, in case of seasonal package it does.
The problem in my case was caused by some mistake in Windows Registry (Win 10), that in turn caused warning System cannot find the path specified when launching CMD.exe or PowerShell, which caused warning inside R as well. So to fix it:
Press Win+R -> regedit
In HKEY_CURRENT_USER\SOFTWARE\Microsoft\Command Processor folder clean the value of Autorun record (it should be empty)
Do the same for Autorun in HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Command Processor
After these actions annoying warning with "has status 1" has gone and seasonal::seas started to work perfectly.
Hope it will be usefull for somebody.
Running system commands from R can be really tricky. In my experience, as long as the exit code is not 127 then the command did run, and you could use the intern=TRUE switch in the system command for a more verbose output. If you run the command again, the warning message could contain a errmsg attribute as well for some more info. hth
I'm running into an issue when building the following package: https://github.com/yoni/rbundler
My test attempts to run rbundler's bundle command on a trivial package which has a single dependency. The test passes on my OSX machine, but fails on my x86_64-redhat-linux-gnu Jenkins server. Both machines are running R 2.15.1 with devtools 0.7.1, which includes this bug fix.
The full test output can be found in this gist.
Here's a short summary of error I'm seeing:
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
Calls: local ... eval.parent -> eval -> eval -> eval -> eval -> source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file 'startup.Rs': No such file or directory
Execution halted
The background for this is that I'm trying to build a dependency management system for R. The idea is that an R project should be able to run without using system-wide or user-wide libraries. Rather, the R project will have it's own library installed under it's root directory.
For my previous Stack Overflow question related to Dependency Management in R, see Dependency management in R
In my case this issue was caused by the environment variable R_TESTS that was set to startup.Rs
When you execute another R process from within your tests (in my case it was submitted via OGS qsub), the presence of this environment variable causes issues.
I can't answer your question directly, but two things you can try get more information about what is happening.
use 'env' to dump environment variables on your OSX machine and the Jenkins host
run the process through strace on Linux and dtruss on OSX to trap the system calls
strace/dtruss should reveal the places in which it is searching for startup.Rs and env output will likely give you a environment variable that differs between the system accounting for the different outcome.
I'm attempting to run a parallel job in R using snow. I've been able to run extremely similar jobs with no trouble on older versions of R and snow. R package dependencies prevent me from reverting.
What happens: My jobs terminate at the parRapply step, i.e., the first time the nodes have to do anything short of reporting Sys.info(). The error message reads:
Error in checkForRemoteErrors(val) :
3 nodes produced errors; first error: cannot open the connection
Calls: parRapply ... clusterApply -> staticClusterApply -> checkForRemoteErrors
Specs: R 2.14.0, snow 0.3-8, RedHat Enterprise Linux Client release 5.6. The snow package has been built on the correct version of R.
Details:
The following code appears to execute fine:
cl <- makeCluster(3)
clusterEvalQ(cl,library(deSolve,lib="~/R/library"))
clusterCall(cl,function() Sys.info()[c("nodename","machine")])
I'm an end-user, not a system admin, but I'm desperate for suggestions and insights into what could be going wrong.
This cryptic error appeared because an input file that's requested during program execution wasn't actually present. Each node would attempt to load this file and then fail, but this would result only in a "cannot open the connection" message.
What this means is that almost anything can cause a "connection" error. Incredibly annoying!