I am installing opencpu on a new windows 10 box. It already runs on two other windows machines.
The library is found but opencpu is not recognized as an object, so the server does not start
> library(opencpu)
Loading config from C:/Users/jake_000/Documents/R/win-library/3.3/opencpu/config/defaults.conf
Loading config from C:\Users\jake_000\AppData\Local\opencpu\opencpu/user.conf
Welcome to OpenCPU!
> opencpu$start(9831)
Error: object 'opencpu' not found
Can anyone suggest what is going wrong here? Hopefully, this is basic human error, but I am at a loss.
It seems Jeroen has recently changed from using opencpu$start() to ocpu_start_server(). From the readme:
To start the single-user development server in R:
library(opencpu)
ocpu_start_server()
Or to start an App:
ocpu_start_app("rwebapps/stocks")
As to why you see different behavior between servers, my guess is you (or someone) did a devtools::install_github("opencpu/opencpu") more recently on one server than the other.
Related
I want to set up rstudio-server on an iMac with support for multiple users and remote login. I followed the steps in the INSTALL tutorial: I built the source, set up the configuration files and the launchd daemon. At first, it works fine, but after some time, I get these warnings/errors when I plot:
2022-06-09 08:02:29.438 rsession[3050:139329] XType: failed to connect - Error Domain=NSCocoaErrorDomain Code=4099 "The connection to service named com.apple.fonts was invalidated: failed at lookup with error 3 - No such process." UserInfo={NSDebugDescription=The connection to service named com.apple.fonts was invalidated: failed at lookup with error 3 - No such process.}
2022-06-09 08:02:29.438 rsession[3050:139329] Font server protocol version mismatch (expected:5 got:0), falling back to local fonts
2022-06-09 08:02:29.438 rsession[3050:139329] XType: unable to make a connection to the font daemon!
2022-06-09 08:02:29.438 rsession[3050:139329] XType: XTFontStaticRegistry is enabled as fontd is not available.
Then I can't plot any more unless I restart R and re-run my code. Do you know what could be the issue? I could not get any help when opening an issue on the rstudio-server github since MacOS is not officially supported.
I was also looking at running rstudio-server via docker, but I couldn't find a good way to map the user namespace from macOS to the container.
Any help or suggestion would be greatly appreciated!
EDIT: It seems I was able to solve the issue by launching the fontd daemon with:
sudo launchctl load -w /System/Library/LaunchAgents/com.apple.fontd.useragent.plist
This seems like an issue with the MacOS font daemon, not with RStudio itself.
Someone reported a similar issue on PhantomJS. Rebooting resolved it for them.
This answer reported the same error for a different build, and they were able to resolve it by installing the correct "Apple Worldwide Developer Relations Certification Authority" in Keychain:
The one I had had an expiration date of February 2023. I deleted that one and went here, downloaded the one called "Worldwide Developer Relations - G3 (Expiring 02/20/2030 00:00:00 UTC)", then retried the build and it worked.
I am trying to run jupyterhub on an Ubuntu 20.04 LTS server. My idea is to run python/jupyterhub in a conda virtual environment as a system service. As I want to be able to limit the resources available to individual users I installed the systemdspawner.
After installing everything and starting the jupyterhub service I can login through my web browser. However, when trying to start the server the spawner stucks and after a while I get an error message saying "Spawn failed: Timeout"
in journalctl I can see the following messages:
User logged in: me 302 POST /hub/login?next= -> /hub/spawn (me#::ffff:[my IP address]) 59.42ms
Adding role server to token: <APIToken('93c8...', user='me', client_id='jupyterhub')
Creating oauth client jupyterhub-user-me
pam_loginuid(login:session): Error writing /proc/self/loginuid: Operation not permitted
pam_loginuid(login:session): set_loginuid failed
pam_unix(login:session): session opened for user me by (uid=0)
Failed to open PAM session for me: [PAM Error 14] Cannot make/remove an entry for the specified session
Disabling PAM sessions from now on. user:me
Unit jupyter-me-singleuser in a failed state. Resetting state.
Disclaimer: My Jupyter/Python installation is replacing an former installation that was setup by someone else and got messed up a bit during time. I tried to remove everything related and start with a clean installation from scratch. However, as I had very little documentation about the old setup there is a certain risk that there might be some left-overs of the previous installation that may cause trouble.
Any ideas?
Solved it out myself. In the end the PAM related messages seem to be non-critical and were not related to the timeout at all. Instead I found a mistake in /etc/systemd/system/jupyterhub.service, where the PATH variable was not including the bin directory of my miniconda installation.
I've been trying to install and run keras in RStudio (Windows) in vain.
i installed keras package using normal package "keras"
(didn't use github)
I've installed latest python (3.6) and Anaconda.
then i use
> library(keras)
> install.keras()
and i get this error:
Creating r-tensorflow conda environment for TensorFlow installation...
Fetching package metadata ... CondaHTTPError: HTTP 000 CONNECTION
FAILED for url
https://repo.continuum.io/pkgs/main/win-64/repodata.json.bz2
Elapsed: -
An HTTP error occurred when trying to retrieve this URL. HTTP errors
are often intermittent, and a simple retry will get you on your way.
ConnectTimeout(MaxRetryError("HTTPSConnectionPool(host='repo.continuum.io',
port=443): Max retries exceeded with url:
/pkgs/main/win-64/repodata.json.bz2 (Caused by
ConnectTimeoutError(, 'Connection to repo.continuum.io timed out.
(connect timeout=9.15)'))",),)
Error: Error 1 occurred creating conda environment r-tensorflow In
addition: Warning message: running command
'"C:\PROGRA~3\ANACON~1\Scripts\conda.exe" "create" "--yes" "--name"
"r-tensorflow" "python=3.6"' had status 1
I've looked up everywhere on the web and can't figure out how to install keras and tensorflow properly. Using latest version of R (3.4.2)
Every method fails somewhere.
just to add to misery, i've also tried:
> devtools::install_github("rstudio/keras")
and i get this error:
Installation failed: Timeout was reached: Connection timed out after
10015 milliseconds
I am not behind any authenticated proxies. So, after multiple failure, i just downloaded the zip file from github and manually installed it using the zip file.
i also tried install.packages("keras") and that didn't give me any error either.
when i call the library i don't get any errors (as shown above)
UPDATE: I was able to install and use the package very easily on another computer that doesn't have python/anaconda installed on it already.
UPDATE 2: my proxy does not need authentication and there is no https_proxy either.
OK,, FINALLY found a solution.
Turns out RStudio uses a lot of default proxy settings, so i needed to change all that and set up my own proxy settings.
First step:
Rstudio --> Tools --> Global Options --> packages --> uncheck both "Use secure download method for HTTP" and "Use Internet Explorer librayr/proxy for HTTP"
Second step, in RStudio type:
> file.edit('./.Renviron')
Either an empty file or some file with already existing proxy settings will open. (Mine was empty). Then I included the following two:
http_proxy=http://myusename:password#proxy.server.com:port/
https_proxy=http://myusename:password#proxy.server.com:port/
(a few notes: I didn't have a https_proxy setting but I still needed to use the http_proxy details for my https_proxy setting. This was one of the culprits for my issue. Also, I needed to include the username:password even though my proxy doesn't need secure authentication. Same thing goes with the port. Port number had to be included, otherwise it wouldn't work.
Step 3:
Saved the new changes in .Renviron file and restarted RStudio.
I checked my proxy settings in RStudio after restart by typing:
> Sys.getenv("http_proxy")
> Sys.getenv("https_proxy")
The first few times i did this i realised that the proxy settings were not being changed in RStudio because i was editing the wrong .Renviron file. So, it's best to use file.edit('~/.Renviron') in step 2 to make sure it's the right file.
After all this, when i ran install.keras(), it installed successfully, including installing Tensorflow. Again, initially i had skipped step 1 so keras started being installed but it failed at installing tensorflow.
It was only going through all the steps that i was able to install both keras and tensorflow successfully over a proxy. Hope this helps.
Uninstalling Anaconda3 and installing Anaconda2 (i.e. Python 2.7) did the trick for me: https://www.anaconda.com/download/
I already installed OpenCPU on a Ubuntu Server - Ubuntu 14.04.1 LTS (GNU/Linux 3.13.0-32-generic x86_64) - and everything worked perfectly without any problems.
Here I want to say that I really like this API and I am very thankful for all the effort from the people (I think mostly Jeroen Ooms) working on it.
Now I installed it again, but on another Server hosted at another provider. It is also a Ubuntu Server - Ubuntu 14.04.1 LTS (GNU/Linux 3.13.0-042stab093.4 x86_64) - and therefore I expected it to work as smoothly as before.
But now I have a problem. After the installation and starting the service, I wanted to check through my browser if everything is OK.
So I just opened http://xxx.xxx.xxx.xxx/ocpu like it worked on my other server. This time my browser doesn't show the OpenCPU API Explorer, but the following message:
Failed to set rlimit. ENOSYS
In call:
rlimit_wrapper("rlimit_as", hardlim, softlim, pid, verbose)
The server only has 1GB of physical memory, so I thought changing the "rlimit.as" to 1e9 instead of the standrd 2e9 would fix the problem (I also tried 750000000 and 500000000), but nothing helped (of course I restarted the service opencpu again after each change).
I also think that this is not the problem, because I guess the server would use virtual memory when an operation uses more than one GB.
I think the problem has to do with RAppArmor. So I tried to disable it and restart opencpu, but the problem didn't vanish:
$ sudo aa-disable usr.bin.r
Disabling /etc/apparmor.d/usr.bin.r.
Traceback (most recent call last):
File "/usr/sbin/aa-disable", line 30, in
tool.cmd_disable()
File "/usr/lib/python3/dist-packages/apparmor/tools.py", line 148, in cmd_disable
raise apparmor.AppArmorException(cmd_info[1])
apparmor.common.AppArmorException: 'Warning: unable to find a suitable fs in /proc/mounts, is it mounted?\nUse --subdomainfs to override.\n'
So does anyone know what the problem here could be or has any suggestions where to look for a solution (I tried to google already, but didn't find anything helpful)?
I don't think anything of the following is the cause of the problem, but since I'm not sure, I add these warnings anyways:
The only strange thing I encountered during the OpenCPU installation was this message (which appeared 4 times):
iptables v1.4.21: can't initialize iptables table `nat': Table does not exist (do you need to insmod?)
Perhaps iptables or your kernel needs to be upgraded.
But afterwards it said:
* Reloading nginx configuration nginx [ OK ]
OK
Setting up opencpu (1.4.4-trusty15) ...
Also when I tried to install RAppArmor separately, I got the following warning:
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = (unset)
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
locale: Cannot set LC_CTYPE to default locale: No such file or directory
locale: Cannot set LC_ALL to default locale: No such file or directory
Selecting previously unselected package r-cran-rapparmor.
And also this one:
Warning: unable to find a suitable fs in /proc/mounts, is it mounted?\nUse --subdomainfs to override.\n
Thanks in advance!
It looks like your new hosting provider uses some sort of virtualization system that has a shared kernel which limits all kind of linux functionality, including rlimit, iptables and probably apparmor. Is an actual cloud host, or something you setup yourself?
It would be helpful to debug this in R (outside of opencpu). On your server, start R in the console and type:
library(RAppArmor, lib="/usr/lib/opencpu/library")
rlimit_as(1e9)
rlimit_fsize(1e9)
rlimit_cpu(1e5)
I'm trying to deploy an ASP MVC project developed on Mono/OSX on my Linux server using mono 2.10.8.1 w/ fastcgi-mono-server4
The webapp always starts fine, but then I start getting random CS0006 compilation errors for various URIs, and once they break, they remain broken until I restart the server application.
An example error:
Server Error in '/' Application
Compilation Error
Description: Error compiling a resource required to service this request. Review your source file and modify it to fix this error.
Compiler Error Message: CS0006: Metadata file `/tmp/root-temp-aspnet-0/ed68754/App_global.asax_40e709ea.dll' could not be found
~/Views/Order/Download.aspx
There is a related thread from January, but both the question and the answer seem to be mod_mono specific and rather hand-wavy. Anyone have any advice on what to try to debug/solve/work around this issue? It's getting very frustrating. In particular, is there any "unsupported" workaround where I can copy something from my Windows Server machines to use an MS implementation instead of the buggy mono one?
(I've filed a bug report too.)
Since the errors appear to be issue with the Mono JIT attempting to compile temporary files that don't exist, I spent a few days trying different methods of working around this issue (vs solving it). One solution that worked was using aspnet_compiler on Windows to create a binary version that could be copied and run as-is on Linux/Mono (as the latest versions of Mono now support precompiled ASP.NET applications).
However, I was looking for a native Linux solution, and I don't want to have to compile and sync binaries (vs syncing a GIT repo of code) to the server, so I was looking for another solution when I came across Mono ahead of time compilation, which is pretty much the equivalent of ngen.exe on Windows.
While it doesn't precompile everything, it seems to have done the trick. For me, this deployment script does the job without any runtime build failures:
xbuild SystemDiscs.sln
mono --aot -O=all SystemDiscs/bin/SystemDiscs*.dll
killall -9 mono
nohup fastcgi-mono-server4 /socket=tcp:127.0.0.1:8000 /applications=/:/var/asp/S
ystemDiscs/SystemDiscs/ > /var/log/systemdiscs.log &
Where SystemDiscs*.dll is the output of the solution compiled with xbuild in the first step. I don't think this precompiles the ASP pages (and --aot=full isn't supported on x86, as far as I can tell), but somehow it did the job. I was waiting to see whether or not that was just a fluke, but it's been going fine with maybe a dozen commits/deploys since I asked this ten days ago, so I reckon its safe to say it works.
I had a similiar problem:
Compilation Error
Description: Error compiling a resource required to service this request. Review your source file and modify it to fix this error.
Compiler Error Message: CS0006: Metadata file `/tmp/<DOMAIN/>/<username/>-temp-aspnet-0/5ed74d00/App_global.asax_34cccb99.dll' could not be found
/Default.aspx
But it didn't have anything to do with precompiling but with a backslash in my username. I use likewise-open to login to a windows domain, so my username is <DOMAIN/>\<username/> while my home-directory is without a backslash: /home/likewise-open/<DOMAIN/>/<username/>. This difference or just the backslash itself caused mono not finding the compiled global.asax in the temp directory. If you look closely to the detailed output you see that the backslash \ in the out parameter is changed to a forward slash /:
dmcs /target:library /lib:"/home/likewise-open/<DOMAIN/>/<username/>/Documents/test9999/test9999/bin" /debug+ /optimize- /warn:4 /out:"/tmp/<DOMAIN/>\<username/>-temp-aspnet-0/5ed74d00/App_Web_17ca7bdd.dll" /r:"/usr/lib/mono/4.0/mscorlib.dll" /r:"/usr/lib/mono/gac/Microsoft.CSharp/4.0.0.0__b03f5f7f11d50a3a/Microsoft.CSharp.dll" /r:"/usr/lib/mono/gac/System/4.0.0.0__b77a5c561934e089/System.dll" /r:"/usr/lib/mono/gac/System.Configuration/4.0.0.0__b03f5f7f11d50a3a/System.Configuration.dll" /r:"/usr/lib/mono/gac/System.Web/4.0.0.0__b03f5f7f11d50a3a/System.Web.dll" /r:"/usr/lib/mono/gac/System.Data/4.0.0.0__b77a5c561934e089/System.Data.dll" /r:"/usr/lib/mono/gac/System.Web.Services/4.0.0.0__b03f5f7f11d50a3a/System.Web.Services.dll" /r:"/usr/lib/mono/gac/System.Xml/4.0.0.0__b77a5c561934e089/System.Xml.dll" /r:"/usr/lib/mono/gac/System.Drawing/4.0.0.0__b03f5f7f11d50a3a/System.Drawing.dll" /r:"/usr/lib/mono/gac/System.EnterpriseServices/4.0.0.0__b03f5f7f11d50a3a/System.EnterpriseServices.dll" /r:"/usr/lib/mono/gac/System.IdentityModel/4.0.0.0__b77a5c561934e089/System.IdentityModel.dll" /r:"/usr/lib/mono/gac/System.Runtime.Serialization/4.0.0.0__b77a5c561934e089/System.Runtime.Serialization.dll" /r:"/usr/lib/mono/gac/System.Xaml/4.0.0.0__b77a5c561934e089/System.Xaml.dll" /r:"/usr/lib/mono/gac/System.ServiceModel/4.0.0.0__b77a5c561934e089/System.ServiceModel.dll" /r:"/usr/lib/mono/gac/System.ServiceModel.Web/4.0.0.0__31bf3856ad364e35/System.ServiceModel.Web.dll" /r:"/usr/lib/mono/gac/System.Core/4.0.0.0__b77a5c561934e089/System.Core.dll" /r:"/usr/lib/mono/gac/System.Web.Extensions/4.0.0.0__31bf3856ad364e35/System.Web.Extensions.dll" /r:"/usr/lib/mono/gac/System.Data.DataSetExtensions/4.0.0.0__b77a5c561934e089/System.Data.DataSetExtensions.dll" /r:"/usr/lib/mono/gac/System.Xml.Linq/4.0.0.0__b77a5c561934e089/System.Xml.Linq.dll" /r:"/usr/lib/mono/gac/System.ComponentModel.DataAnnotations/4.0.0.0__31bf3856ad364e35/System.ComponentModel.DataAnnotations.dll" /r:"/usr/lib/mono/gac/System.Web.DynamicData/4.0.0.0__31bf3856ad364e35/System.Web.DynamicData.dll" /r:"/usr/lib/mono/gac/System.Data.Linq/4.0.0.0__b77a5c561934e089/System.Data.Linq.dll" /r:"/usr/lib/mono/gac/System.Web.ApplicationServices/4.0.0.0__31bf3856ad364e35/System.Web.ApplicationServices.dll" /r:"/home/likewise-open/<DOMAIN/>/<username/>/Documents/test9999/test9999/bin/test9999.dll" /r:"/tmp/<domain/>/<username/>-temp-aspnet-0/5ed74d00/App_global.asax_34cccb99.dll" /nowarn:0169 /d:DEBUG -- "/tmp/<DOMAIN/>\<username/>-temp-aspnet-0/5ed74d00/App_Web_17ca7bdd_0.cs"
So:
/out:"/tmp/<DOMAIN/>\<username/>-temp-aspnet-0/5ed74d00/App_Web_17ca7bdd.dll
becomes
/tmp/<DOMAIN/>/<username/>-temp-aspnet-0/5ed74d00/App_global.asax_34cccb99.dll
If I copy the directory 5ed74d00 to /tmp/<DOMAIN/>/<username/>-temp-aspnet-0/ the application works as expected.
It took me almost 2 days to see this, so hopefully I can help others with this answer.