I have a RM Server running on a VM (Ubuntu) on top of my Win10 machine.
I have a process to read a .csv file and write its contents on a MySQL database on a MySQL Server which also runs on the same VM.
The problem is that the read file operator does not seem to be able to find the file.
Scenario1.
When I try as location-name in the read csv operator ../data/myFile.csv
and run the process on Server I am getting Failed to execute initialization process: Error executing process /apps/myApp/process/task_read_csv_to_db: The file 'java.io.FileNotFoundException: /root/../data/myFile.csv (No such file or directory)' does not exist.
Scenario2.
When I try as location-name in the read csv operator /apps/myApp/data/myFile.csv
and run the process on Server I am getting Failed to execute initialization process: Error executing process /apps/myApp/process/task_read_csv_to_db: The file 'java.io.FileNotFoundException: /apps/myApp/data/myFile.csv (No such file or directory)' does not exist.
What is the right filepath that I should give to the Read CSV operator?
Just to update with the answer. After David's suggestion, I resulted in storing the .csv file outside of the /rapidminer-server-home/data/repository since every remote repository seems to be depicted with an integer instead of its original name, making the use of the actual full path of the file not usable.
I would say, the issue is that depending on the location of the JobAgent that is executing your process, the relative path might be varying.
Is /apps/myApp/data/myFile.csv the correct path to the file? If not, I would suggest to use the absolute path to the file. Hope this helps.
Best,
David
I need to delete files from an FTP site once I have processed them in R (parsing content). However, nothing I try seems to work.
this is what ive trying, and variations of.
library(RCurl)
curlPerform(url="sftp://user:password#sftplocation/folder/", quote="DELE filename.pdf")
curlPerform(url="ftp://xxx.xxx.xxx.xxx/", quote="DELE file.txt", userpwd = "user:pass")
Error is
Error in function (type, msg, asError = TRUE) : Unknown SFTP command
When I run the following code, I get a lovely list of all the files (which is used to download them). So I know the connection is working just great, and the parsing from the downloaded files works great!
curlPerform(url="sftp://user:password#sftplocation/folder/")
Thanks,
Siobhan
To delete over sftp, use rm instead of DELE - which looks like an ftp rather than an sftp command.
Then make sure you have the full file path. This works for me:
curlPerform(
url="sftp://me#host.example.com/",
.opts=list(
ssh.public.keyfile=pub,
ssh.private.keyfile=pri),
verbose=TRUE,
quote="rm /home/me/test/test.txt")
Note I've put my credentials in some key files so I don't put the password in plain text in the code.
I'm not convinced this is the best way to do it, since I can't stop it printing the contents of the URL... There's might be an option...
I would like to use VS Code for python development. For this I need to install an extension, but searching for extensions results in an "ECONNREFUSED" error (407 when I'm using the Insiders build).
My settings.json file contains the following two lines:
"http.proxy": "http://username:password#proxyurl:port",
"http.proxyStrictSSL": false
The password does contain the # symbol, but that's escaped with %40.
I have already double-checked for any spelling mistakes, and I'm still getting the same error. I also tried leaving out either of the two lines or both, but to no avail.
Check the official documentation about proxy-server-support.
As it's written, VS Code has exactly the same proxy server support as Google Chromium, refer the chromium network-settings for more detais.
Assume the proxy uri is http://127.0.0.1:8118, use command like bellow:
code --proxy-server="http=127.0.0.1:8118;https=127.0.0.1:8118"
Or a simple trick with alias if you are in linux, put following line at the end of you ~/.bashrc or ~/.profile file.
alias code='code --proxy-server="http=127.0.0.1:8118;https=127.0.0.1:8118"'
I am uploading a file from a collection of different servers to one data server. I am using psftp and one out of 20+ servers is producing a permissions problem.
Remote working directory is /
psftp> cd Remote_Directory\
Remote directory is now /Remote_Directory/
psftp> put C:\folders\containing\file\FILE.zip
/Remote_Directory/: open for write: failure
psftp> quit
It appears like a permissions issue on the remote directory, however, why am I only getting the issue on one server? The batch is identical on all of the 20+ servers.
PUT command expects a file name at the end of the destination location.
Please try the following code
put C:\folders\containing\file\FILE.zip /Remote_Directory/FILE.zip
The path in the error message is an exact path to the remote file the psftp tried to create. See outfname in below code snippet:
req = fxp_open_send(outfname,
SSH_FXF_WRITE | SSH_FXF_CREAT | SSH_FXF_TRUNC,
&attrs);
...
printf("%s: open for write: %s\n", outfname, fxp_error());
As the path is obviously not correct (lacks file name), it seems that psftp got confused somehow. I believe it's likely due to wrong (back)slash you have used in the cd command.
Try cd Remote_Directory/.
In my case, it's a permission issue on the remote server, i.e. the account you are using to log on doesn't have the write permission for the remote folder.
I'm trying to run two things: first, I'm creating a PDF with 4x5, ending with dev.off(), and then trying to create a new graph. However, after starting the second plot, I get:
Error in gzfile(file, "wb") : cannot open the connection
In addition: Warning message:
In gzfile(file, "wb") :
cannot open compressed file '/var/folders/n9/pw_dz8d13j3gb2xgqb6rfnz00000gn/T/RtmpTfm1Ur/rs-graphics-822a1c83-b3fd-46c3-8028-4e0778f91d0c/4db4b438-ac35-403b-b791-e781baba152c.snapshot', probable reason 'No such file or directory'
Graphics error: Error in gzfile(file, "wb") : cannot open the connection
What is this error? The working directory is one I have read/write access to, and my hard drive isn't full.
Also, I'm using RStudio.
This is a bit late but for anyone coming here for help, I got this error when I was trying to write a file from RStudio and my destination file path was very long. I realized this could be a problem because when I wrote the file to another location with a shorter name and tried to copy it into my original destination, Windows gave me an error saying "File path too long". You might need to save the original file into another location with a shorter absolute path.
Maybe you should look here. At the end it says
Note:
The most common reason for failure is lack of write permission in the current directory. For save.image and for saving at the end of a session this will shown by messages like
Error in gzfile(file, "wb") : unable to open connection
In addition: Warning message:
In gzfile(file, "wb") :
cannot open compressed file '.RDataTmp',
probable reason 'Permission denied'
So rapidly, if you try getwd(), look at where is your working directory set. If you're trying to save your document in a place where it's not in your current working directory, it will throw you this error.
At the end of your error message, it says probable reason 'No such file or directory'
Graphics error: Error in gzfile(file, "wb") : cannot open the connection
My diagnosis would be simply that it's trying to save your item in the wrong place and RStudio is not able to find the right place.
This burned me so hopefully saves someone else some toil. The issue was that the classifiers loaded just fine on OS X but on the Linux deployment system they would fail with the error listed in the question. The issue was the the files on the disk had extension abc.RData but the code modelAbc <- readRDS(file="abc.Rdata"). The difference in the upper and lowercase D in the .RData vs .Rdata extension would fail on Linux. It was not very noticeable but check your extensions for case.
You may have no permission to save file in the directory.
On RStudio, get your working directory by getwd().
Then, go to the directory in linux and observe its owner by ls -l.
Now you can change the owner of the directory by chown -R username directoryname.
But you must be root.
Problem resolved by specifying full file path:
saveRDS(df,'C:\\users\\matt\\desktop\\code\\df.Rdata')
I faced this issue lately. Try turning off your anti-virus and build the package, it might help. It worked for me. Usually anti-virus blocks the permissions and you could avoid it by disabling for sometime just before building a package.
I was trying to save an RDS file to my local Dropbox folder so it syncs with my Dropbox.
I figured out I got the same error because I was trying to create a new folder and looks like saveRDS cannot create a new folder, but it can add files to existing folders. So I changed the path to add the file into an existing folder and it worked!
In my case it was Windows Defender which was preventing Rstudio to write any file on hard drive. Either you need to turn Controlled Folder Access off or add Rstudio in the exclusion list.
I also had this problem when working with RStudio and R Markdown. I was getting this error message and had an annoying number of fatal errors which closed RStudio. My issue was that I was working off a network drive and either the name was too long, as in #AHedge above or my network firewalls were giving me trouble. For the moment, I have moved my working files to my desktop and things seem to be working fine. Not sure what this means for my file management over time.
Just want to add more clarity(scenarios in my experience) to what M Beausoleil mentioned.
When you are using a shared-working-directory and trying to rewrite the RDS files which are already existing in a working-directory written by some other user, you get this error.
As some people have already quoted that deleting the existing RDS files or changing the working directory works. It's not a magic. It just works because you are writing a new RDS file and not trying to re-write the old ones.
I came into the same problem after I re-install a new version of RStudio.
The Rmarkdown file I created using old version of RStudio shows the same problem.
When I use ggplot() to draw a picture the error code are as follow:
Warning in gzfile(file, "wb") :
cannot open compressed file 'I:/Rlearning/.Rproj.user/shared/notebooks/58A1385C-PCA作图/1/2C15461A183AC56C/cco192gb0pow1_t\_rs_rdf_32004888ecb.rdf', probable reason 'No such file or directory'
Error in gzfile(file, "wb") : cannot open the connection
Solution:
Create a new Rmarkdown file
Delete all codes
Copy your old Rmarkdown code into it.
I had the same problem.For me, it was caused due to not having enough disk space on the drive where R studio was installed.Freeing up space works.
The reason for the error is that your username is Chinese.Please create new user folder with English in the user directory.For example, you could name the folder for "DavidSmith".Then, you need create three folders("AppData","Local","Temp").File directory C:\Users\DavidSmith\AppData\Local\Temp.
In the Advanced system settings which will modify the environment variables TMP and TEMP C:\Users\DavidSmith\AppData\Local\Temp.Save them.
After modification, open RStudio and try again.
Notice:TMP and TEMP are modified in the USER VARIABLE.
I just ran into this problem after changing my system locale.
Check your locale using Sys.getlocale().
Change it to appropriate one using Sys.setLocale("LC_ALL","ENG") (replace "ENG" with appropriate one)
I can't say with certainty which locale would be appropriate, but it seems to be coherent with default OS one.
Hope this helps!
I had this error because of an invalid character in the filename to be used to save the file, in my case "/" (there are many such characters that cannot be used in a filename). I removed the character and it was solved.
In my case, I received the error "Error in gzfile(file, "wb") : cannot open the connection" when trying to exit R in the Anaconda Prompt and saving workspace image. I am using Windows 10 and R-3.5.2. To fix it, I had to go to the Program Files folder, right click and the R folder, then selected Properties. Selected the Security tab, then, in the Group or user names box, selected Users, then clicked Edit. In the Permissions for Users, I checked Full control and Modify and saved the changes. Then I was able to save the workspace image.
I have another instance of this error which seems to be new (or at least not listed here or here: apparently it's not OK to save a file with the name aux.RData. I guess it's a reserved filename.
x <- rnorm(9000)
save(x, file = "aux.RData")
Error in gzfile(file, "wb") : no se puede abrir la conexión
Also: Warning message:
In gzfile(file, "wb") :
cannot open compressed file 'aux.RData', probable reason 'No such file or directory'
But when I change the filename saves with no problem:
save(x, file = "aux_file.RData")
Haven't seen this case in the other answers:
if this seems to happen all the time, and to be very persistent when it does happen, check the default directory in your file handling software connection.
In my case FileZilla was logging on to my DigitalOcean droplet as "root" and whenever I used FileZilla to create a directory it was setting write permissions to "root", whereas my RStudio on the same droplet read/wrote as "My_Name". Anytime I set something up in FZ (e.g. large imported files, renamed or copied) the permissions would switch and I'd get this error.
If this is what is causing frequent error messages it can be solved instantly with chown -R My_Name directoryname but in the longer run, if you are going to be using your file handler to define and create a lot of directories, it will pay to create a connection whose default name is the same name you use for RStudio.
In my case, when it happened first, months ago, the solution here worked.
But recently, it came back, constantly... What solved this time was to change the anti-virus. I have not just the Windows defender, but also a 2nd anti-virus, the same in both times. I ended up deinstalling it and installing another antivirus... After this, the problem did not happen again...
After several days trying to solve this same ERROR or problem in my case (Windows 10 and R), I tried to save my file(file.RData) in D disk instead of C disk (where I always was working and I have installed R) and it was fine, without problems,my file was saved in D:/Users.When I tried many times to save it in C disk, always gave me Permission denied.
save(Myfile, file="D:/Users/Myfile.RData")
I encountered this same issue when trying to save an Rds file from an Markdown file. Changing my relative file path to an absolute file path worked for me.
In my case, this error was because the file that I wanted to re-write, was read-only (for whatever reason, I didn't do it myself). I just right-click on the file's name in the folder and unchecked the read-only property. After that it worked.