I use R/exams to generate a PDF exam like this:
exams2pdf("swisscapital")
However, this results in the following error:
Loading required namespace: tinytex
sh: : Permission denied
Doing the same with exams2html() works well.
What is the problem and how can I fix it?
Given that this does not produce an "error" within R but only on the shell (sh), this is probably just a problem of displaying the PDF interactively at the very end. You can check whether
getOption("pdfviewer")
is correctly set to an application for viewing PDFs (e.g., "/usr/bin/evince") and whether you have permission to use that application.
If there are problems with getting a proper PDF viewer called from within R, then simply use
exams2pdf("swisscapital", dir = ".")
which will write the PDF to your current working directory rather than displaying it in the PDF viewer. And then you can manually open the PDF outside of R.
I'm building a R package for binary classification and I'm using opencpu to host it. Currently I've saved the h5 file as .RData file(serialized), which is then loaded in the environment using the .onLoad() function in R. This enables the R script to use the environment variable to load keras model using keras::unserialized_model().
I've tried directly using keras::load_model_hdf5() in the code, but after building and deploying on opencpu, when I try to hit the prediction API, I get error
ioerror: unable to open file (unable to open file: name = '/home/modelfile_26feb.h5', errno = 13, error message = 'permission denied', flags = 0, o_flags = 0)
I have changed permission for the file(777) and even the groups but still getting the error.
I even tried putting the file in inst/extdata folder so that it gets in the package but still same error.
Can anyone help on this, or suggest some alternative to load the h5 model directly?
Which OS does OpenCPU run on? Why does it try to write in /home/, this is very unusual? The best solution is to adapt your code to write in getwd() or tempdir(). Even better is to store data in a local database or redis server and let R read it from there, so you don't need disk access at all.
If you run on Ubuntu Server, reading from /home/ is not permitted by default. If you want to allow this, you need to add apparmor rules, see section 3.5 of the server manual.
Some relevant topics from the opencpu mailing list:
write in home dir: https://groups.google.com/d/msg/opencpu/5vRvgSKY-qE/4xMzZCGJBAAJ
keras in opencpu: https://groups.google.com/d/msg/opencpu/HhRzFVVFdaA/n5Nu1sxyFgAJ
write tmp folder: https://groups.google.com/d/msg/opencpu/Y1tYhaQUzwU/ubSEd_CDCgAJ
I am trying to build PhantomJS 2.0 on Windows from the c:\fastio\phantomjs\phantomjs directory. For some reason, the build process fails after a while, with 2 errors (see error message below):
1) It tries to access "C:fastiophantomjsphantomjssrcqtqtbasebinmoc.exe". Obviously, the backslash characters between directory names are somehow getting stripped away deep in the build process - possibly a mismatch between Windows-style "\" and Linux-style "/" (but this is only a guess).
2) There's another error, "Failed to read names from file: C:/fastio/phantomjs/phantomjs/src/qt/qtwebkit/Source/WebCore/mathml/mathtags.in".
If I remove sh.exe from the PATH, the build still gets to this point, and only error #2 appears, leading me to think that error #2 is the real problem here.
Here is the full error message (as far as I can tell this is happening while building WebKit):
sh: C:fastiophantomjsphantomjssrcqtqtbasebinmoc.exe: command not found
Failed to read names from file: C:/fastio/phantomjs/phantomjs/src/qt/qtwebkit/Source/WebCore/mathml/mathtags.in at C:/fastio/phantomjs/phantomjs/src/qt/qtwebkit/Source/WebCore/dom/make_names.pl line 315.
NMAKE : fatal error U1077: 'C:\Users\Eugene\AppData\Local\GitHub\PortableGit_c2ba306e536fdf878271f7fe636a147ff37326ad\bin\perl.EXE' : return code '0x7f'
Stop.
(By the way, I saw this question but I'm already past the issues described there, my error is happening later in the build process.)
How can I make this work?
Full logs below:
Console output:
http://pastebin.com/btMeNPz4
QT build log file build_qt_4-285-20-0859.log:
http://pastebin.com/LUEJz7E0
WebKit build log file build_webkit_4-285-20_0859.log:
http://pastebin.com/494TivXF
PhantomJS build log file build_phantomjs_4-285-20_0859.log:
Empty
Looks like I found the solution myself, here were my steps:
Remove as much as possible from the PATH leaving only the entries critical to the build process
Most importantly, remove all GitHub's git directories from the PATH
Install GIT separately (not from GitHub but from git-scm.com), add its cmd directory only (not its bin directory) to the PATH
Install ActivePerl separately, add it to the PATH
It's moving past the error I asked about with the steps above (still not sure if it will finish the build successfully, it's taking a while).
Okay - so here is what I'm trying to do.
I've got this password protected CSV file I'm trying to import into R.
I can import it fine using:
read.csv()
and when I run my code in RStudio everything works perfect.
However, when I try and run my .R file using a batch file (windows .bat) it doesn't work. I want to use the .BAT file so that I can set up a scheduled task to run my code every morning.
Here is my .BAT file:
"E:\R-3.0.2\bin\x64\R.exe" CMD BATCH "E:\Control Files\download_data.R" "E:\Control Files\DailyEmail.txt"
And here is my .R file:
url <- "http://username:password#www.url.csv"
data <- read.csv(url, skip=1)
** note, I've put my username/password and the exact location of the CSV in my code. I've used generic stuff here, as this is work related and posting usernames and passwords is probably frowned upon.
As I've said, this code works fine when I use it in RStudio. But fails when I use the .BAT file.
I get the following error message:
Error in download.file(url, "E:/data/data.csv") :
cannot open URL 'websiteurl'
In addition: Warning message:
In download.file(url, "E:/data/data.csv") :
unable to resolve 'username'
Execution halted
** above websiteurl is the http above (I can't post links)
So obviously, the .BAT is having trouble with the username/password? Any thoughts?
* EDIT *
I've gone so far as trying this on Linux. Thinking maybe windows was playing silly bugger.
Just from the terminal, I run Rscript -e "download_data.r" and get the EXACT same error message as I did in Windows. So I suspect this may be a problem with where I'm getting the data? Could the provider be blocking data from the command line, but not from with Rstudio?
I have had similar problems which had to do with file permissions. The .bat file somehow does not have the same privileges as you running the code directly from Rstudio. Try using rscript (http://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html) within your .bat file like
Rscript "E:\Control Files\download_data.R"
What is the purpose of the argument "E:\Control Files\DailyEmail.txt"? Is the program suppose to use it in any way?
So, I've found a solution, which is likely not the most practical for most people, but works for me.
What I did was migrated my project over to a Linux system. Running daily scripts, is easier on Linux anyways.
The solution makes use of the "wget" function in linux.
You can either run the wget right in your shell script, or make use of the system() function in R to run the wget.
code looks like:
wget -O /home/user/.../file.csv --user=userid --password='password' http://www.url.com/file.csv
And you can do something like:
syscomand >- "wget -O /home/.../file.csv --user=userid --password='password' http://www.url.com/file.csv"
system (syscommand)
in R to download the CSV to a location on your hard drive, then grab the CSV using read.csv()
Doing it this way gave me some more insight into the potential root cause of the problem. While the system(syscommand) is running, I get the following output:
Connecting to www.website.com (www.website.com)|ip.ad.re.ss|:80... connected.
HTTP request sent, awaiting response... 401 Unauthorized
Reusing existing connection to www.weburl.com:80.
HTTP request sent, awaiting response... 200 OK
Not sure why it has to send the request twice? And why I'm getting a 401 Unauthorized the first try?
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.