This is the error message:
> h2o.init()
Error in dirname(path) : path too long
In addition: There were 12 warnings (use warnings() to see them)
This is one of the warning messages (the others are similar):
> warnings()
Warning messages:
1: In normalizePath(path.expand(path), winslash, mustWork) :
path[1]="\\FILE-EM1-06/USERDATA2$/john134/My Documents/./../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../..": The filename or extension is too long
Any idea how to work around this error?
Thanks
It seems that Windows path string is limited to (maybe) 256 length. Usually, setting a the path setwd(shorterExistingWorkDir) works and should address your issue.
I struggled with this issue quite a bit, including upgrading.
Most folks are assuming that you've literally just set an incredibly long path. I don't think this is the case (it wasn't for me, at least). It's that the PATH may be set on a network drive or other device where the underlying mapped paths are more complicated.
A related thread is here on the H2O forum:
Main issue is the user had a Windows drive that did not conform to the norm, i.e., "C://", etc. Instead, the user had a network drive
(DTCHYB-AZPX015/). This caused issues in the search for a config
file as there was no "root" (In this case, "root" is reaching your Win
drive). Since there was no "root", the path to search kept expanding
until it caused R to error out with the above exception.
The fix is to NOT search for a config when h2o.init() is called. Rather, only search for a config if a user asks to do so. My proposal
is to add a new field to h2o.init()called ignore_config. This
field will be set to TRUE by default.
When calling h2o.init() the R environment signal the launching of h2o application (actually a web server) in the backend which was installed when you install H2O package into R. The local runtime environment uses the full path of the location where H2O jar file is located. Because the packages is installed deep inside the nested folders in your file system it cross the valid limit of OS path 256 character length and fails to launch the backend H2O server and you see this error. In your case you are using external path so adds up more characters in the path to make the problem worse..
For example the h2o.jar is located in my OSX machine as below:
/Library/Frameworks/R.framework/Resources/library/h2o <-- H2O package Path
/Library/Frameworks/R.framework/Resources/library/h2o/java/h2o.jar <-- Jar Path
As you are using Windows, what you need is to find ways to reduce this path to OS limit and it will work.
The other solution is to run h2o.jar separately and then just use R to connect to H2O cluster. The steps are as below:
Download H2O 3.10.4.2 and unzip to a folder close to root so you do not hit 265 char limit again. Also install 3.10.4.2 R Package. (Try to keep the same version)
Run H2O > java -jar h2o.jar
From RStudio console try > h2o.init()
So if there is already H2O cluster running the h2o.init() will connect to a running H2O cluster instead to start one and you will by pass above problem.
If you hit any problem write here and we will help you.
Related
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 am trying to use XLConnect library in R. If I execute
library(XLConnect)
I get the following error message:
JAVA_HOME cannot be determined from the Registry
To resolve this problem I set first the JAVA_HOME variable:
Sys.setenv(JAVA_HOME='C:/Program Files (x86)/Java/jre1.8.0_65')
library(XLConnect)
It looks like it helps me to come further but then I get another problem:
unable to load shared object 'C:/Program Files/R/R-3.2.2/library/rJava/libs/x64/rJava.dll'
It wonder why R cannot load rJava.dll. At least this file is located in the folder where R searches for it:
C:\Program Files\R\R-3.2.2\library\rJava\libs\x64
ADDED
Please note that the rJava.dll file exists and it is located there, where R is searching for it. I guess that the problem is in incompatibility between 32bit and 64bit versions. I assume that because R complains:
% 1 is not a valid Win32 application
Well, why do R expect it to be a Win32 application`? First, my OS is 64bit, second my Java is also for the 64bit and finally, the `rJava.dll` object is located in the folder withx64` in the name (so, I assume it is also a 64bit version).
I faced the same issue . Please locate jvm.dll
should be in (your JRE version could be different )
C:\Program Files (x86)\Java\jre1.8.0_65\bin\client
or
C:\Program Files (x86)\Java\jre1.8.0_65\bin\server
add this path to your windows system path and you are good to go .but keep in mind the version of jre and R should be consistent,if your java is in Program Files its 64 bit so launch from 64 bit R if its in Program Files (x86)its 32 bit so use 32 bit R
like in my case it showed error in 64 bit
but worked perfectly in 32 bit
You did use / instead of \.
Sys.setenv(JAVA_HOME='C:\\Program Files (x86)\\Java\\jre1.8.0_65')
library(XLConnect)
I am using UNIX. Therefore I cannot test it by myself but your path might be wrong as well.
According to this post you can search it by using this:
find.java <- function() {
for (root in c("HLM", "HCU")) for (key in c("Software\\JavaSoft\\Java Runtime Environment",
"Software\\JavaSoft\\Java Development Kit")) {
hive <- try(utils::readRegistry(key, root, 2),
silent = TRUE)
if (!inherits(hive, "try-error"))
return(hive)
}
hive
}
credit goes to #nograpes for the function and this article for helping me giving you the answer.
I am downloading data from data.gov website and I get following two types of errors in the process:
fileUrl <- "http://catalog.data.gov/dataset/expenditures-on-children-by-families"
download.file(fileUrl,destfile=".data/studentdata.csv",method="curl")
Warning message:
In download.file(fileUrl, destfile = ".data/studentdata.csv", method = "curl") :
download had nonzero exit status
I tried to remove the method="curl" as suggested in other forum, but again I get this new error
download.file(fileUrl,destfile=".data/studentdata.csv")
Error in download.file(fileUrl, destfile = ".data/studentdata.csv") :
cannot open destfile '.data/studentdata.csv', reason 'No such file or directory'
I think there are two major factors why your curl doesn't work well.
First, the problem is on your URL. fileUrl <- "http://catalog.data.gov/dataset/expenditures-on-children-by-families". In your URL, it is not referred to a csv file. So, they won't work even if you set the destination into a csv file such as destfile = ".data/studentdata.csv"
I have an example of getting a csv dataset using the same code (different dataset):
DataURL<- "https://data.baltimorecity.gov/api/views/dz54-2aru/rows.csv?accessType=DOWNLOAD" (This link refers to a rows.csv file)
download.file(DataURL, destfile="./data/rows.csv", method="curl") (The method is quite same, using curl)
Second, previously I had the same problem that the curl does not work, even I used a proper URL that refers to a csv file. However, when I diagnosed a bit deeper, I found something interesting fact about why my curl method cannot work properly. It was my R session program. I used a 32-bit R, in which the error occurs. Later then, I tried to change the session into a 64-bit R. Amazingly, and the download status was running at that time. To see your R session architecture (whether you are using 32-bit or 64-bit), type in your R:
sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-ming32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
You have to switch your R, from 32-bit to 64-bit to avoid 'curl' call had nonzero exit status. You go to your R directory folder, and then you run a 64-bit R.
If you are using a Windows OS and installing the R in a default path folder, you can run this C:\Program Files\R\R-3.5.3\bin\x64\R.exe. (I used a version of 3.5.3, so it may be different with your version)
If you are using R-studio, you can switch the R session on the menubar Tools -> Global Options -> R version -> Change -> Use your machine's default version of R64 (64-bit) -> OK. Then restart your R-studio.
However, it depends on your OS architecture. If you are using a 32-bit OS, hence you have to find another way to solve this.
So looking at the code for download.file(...), if you specify method="curl" the function tries to use the curl shell command. If this command does not exist on your system, you will get the error above.
If you do not specify a method, the default is to use an internal R method to download, which evidently works on your system. In that case, the function is trying to put the file in .data/studentdata.csv but evidently there is not .data directory. Try taking out the ..
When this download works, you will get a text/html file, not a csv file. Your url points to a web page, not a download link. That page does have a download link, but unfortunately it is a pdf, not a csv.
Finally, if your goal is to have the data in R (is it?), and if the link actually produces a csv file, you could more easily use
df <- read.csv(fileUrl)
If I'm not very much mistaken you just have a simple typo here. I suspect you have a "data" directory, not a ".data" directory - in which case your only problem is that your destfile string needs to begin "./data", not ".data".
I was having the same problem.
Then I realized that I forget to create the "data" directory!
So try adding this above your fileURL line to create the directory first.
if(!file.exists("data")){
dir.create("data")
}
Also, if you are running a Mac, then you want to keep method="curl" when downloading a https file. I don't believe Windows has that problem hence the suggestions to remove it.
Try this:
file<-'http://catalog.data.gov/dataset/expenditures-on-children-by-families'
file<- read.csv(file)
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 trying to get R (running on Windows) to download some packages from the Internet, but the download fails because I can't get it to correctly use the necessary proxy server. The output text when I try the Windows menu option Packages > Install package(s)... and select a CRAN mirror is:
> utils:::menuInstallPkgs()
--- Please select a CRAN mirror for use in this session ---
Warning: unable to access index for repository http://cran.opensourceresources.org/bin/windows/contrib/2.12
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.12
Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = type) :
no packages were specified
In addition: Warning message:
In open.connection(con, "r") :
cannot open: HTTP status was '407 Proxy Authentication Required'
I know the address and port of the proxy, and I also know the address of the automatic configuration script. I don't know what the authentication is called, but when using the proxy (in a browser and some other applications), I enter a username and password in a dialog window that pops up.
To set the proxy, I tried each of the following:
Sys.setenv(http_proxy="http://proxy.example.com:8080")
Sys.setenv("http_proxy"="http://proxy.example.com:8080")
Sys.setenv(HTTP_PROXY="http://proxy.example.com:8080")
Sys.setenv("HTTP_PROXY"="http://proxy.example.com:8080")
For authentication, I similarly tried setting the http_proxy_user environment variable to:
ask
user:passwd
Leaving it untouched
Am I using the right commands in the right way?
You have two options:
Use --internet2 or setInternet2(TRUE) and set the proxy details in the control panel, in Internet Options
Do not use either --internet2 or setInternet2(FALSE), but specify the environment variables
EDIT: One trick is, you cannot change your mind between 1 and 2, after you have tried it in a session, i.e. if you run the command setInternet2(TRUE) and try to use it e.g. install.packages('reshape2'), should this fail, you cannot then call setInternet2(FALSE). You have to restart the R session.
As of R version 3.2.0, the setInternet2 function can set internet connection settings and change them within the same R session. No need to restart.
When using option 2, one way (which is nice and compact) to specify the username and password is http_proxy="http://user:password#proxy.example.com:8080/"
In the past, I have had most luck with option 2
If you want internet2 to be used everytime you use R you could add the following line to the Rprofile.site file which is located in R.x.x\etc\Rprofile.site
utils::setInternet2(TRUE)
I've solved my trouble editing the file .Renviron as documented in Proxy setting for R.
EDITED
The solutions based on the setInternet2 statement do not work with the recent R versions because setInternet2 is declared defunct.
I'm using the 4.2.1 (on Win 11Pro) while I never had any problems in previous versions .
So to solve the problem need to modify some config files in order to fix the proxy issue not only for packages installation but, in general, also to acced to a remote resource (ie. boundary maps in my case).
The question "Proxy setting for R" collect a lot of solutions. I've found that this one has solved both my problems (packages installation and remote resources) explaining step-by-step how to edit the file .Renviron
Other solutions based on the customization of the file Renviron.site for me doesn't work
install.packages("RCurl")
that will solve your problem.