I'm working with a Mac Os 10.9.2 and a R version 3.0.2.
I used dbDriver() and dbConnect() to initiate the connection to my database. Next, I tried to connect to my postgres database using
c = readOGR("PG:dbname=OB", layer="geo.countries")
This does not work, and always returns a "Cannot open file" error.
I understood from https://stat.ethz.ch/pipermail/r-sig-geo/2010-January/007519.html that the reason for this is the absence of a driver for PostgreSQL. As can be seen by using the command ogrDrivers()
Does anybody can help me on how to install the driver? Or how I can make this work? Any help is much appreciated!
Thanks!
In the absence of the right driver, gdal/ogr usually throws and error like
Unable to find driver PostgreSQL
First, make sure that the database and layer exist. If it's true that the driver for Postgres isn't installed, you'll have to re-install gdal. Using homebrew:
brew uninstall gdal
brew install gdal --with-postgresql
See also this question.
If you are really sure that gdal is properly installed, make sure that your dns is fully specified (it has more parameters than dbname)
dsn="PG:dbname=DB host=HOST user=USER password=PSSWD port=5432"
Moreover, if your table contains more than one spatial columns (layers), you have to specify the one you want:
layer = "DB.TABLE(YOUR_SPATIAL_COLUMN)"
Took me a while to find out. But it was obvious after calling function
ogrListLayers()
It works for me. Just one issue, if you have some raster column in you table, it will not be excluded (as all other layers/spatial columns). Instead, it will be loaded into spatialobject#data dataframe as text column. Quite annoying in case of big rasters. I have posted question for this.
Related
I've found a number of different methods that can be used to install packages on a machine that isn't connected to the internet. This post offers a fairly straightforward method to download the packages, transfer to the disconnected machine, and then to point the R installation at this custom repository.
After transferring the files, I ran the following command on the machine not connected to the internet:
update.packages(repos="C:/Users/username/Documents/R/R Repository/3.4",repos = NULL,type = "source")
After running the above line, I am getting the following error:
Error in update.packages(repos = "C:/Users/username/Documents/R/R Repository/3.4", :
formal argument "repos" matched by multiple actual arguments
Another thing I noticed is that the downloaded packages are all ".tar.gz" files, and this is a windows machine (as was the machine in the linked post above). Could this be part of the problem?
Any help would be much appreciated, thank you!
It looks like you have "repos =" twice in your call. Take out "repos = NULL" and try it again.
I am using windows 10. I successfully installed NotesSQL 9.0 but unable to add ODBC driver and getting the such a error:
The setup routines for the Lotus Notes SQL driver (*.nsf) ODBC driver could not be loaded due to system error code 126: The specified module could not be found. (C:\NotesSQL\nsqlc32.dll).
I checked the .dll and it is existing in the path that it showed. I did many different way of fixing this issues but could not fix it. Please anyone help to advise? Thank you.
Make sure you have added your notes.ini file to the PATH variable. This file is required by ODBC driver to run. By default your notes.ini should be in:
C:\Program Files (x86)\IBM\Lotus\Notes\notes.ini
After spending a lot hours trying to find out a solution, I discovered one that solves to me: add the path of your Notes client at your path environment (user and system path) and it will work fine! Tell us if its solves for you.
devtools::install_github("SeaAroundUs/rseaaroundus")
library("seaaroundus")
regionmap("eez")
#> Error in ogrListLayers(url): Cannot open data source
Internally regionmap() is using the url http://api.seaaroundus.org/api/v1/eez/?geojson=true in a call to readOGR(dsn=url, layer=ogrListLayers(url))
ogrListLayers fails, but even if you get they layer (OGRGeoJSON) specified manually, readOGR() fails with Cannot open file
Any help greatly appreciated. I'm not a windows user, so not sure where things are going wrong.
Using: rgdal v1.1.1, GDAL v.1.11.2, R v.3.2.3, on Windows XP
There's no problem on *nix systems
I don't know what is going on, everything was working great but suddenly I started to have this error message on the documentation:
Error in fetch(key) : lazy-load database '......descopl.rdb' is
corrupt
I removed almost all my code and build again then publish to Github, but when I use the other laptop to download the package, the package is being downloaded and loaded but I can't call any of the functions, and the documentation states that error.
I don't know what caused the problem, I am using roxygen to generate the documentation.
https://github.com/WilliamKinaan/descopl
It seems that the error arises when the package cannot be decompressed by R (as #rawr established, it is corrupt). This solutions have worked for me:
1) Check for possible errors in the creation of the .Rdb files
2) Try restarting your R session (e.g. .rs.restartR() if in RStudio)
3) The package might have been installed in your computer (even though it does not work). Remove it using ?remove.packages()
I have had this problem with roxygen2 as well. Couldn't see any problem with any of my functions. In the end deleting the .rdb file and then getting roxygen2 to rebuild it seemed to solve the problem.
I think the explanation for what is causing this is here.
It's related to devtools.
Per #Zfunk
cd ~/Rlibs/descopl/help
rm *.rdb
Restart R. Look at the help for the package again. Fixed!
I received this error after re-installing a library whilst another R session was running.
Simply restarting the existing R session(s) solved for me (i.e. running .rs.restartR() to restart the sessions)
If you are using R-studio:
1) ctrl+shift+f10 to restart r session
2) tools -> Check for package updates -> update all packages
3) library(ggmap)
Problem is solved.
Basically all answers require restarting R to resolve the issue, but I found myself in an environment where I really didn't want to restart R.
I am posting here a somewhat hack-ish solution suggested by Jim Hester in a bug report about the lazy-load corruption issue.
The gist of it is that the package may have some vestigial S3 methods listed in session's .__S3MethodsTable__. environment. I don't have a very systematic way of identifying which S3 methods in that environment come from where, but I think a good place to start is the print methods, and looking for S3method registrations in the package's NAMESPACE.
You can then remove those S3 methods from the .__S3MethodsTable__. environment and try again, e.g.
rm(list="print.object", envir = get(".__S3MethodsTable__.", envir = baseenv()))
You may also need to unload some DLLs if some new messages come up like
no such symbol glue_ in package /usr/local/lib/R/site-library/glue/libs/glue.so
You can check getLoadedDLLs() to see which such files are loaded in your session. In the case of glue here, the following resolved the issue:
library.dynam.unload('glue', '/usr/local/lib/R/site-library/glue')
I got this error on RStudio on mac OS - updating all the packages and restarting r session did the trick.
Just updated to R 3.0 and updated all the packages, including DBI. To my surprise, a script that I often use stopped working.
I am unable to connect to a MySQL database using dbConnect. The code script instantly, so only a few lines will reproduce the problem
> require("RMySQL")
> m = dbDriver("MySQL")
> dbConnect(m, user = 'user', password = 'pass', dbname = 'dbname', host = 'localhost', client.flag = CLIENT_MULTI_STATEMENTS)
Error in as.integer(from) :
cannot coerce type 'S4' to vector of type 'integer'
Calls: dbConnect ... mysqlNewConnection -> isIdCurrent -> as -> asMethod
Also tried it as:
dbConnect(MySQL(), user = 'user', password = 'pass', dbname = 'dbname', host = 'localhost', client.flag = CLIENT_MULTI_STATEMENTS)
but the same problem
Also tried removing other parameters, but the same issue from the dbDriver.
What changed in the DBI package with the latest update? How can I fix this?
I noticed that the DBI package is orphaned so don't know who to ask.
I had the same issue with R 3.0.1 on ubuntu.
Installing the latest version of the RMySQL-package resolved the problem:
> install.pacakges("RMySQL")
Make sure to restart R after the installation.
I'm still digging into the issue, but I think I've identified multiple causes of this issue. At their root, they all have to do with R expecting an S4 object but getting back an integer instead. I believe these are generally a result of the connection failing to establish.
Why is it failing? One thing I've noticed is that if you fail to close to many of your connections (~16 [see the number of maximum connections specified in the driver handle call] open) DBI won't/can't open a new connection. Make sure you are calling dbDisconnect as needed. Usually, this sort of problem results in a sensible error message, however sometimes results in the above referenced error. If possible access the DB through an abstraction layer, e.g. dplyr as some will monitor the db connections and kill them if they are inactive. Whereas, AFIK if you open a connection in a function and the function breaks, you have no way to close the open connection unless you returned the driver object from your initial call to dbConnect. In this case you have no choice but to restart your instance of R (possibly resetting your machine and clearing your workspace as well).
The other issue I recently encountered is that if RMySQL masks RPostgreSQL, then RPostgreSQL will fail. The reverse does not appear to be the case, but because others have mentioned RPostgreSQL in here as showing the same error message, it seemed worthy of note.
Update
The latest version of RMySQL (0.10.1) seems to have finished off RPostgreSQL - RPostgreSQL now fails to work regardless of load order. The same people working on RMySQL appear to be working on RPostgres (https://github.com/rstats-db/RPostgres) and this conflict appears to be a non-issue if using that package instead of RPostgreSQL. Specifically, use RPostgres::Postgres() in the place of RPostgreSQL::PostgreSQL() when specifying the driver in dbConnect. Other packages, e.g. dplyr, currently assume RPostgreSQL, so this issue can still bite (but it seems a resolution is in the works (https://github.com/rstats-db/RMySQL/issues/28).