I've had a working R script that uses the dbWriteTable command to write to a SQL Server table. It has worked well without issue for a while ... until the last few days.
Now when I run the dbWriteTable command, I get the following warning:
Found more than one class "blob" in cache; using the first, from namespace 'blob'
Also defined by ‘jsonlite’
Interestingly enough the table appears to write successfully.
Here is some sample code:
library("DBI")
db_test <- dbConnect(
odbc(),
driver = "SQL Server",
server = "test_server",
port = 1234,
database = "test_db"
)
dbWriteTable(
conn = db_test,
name = SQL("dbo.swc_test_write_table"),
value = df_test,
overwrite = TRUE
)
I've tried explicitly naming the package, DBI::dbWriteTable, but it throws the same warning. For reference, I'm not using using the jsonlite package, but I have it installed.
Any thoughts on why this is happening?
This seems to be a bug, which is caused by the jsonlite package in its latest release 1.7.3.
See the bug report https://github.com/jeroen/jsonlite/issues/373
It seems to be fixed upstream and as of now there's also an updated version available, Changelog from 1.7.3 to 1.8.0.
Same problem here, seems to be interfering with encoding, possibly
EDIT:
Sorry for the "me too" post. I checked around a bit more and it's caused for me at least by the loading of the tidyverse library. Loading only DBI and odbc for me resolves the warning.
Related
I am trying to connect to an Oracle database with dplyr and dbplyr backend. However since the upgrade of dbplyr to version 2.0.0 it no longer works and getting the following error.
x <- tbl(con, in_schema("dm", "DM_CLT_POS_OVL_LIAB_HEDGE"))
Error in .oci.GetQuery(conn, statement, data = data, prefetch = prefetch, :
ORA-00942: table or view does not exist
In the previous version of dbplyr I could make it work with the redirection functions ( see below) but they have been removed with the upgrade.
#below are required to make the translation done by dbplyr to SQL produce working Oracle
SQLsql_translate_env.OraConnection <- dbplyr:::sql_translate_env.Oracle
sql_select.OraConnection <- dbplyr:::sql_select.Oracle
sql_subquery.OraConnection <- dbplyr:::sql_subquery.Oracle
Any help would be appreciated.
Came across the same issue using RJDBC package instead of an ODBC driver based approach and found the solution for it on the github page of dbplyr.
I'm not sure, whether it works and cannot try it myself but you might try to replace your assignments with these here:
SQLsql_translate_env.OraConnection <- dbplyr:::sql_translation.Oracle
sql_select.OraConnection <- dbplyr:::sql_query_select.Oracle
sql_subquery.OraConnection <- dbplyr:::sql_query_wrap.Oracle
I have to following code
drv <- RPostgreSQL::PostgreSQL()
con <- DBI::dbConnect(drv, dbname = 'dbname', user = 'user',
host = 'host.name', port = 5432, password = 'password')
When I run it on server (Ubuntu server 16.04 with latest updates) running the database I get the following error:
Error in .valueClassTest(ans, "data.frame", "dbGetQuery") :
invalid value from generic function ‘dbGetQuery’, class “NULL”, expected “data.frame”
But when I run R from commandline with sudo, it works, when I run it from different my laptop connecting to the DB on the server it also works. So it shouldn't be connection problem. I am thinking about problem with access rights to some libraries/executables/configs on the system? Any help will be appreciated.
When I run the dbConnect multiple times and it ends with the error, when I run drv_info <- RPostgreSQL::dbGetInfo(drv), I still get multiple connectionIds in the drv_info:
drv_info <- RPostgreSQL::dbGetInfo(drv)
> drv_info
$drvName
[1] "PostgreSQL"
$connectionIds
$connectionIds[[1]]
<PostgreSQLConnection>
$connectionIds[[2]]
<PostgreSQLConnection>
$fetch_default_rec
[1] 500
$managerId
<PostgreSQLDriver>
$length
[1] 16
$num_con
[1] 2
$counter
[1] 2
Found a source of confusion, but not necessarily the root problem. (I was assuming RPostgres, while you are using RPostgreSQL (github mirror).)
If you check the source, you'll find that the method is calling postgresqlNewConnection, which includes a call to dbGetQuery. The problem you're seeing is that your call to dbConnect is failing (my guess is at line 100) and returns something unexpected, but postgresqlNewConnection continues.
I see three options for you:
try calling dbConnect(..., forceISOdate=FALSE) to bypass that one call to dbGetQuery (note that this doesn't fix the connection problem, but it at least will not give you the unexpected query error on connection attempt);
raise an issue for the package maintainers; or
switch to using RPostgres, still DBI-based and actively developed (it looks like RPostgreSQL has not had significant commits in the last few years, not sure if that's a sign of good code stability or development stagnation)
One lesson you may take from this is that you should check the value returned from dbConnect; if is.null(con), something is wrong. (Again, this does not solve the connection problem.)
I am using Cassandra CQL- system in DBeaver database tool. I want to connect this cassandra to R to read data. Unfortunately the connection takes more time (i waited for more than 2 hours) with RCassandra package. but it does not seem to get connected at all and still loading. Does anyone has any idea on this?
the code as follows:
library(RCassandra)
rc <- RC.connect(host ="********", port = 9042)
RC.login(rc, username = "*****", password = "******")
after this step RC.login, it is still loading for more than 2 hours.
I have also tried using RJDBC package like posted here : How to read data from Cassandra with R?.
library(RJDBC)
drv <- JDBC("org.apache.cassandra.cql.jdbc.CassandraDriver",
list.files("C:/Program Files/DBeaver/jre/lib",
pattern="jar$",full.names=T))
But this throws error
Error in .jfindClass(as.character(driverClass)[1]) : class not found
None of the answers are working for me from the above link.I am using latest R version 3.4.0 (2017-04-21) and New version of DBeaver : 4.0.4.
For your first approach, which I am less familiar with, should you not have a line that sets the use of the connection?
such as:
library(RCassandra)
c <- RC.connect(host ="52.0.15.195", port = 9042)
RC.login(c, username = "*****", password = "******")
RC.use(c, "some_db")
Did you check logs that you are not getting some silent error while connecting?
For your second approach, your R program is not seeing a driver in a classpath for Java (JMV).
See this entry for help how to fix it.
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).
I'M running the following code in R:
library(GEOquery)
mypath <- "C:/Users/Farzin/Desktop/BIOC"
GDS1 <- getGEO('GDS1',destdir=mypath)
But I'm getting the following error:
Using locally cached version of GDS1 found here:
C:/Users/Farzin/Desktop/BIOC/GDS1.soft.gz
Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
invalid 'nlines' argument
Could anyone please tell me how I could get rid of this error?
I have had the same error using GEOquery (version 2.23.5) with R and Bioconductor from ubuntu (12.04), whatever GDS file I queried. Could it be that the GEOquery package is faulty ?
In my experience, getGEO is extremely finicky. I commonly experience issues connecting to the GEO server. If this happens during download, getGEO leaves a partial file. But since the partial file is there, when you try to re-download, it will use this cached, partially downloaded file, and run into the error you see (which you want, because its not the full file).
To solve this, delete the cached SOFT file and retry the download.