Looking for odbc library for R

[矢作英幸]

There is dbi library for R, but no odbc library.
How can I access to Db2 for i from R on i?

I tried install.packages("odbc") from “1: 0-Cloud [https]” but it failed by TZ issue.
Thank you for your help.

Uzaemon@Japan

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[Jesse G]

I believe the TZ messages you are seeing are only warnings. Do you have the full output?

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Also, if you haven’t already, you will need to install developer tools (yum group install "Developer Tools"), R-devel (R-devel), and unixODBC-devel (yum install unixODBC-devel). Plus, you need to install the ODBC driver itself as documented at https://github.com/IBM/ibmi-oss-examples/blob/master/odbc/odbc.md

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[矢作英幸]

Thank you very much for your reply!

Do you have the full output?

Yes. Please check out “install_log.txt”.

Also, if you haven’t already,

I think I’ve installed all pre-requisites.

• Packages → yum_list.txt
• odbc → odbcinst_j.txt (working well with “pyodbc”)

If you need more info, please let me know.
I very much appreciate your help.

uzaemon@Japan

[Kevin Adler]

The problem is here:

ar: 0707-126 time_zone_format.o is not valid with the current object file mode.
        Use the -X option to specify the desired object mode.

The default for most tools within PASE are for 32-bit mode, but we build everything as 64-bit by default so you have to set some flags that most software doesn’t know about.

You can get around this by setting OBJECT_MODE=64 before running the install:

export OBJECT_MODE=64

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[矢作英幸]

Thank you Kevin, odbc now works with R!

List all packages:

> str(allPackage <- installed.packages(.Library))
 chr [1:43, 1:16] "BH" "DBI" "KernSmooth" "MASS" "Matrix" "Rcpp" "base" ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:43] "BH" "DBI" "KernSmooth" "MASS" ...
  ..$ : chr [1:16] "Package" "LibPath" "Version" "Priority" ...
> allPackage [, c(1,3:5)]
           Package      Version    Priority
BH         "BH"         "1.72.0-3" NA
DBI        "DBI"        "1.1.0"    NA
(SNIP)
odbc       "odbc"       "1.2.2"    NA

Test run:

> library(odbc)
> con <- dbConnect(odbc(), "*LOCAL")
> library(DBI)
> dbGetQuery(con, 'select SCHEMA_NAME, SCHEMA_OWNER, SCHEMA_CREATOR,  CREATION_TIMESTAMP from qsys2.sysschemas')
                 SCHEMA_NAME SCHEMA_OWNER SCHEMA_CREATOR  CREATION_TIMESTAMP
1                    #CGULIB         QSYS     QLPINSTALL 2018-09-01 02:06:46
2                    #COBLIB         QSYS        QSECOFR 2018-09-25 09:43:14
(SNIP)
Warning messages:
1: In as.POSIXlt.POSIXct(x, tz) : unknown timezone '<JST>-9'
2: In format.POSIXlt(as.POSIXlt(x, tz), format, usetz, ...) :
  unknown timezone '<JST>-9'

Is there any way to remove “timezone” warnings?

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• I checked valid tz by OlsonNames() and ran code below replacing “xxx” to “Japan”, “Asia/Tokyo”, “GMT”, “UTC”, etc. but nothing worked.

> Sys.setenv(TZ="xxx")
> Sys.getenv("TZ")
[1] "xxx"
> as.POSIXct(t, tz=getOption("tz"))
Error in as.POSIXct.default(t, tz = getOption("tz")) :
  do not know how to convert 't' to class "POSIXct"

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Thank you for your kind support.

Uzaemon@Japan