[Bioc-devel] Problem loading Rdbi (again)

Mon, Nov 5, 2007 4:08 PM

Benno Puetz wrote:

Herve Pages wrote:

Hi Benno,


Benno Puetz wrote:

After successfully installing and using Rdbi (1.12.0, on R 2.6.0) 
yesterday, I started getting error messages when trying to load the 
library today (... cyclic dependencies ...).

On my system 'library(Rdbi)' is desperately quiet ;-)

It's hard to believe that Rdbi has a circular dep problem since it depends
on nothing except R >= 1.2. What message do you get _exactly_? and after doing
what? Please show us the full session.

Also, we need your sessionInfo(). Here is mine:

sessionInfo()

R version 2.6.0 (2007-10-03)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Rdbi_1.12.0

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17 tools_2.6.0

I thought I had a clean R when doing:

[Workspace restored from /Volumes/User/bpuetz/.RData]

 > sessionInfo()

R version 2.6.0 (2007-10-03)
powerpc-apple-darwin8.10.1

locale:
de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets
[6] methods   base

 > library(Rdbi)

Lade n?tiges Paket: Rdbi
Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = 
keep.source) :
  zyklische Abh?ngigkeiten von Namensr?umen werden nicht unterst?tzt
Error : Paket 'Rdbi' konnte nicht geladen werden
Error : .onLoad in 'loadNamespace' f?r 'Rdbi' fehlgeschlagen
Fehler: Laden von Paket/Namensraum f?r 'Rdbi' fehlgeschlagen

then I noticed the first line and wanted to make sure it was. After

rm (list=ls())

library(Rdbi)

is quiet as it should be... although I seem to have to load RdbiPgSQL 
manually -

    primer.conn <- dbConnect(PgSQL(),
                             host='localhost',
                             dbname='primer')

yields

Fehler in dbConnect(PgSQL(), host = "localhost", dbname = "primer") :
  konnte Funktion "PgSQL" nicht finden

But I can live with that ...

Thanks for helping me remove the culprit - whatever it may have been

I think if one has a previous connection saved in the workspace, this 
will cause the problem.  After rm(list=ls()), the connection is removed; 
hence, no further problems.  I have simply gotten in the habit of not 
saving connections in the workspace.

Sean

[Bioc-devel] Problem loading Rdbi (again)

Thread (4 messages)