RSQLite reverse dependencies
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biostR ▴ 10
@biostr-13494
Last seen 4.3 years ago

Hi,

This is the first time I am posting an issue online, I also posted this on Biostars:

https://www.biostars.org/p/262617/#262622

I updated R to the latest version. When I tried to use latest version of affycoretools package an error message told me that I should use an updated version of RSQLite:

When I upgraded RSQLite to 2.0 version attaching affycoretools package gives the following error:

library(affycoretools)

No methods found in "RSQLite" for requests: dbGetQuery

Trying to upload an annotation package is also problematic:

biocLite("pd.hg.u133.plus.2")

...

No methods found in "RSQLite" for requests: dbGetQuery
*** arch - x64
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (pd.hg.u133.plus.2)

Any suggestions?

Thank you very much in advance.

R RSQLite • 2.6k views
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@james-w-macdonald-5106
Last seen 3 hours ago
United States

This issue is due to a problem with the NAMESPACE for affycoretools (and oligoClasses as well), where both packages are importing dbGetQuery from RSQLite, rather than the DBI package. The function is defined in DBI and is imported and then exported by RSQLite, and importing the function from RSQLite used to be copacetic, but apparently no longer. Although weirdly this only pops up with the devel version of Bioconductor, not the released version:

> library(oligoClasses)
Welcome to oligoClasses version 1.38.0
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

> library(oligoClasses)
No methods found in "RSQLite" for requests: dbGetQuery
Welcome to oligoClasses version 1.39.0
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

The fixes will appear in affycoretools 1.49.4 and oligoClasses 1.39.1, which will propagate through the build servers in a day or so.

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Thanks.

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tcalvo ▴ 70
@tcalvo-12466
Last seen 12 weeks ago
Brazil

Are you using R in which operating system? If linux, you may have to install some dependencies via terminal, such as RSQLite.

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This is not the answer to the user's problem.