IlluminaHumanMethylation450k.db has undeclared dependency on AnnotationForge
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Simon Anders ★ 3.7k
@simon-anders-3855
Last seen 22 months ago
Zentrum für Molekularbiologie, Universi…

Hi

I have just installed IlluminaHumanMethylation450k.db using biocLite, then tried to load it and got the error message "there is no package called ‘AnnotationForge’".

Only after installing AnnotationForge could I load the package. It seems that the db package depends on AnnotationForge, without this being declared in its DESCRIPTION file. I assume, however, that it shouldn't depend on the forge package anyway.

Maybe soembody with more knowledge on AnnotationDbi packages could have a look?

Cheers

  Simon

 

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.14.2

loaded via a namespace (and not attached):
[1] tcltk_3.1.1 tools_3.1.1

 

annotationforge • 1.7k views
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Correction: The error occurs already when biocLite is run, not only when I try to load the package.

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Tim Triche ★ 4.2k
@tim-triche-3561
Last seen 20 months ago
United States

Gah.  It's because of crap like this:

IlluminaHumanMethylation450kDESIGN <- AnnotationForge:::createSimpleBimap("probedesign","Probe_ID","Infinium_Design_Type",datacache,"DESIGN","IlluminaHumanMethylation450k.db")

Either I should be requiring the AnnotationForge package properly or figuring out where this really ought to come from otherwise.

I'm ashamed to have written this... or autogenerated it... or however zzz.R got there.  oopsie.  Will patch (even though I would like to get rid of it entirely, hence the deprecation notice... sadly even Illumina seems to have used the package, so it may never go away...)

 

 

 

 

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Tim Triche ★ 4.2k
@tim-triche-3561
Last seen 20 months ago
United States

Alright I added AnnotationForge to the imports: line.  This is ridiculous, but the createSimpleBimap function doesn't seem to exist anywhere else, and I couldn't understand the instructions in the AnnotationDbi code well enough to just patch the idiocy.

Just in time for a new release!  (ugh)  I will upload 2.0.8 with this patched as soon as I get a chance.  I think Marc will bug those of us who were silly enough to write .db0 packages in the near future... this time around I'll have something to upload. 

Thanks for reporting this.

--t

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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.8 years ago
United States

I am moving this function from AnnotationForge back to AnnotationDbi to eliminate the need for unnecessary dependencies.  This will only affect a tiny handful of annotation packages and I plan to make sure that the affected ones are all updated for the new release.

 Marc

 

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