Problems during the installation of AnnotationDbi and pasilla
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@cacaucenturion2-6961
Last seen 7.1 years ago

I got the same error messages as follows when installing AnnotationDbi and pasilla. Could anyone let me know what the problem is?

 

Error : 'quantile.default' is not an exported object from 'namespace:stats'
Error : unable to load R code in package 'IRanges'
ERROR: lazy loading failed for package 'IRanges' *

 

 

 

AnnotationDbi • 1.9k views
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Could you provide a bit more information. Here is what I get when installing the packages:

> library("BiocInstaller")
Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help
> biocLite(c("AnnotationDbi", "pasilla"))
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.1.
Installing package(s) 'AnnotationDbi' 'pasilla'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/AnnotationDbi_1.28.1.tar.gz'
Content type 'application/x-gzip' length 4254796 bytes (4.1 Mb)
opened URL
==================================================
downloaded 4.1 Mb

trying URL 'http://bioconductor.org/packages/3.0/data/experiment/src/contrib/pasilla_0.5.1.tar.gz'
Content type 'application/x-gzip' length 3886708 bytes (3.7 Mb)
opened URL
==================================================
downloaded 3.7 Mb

* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘toString’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AnnotationDbi)
* installing *source* package ‘pasilla’ ...
** data
** inst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pasilla)

with a recent R and Bioc

> sessionInfo()
R version 3.1.1 Patched (2014-09-02 r66514)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.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_1.16.0

loaded via a namespace (and not attached):
[1] tools_3.1.1
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I got the similar problem when install IRange

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But without any details, in particular sessionInfo, it is difficult to help. In many cases, an updated with biocLite() is the solution.

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BiocInstaller::biocValid() may also help to track down incompatibilities between installed packages..

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