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Question: Package dependency GenomicFeatures is installed but cannot be found
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gravatar for cqe20
7 months ago by
cqe200
cqe200 wrote:

Hi all,

While trying to install the OrganismDbi package, I am getting an error saying that its dependency GenomicFeatures cannot be found.

I was able to install GenomicFeatures without any issues by running biocLite('GenomicFeatures'), however, and library(GenomicFeatures) loads it successfully. 

What might prevent GenomicFeatures from being found by other packages that require it?

Any help would be much appreciated.

Thanks in advance!


Error message following biocLite("OrganismDbi"):

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
Installing package(s) ‘OrganismDbi’, ‘binary’
trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/OrganismDbi_1.16.0.tar.gz'
Content type 'application/x-gzip' length 194540 bytes (189 KB)
==================================================
downloaded 189 KB

* installing *source* package ‘OrganismDbi’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error : package ‘GenomicFeatures’ required by ‘OrganismDbi’ could not be found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/mhome/stats/r/cqe20/R/x86_64-pc-linux-gnu-library/3.1/OrganismDbi’

The downloaded source packages are in
	‘/tmp/cqe20-vncsessionKcSmro/RtmppQpUP3/downloaded_packages’

sessionInfo():

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             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_1.24.0

loaded via a namespace (and not attached):
[1] tools_3.3.3

sessionInfo() with the 'missing' GenomicFeatures package loaded:

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicFeatures_1.26.4 AnnotationDbi_1.36.2   Biobase_2.34.0         GenomicRanges_1.26.4   GenomeInfoDb_1.10.3   
[6] IRanges_2.8.2          S4Vectors_0.12.2       BiocGenerics_0.20.0    BiocInstaller_1.24.0  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10               XVector_0.14.1             GenomicAlignments_1.10.1   zlibbioc_1.20.0           
 [5] BiocParallel_1.8.2         lattice_0.20-35            tools_3.3.3                grid_3.3.3                
 [9] SummarizedExperiment_1.4.0 DBI_0.6-1                  digest_0.6.12              Matrix_1.2-8              
[13] rtracklayer_1.34.2         bitops_1.0-6               RCurl_1.95-4.8             biomaRt_2.30.0            
[17] memoise_1.0.0              RSQLite_1.1-2              Biostrings_2.42.1          Rsamtools_1.26.2          
[21] XML_3.98-1.6 
ADD COMMENTlink written 7 months ago by cqe200

This seems tricky. What does .libPaths() say? And packageDescription("GenomicFeatures"), especially the final line 'File:...'?

ADD REPLYlink written 7 months ago by Martin Morgan ♦♦ 20k
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