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cqe20
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@cqe20-12797
Last seen 7.3 years ago
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
This seems tricky. What does
.libPaths()
say? AndpackageDescription("GenomicFeatures")
, especially the final line 'File:...'?