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federico.comoglio ▴ 100@federicocomoglio-4524
Last seen 5.9 years ago
I just downloaded the latest GenomicFeatures, and noticed that although the Drosophila dm6 genome is within the output returned by ucscGenomes(), neither refGene, ensGene or flyBaseGene tables can be retrieved using:
txdb <- makeTxDbFromUCSC( "dm6", tablename = "ensGene" ) Error in `genome<-`(`*tmp*`, value = "dm6") : Failed to set session genome to 'dm6'
Am I missing something? A quick look into the source indicates that the error is raised from setReplaceMethod("genome","UCSCSession",...)
Thanks a lot for your help.
> sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server 7.0 (Maipo) locale:  LC_CTYPE=C LC_NUMERIC=C  LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8  LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8  LC_PAPER=en_US.utf8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages:  stats4 parallel stats graphics grDevices utils datasets  methods base other attached packages:  BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 BSgenome_1.36.0  rtracklayer_1.28.2 BiocInstaller_1.18.1  GenomicFeatures_1.20.0 AnnotationDbi_1.30.1  Biobase_2.28.0 VariantAnnotation_1.14.1  Rsamtools_1.20.1 Biostrings_2.36.0  XVector_0.8.0 GenomicRanges_1.20.3  GenomeInfoDb_1.4.0 IRanges_2.2.1  S4Vectors_0.6.0 BiocGenerics_0.14.0 loaded via a namespace (and not attached):  zlibbioc_1.14.0 GenomicAlignments_1.4.1 BiocParallel_1.2.1  tools_3.2.0 DBI_0.3.1 lambda.r_1.1.7  futile.logger_1.4.1 futile.options_1.0.0 bitops_1.0-6  RCurl_1.95-4.6 biomaRt_2.24.0 RSQLite_1.0.0  XML_3.98-1.
I also tried to supply a different genome argument (e.g. hg19, mm9 or dm3) and I get the same error.
Not sure what's going on but note that there is no ensGene or flyBaseGene table for dm6. Using the refGene table works for me:
FWIW a more direct way to reproduce your problem would be for you to try:
Can you confirm? If so, it looks like a network issue to me (proxy, firewall, etc...)
thanks for your message. The problem seems to be generalized, though. I get:
I'm running this code on the server I regularly use for my R/BioC work, which is connected to the internet with unmodified network settings.
Let me know if you have an idea on how to fix this issue. Thanks a lot,
This is just another one of those rtrackalyer issues that varies by internet connection. You could try debugging it on your end, but otherwise, there is nothing that we can really do.
Thank you, Michael.