User: jessica.hekman
jessica.hekman • 40
- Reputation:
- 40
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- New User
- Location:
- United States
- Last seen:
- 3 years, 11 months ago
- Joined:
- 4 years, 10 months ago
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- j*************@gmail.com
Posts by jessica.hekman
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... Amazing that it took me this long to get back to this! (In the meantime I went to Siberia, passed my prelims, presented my research twice. and helped submit an NSF proposal... All of which prevented me from getting to my own research.)
Anyways: It works! Thanks again to Leo and Rafa for your suppor ...
written 4.0 years ago by
jessica.hekman • 40
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Comment:
C: sqliteSendQuery in AnnotationDbi
... Ah, thank you! Yes, I'll go change that now.
...
written 4.2 years ago by
jessica.hekman • 40
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... The solution was:
library("AnnotationDbi")
library("biomaRt")
library("GenomicFeatures")
dogTxDb <- makeTxDbFromBiomart(biomart="ensembl",
dataset="cfamiliaris_gene_ensembl",
transcript_ids=NULL,
circ_s ...
written 4.2 years ago by
jessica.hekman • 40
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Comment:
C: sqliteSendQuery in AnnotationDbi
... Thanks James!
Martin: yeah, I do intend to create a dog transcripts package at some point, but first I just wanted to make sure everything worked as expected. (I will also admit that I'm nervous about sharing a package with others as I'm still pretty new to Bioconductor, but I suppose I need to suc ...
written 4.2 years ago by
jessica.hekman • 40
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Comment:
C: sqliteSendQuery in AnnotationDbi
... Sorry -- dogTxEnsembl.rda contains dogTx which was built like so:
dogTx <- makeTranscriptDbFromBiomart(biomart="ensembl",
dataset="cfamiliaris_gene_ensembl",
transcript_ids=NULL,
circ_seqs=DEFAULT ...
written 4.2 years ago by
jessica.hekman • 40
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... HI all. I am trying to run derfinder, but am running into a problem with its calls to AnnotationDbi. I seem to have isolated the problem like so:
> library ("AnnotationDbi")
> load("dogTxEnsembl.Rda")
> class(dogTx)
[1] "GenomicFeatures"
> organism(dogTx)
Error in sqliteSendQuery(con, ...
written 4.2 years ago by
jessica.hekman • 40
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... Loopback, not lookback.
...
written 4.3 years ago by
jessica.hekman • 40
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... OK! I contacted my sysadmin for help in finding an appropriate port to use with R_PARALLEL_PORT, and he said "oh, looks like loopback is blocked -- I opened it back up, see if things work now." And now they do.
So the answer is: check loopback and make sure it's open.
Thanks to both of you for all ...
written 4.3 years ago by
jessica.hekman • 40
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... That's so helpful, thanks! I'm going to be out of the country for a week starting today, but when I get back I'll sit down and try to figure this out. I'll post whatever I find here (hopefully an answer about what ports to open, for the benefit of future answer seekers).
...
written 4.4 years ago by
jessica.hekman • 40
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... I just installed 3.2: R version 3.2.0 alpha (2015-03-26 r68103). In a new session with nothing loaded:
> x <- parallel::mclapply(1:10, sqrt)
> cl <- parallel::makeCluster(2, "PSOCK")
Again parallel:makeCluster() hung and I had to exit with ^C. I conclude that 3.2 vs 3.3 isn't the ...
written 4.4 years ago by
jessica.hekman • 40
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For derfinder: analyzeChr() breaks on chromosomes > 22
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