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Question: getSRAdbFile cannot open URL
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gravatar for Nicholas Stong
5.2 years ago by
Nicholas Stong10 wrote:
Used SRAdb in the past but couldn't load the database today. > getSRAdbFile() trying URL 'http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz' Error in download.file(url_sra, destfile = localfile, mode = "wb", method = method) : cannot open URL 'http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz' I see that this backup database url is not found, and the primary URL, http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz, says forbidden. Is this version and links out of date? Any help would be appreciated. Nick -- Nick Stong PhD Candidate Genomics and Computational Biology Riethman Lab The Wistar Institute [[alternative HTML version deleted]]
ADD COMMENTlink modified 5.2 years ago by Martin Morgan ♦♦ 20k • written 5.2 years ago by Nicholas Stong10
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gravatar for Martin Morgan
5.2 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:
On 09/10/2012 01:40 PM, Nicholas Stong wrote: > Used SRAdb in the past but couldn't load the database today. > >> getSRAdbFile() > trying URL 'http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz' > Error in download.file(url_sra, destfile = localfile, mode = "wb", method = > method) : > cannot open URL 'http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz' this 'worked for me'; maybe it was transient or you're behind a firewall? Can you access the url in a web browser? Martin > sessionInfo() R version 2.15.1 Patched (2012-08-26 r60438) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] SRAdb_1.10.0 RCurl_1.91-1 bitops_1.0-4.1 [4] graph_1.34.0 RSQLite_0.11.1 DBI_0.2-5 [7] BiocInstaller_1.4.7 loaded via a namespace (and not attached): [1] Biobase_2.16.0 BiocGenerics_0.2.0 GEOquery_2.23.5 tools_2.15.1 [5] XML_3.9-4 > > I see that this backup database url is not found, and the primary URL, > http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz, says forbidden. Is > this version and links out of date? Any help would be appreciated. > > Nick > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD COMMENTlink written 5.2 years ago by Martin Morgan ♦♦ 20k
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gravatar for Frank Schwach
5.2 years ago by
Frank Schwach20 wrote:
Hi, does anybody know if there is any way in the topGO package to force full-length descriptions of the GO terms to be printed in the graph? By default, only about 20 characters of the descriptions are printed. Thanks for your help! Frank -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
ADD COMMENTlink written 5.2 years ago by Frank Schwach20
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