Cevap: Re: SRAdb error
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 7 months ago
United States
Hi Ayten, Let's keep the bioconductor list in this thread because that way more people have the opportunity to help you. 2012/3/26 Ayten YIGITER <yigiter at="" hacettepe.edu.tr="">: > ?Hi Dan, > > Thank you for your?helps. > > When I write "sessionInfo()"?on the command window, I see the information > below. > Could you write what was wrong or what?I should do? > > ?Thanks again. > > Dr. Ayten Yi?iter > Hacettepe University > Faculty of Science > Department of Statistics > Ankara/Turkey > Phone: +90 312 2977900 > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: i386-pc-mingw32/i386 (32-bit) > locale: > [1] LC_COLLATE=Turkish_Turkey.1254? LC_CTYPE=Turkish_Turkey.1254 > [3] LC_MONETARY=Turkish_Turkey.1254 LC_NUMERIC=C > [5] LC_TIME=Turkish_Turkey.1254 > attached base packages: > [1] stats???? graphics? grDevices utils???? datasets? methods?? base > other attached packages: > [1] SRAdb_1.8.0??? RCurl_1.91-1.1 bitops_1.0-4.1 graph_1.32.0 > RSQLite_0.11.1 > [6] DBI_0.2-5 > loaded via a namespace (and not attached): > [1] Biobase_2.14.0? GEOquery_2.20.8 tools_2.14.1??? XML_3.9-4.1 > As Sean said in an earlier message, you need to provide all the commands you are running, specifically the one(s) that produce the error. When I run sqlfile <- getSRAdbFile() I get: trying URL 'http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz' Content type 'application/octet-stream' length 187043912 bytes (178.4 Mb) opened URL ================================================ downloaded 178.4 Mb Unzipping... Metadata associate with downloaded file: c("schema version", "creation timestamp")c("1.0", "2012-02-29 02:52:37") I don't get any errors. Dan > 03/23/12, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> yazm??: > > Hi Ayten, > > 2012/3/22 Ayten YIGITER <yigiter at="" hacettepe.edu.tr="">: >> Hi, I am trying to get the SRAdb package work. I have successfully >> installed the SRAdb package and then I have got the following error: >> >> >> library(SRAdb) >> sqlfile <- getSRAdbFile() >> URL 'http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz' deneniyor >> Content type 'application/octet-stream' length 187043912 bytes (178.4 Mb) >> URL a??ld? >> downloaded 178.4 Mb >> Unzipping... >> Error: sqliteNewConnection(drv, ...) : >> RS-DBI driver: (could not connect to dbname: >> unable to open database file" >> >> >> Could you help me at this point? > > Can you post the output of R's > sessionInfo() > command? > That will give us the information we need to help you. > Thanks, > Dan > > >> >> Sincerely yours >> >> Dr. Ayten Yi?iter >> Hacettepe University >> Faculty of Science >> Department of Statistics >> Ankara/Turkey >> Phone: +90 312 2977900 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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