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Question: SRAdb error
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gravatar for Ayten YIGITER
5.7 years ago by
Ayten YIGITER10 wrote:
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? Sincerely yours Dr. Ayten Yi?iter Hacettepe University Faculty of Science Department of Statistics Ankara/Turkey Phone: +90 312 2977900
ADD COMMENTlink modified 5.7 years ago by Sean Davis21k • written 5.7 years ago by Ayten YIGITER10
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gravatar for Dan Tenenbaum
5.7 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
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
ADD COMMENTlink written 5.7 years ago by Dan Tenenbaum ♦♦ 8.2k
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gravatar for Sean Davis
5.7 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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? In addition to sessionInfo() output, could you show us the commands that lead to the error? It seems there might be something missing in the commands you pasted since getSRAdbFile() should not be attempting to connect to the database. Sean
ADD COMMENTlink written 5.7 years ago by Sean Davis21k
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