error in SRAdb
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@faryabi-robert-nihnci-f-5145
Last seen 9.6 years ago
Hello list, I'm having problem with SRAdb package. Any suggestion is appreciated. I'm getting the following error after trying to update my sqlite file using getSRAdbFile() command. > getSRAdbFile() trying URL 'http://dl.dropbox.com/u/51653511/SRAmetadb.sqlite.gz' Error in download.file(url_sra, destfile = localfile, mode = "wb", method = method) : cannot open URL 'http://dl.dropbox.com/u/51653511/SRAmetadb.sqlite.gz' > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] SRAdb_1.18.0 RCurl_1.95-4.1 bitops_1.0-6 graph_1.42.0 RSQLite_0.11.4 [6] DBI_0.2-7 loaded via a namespace (and not attached): [1] Biobase_2.24.0 BiocGenerics_0.10.0 GEOquery_2.30.1 [4] XML_3.98-1.1 parallel_3.1.0 stats4_3.1.0 [7] tools_3.1.0 Best, Robert Robert Babak Faryabi, PhD Laboratory of Genome Integrity NCI/NIH Building 37, Room 1108 37 Convent Drive Bethesda, MD 20892 Tel: (301)594-6485 Fax: (301)402-0711 URL: http://ccr.cancer.gov/labs/lab.asp?labid=920
SRAdb SRAdb • 3.4k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 3.2 years ago
United States
CC'ing the maintainer of SRAdb. Dan ----- Original Message ----- > From: "Robert Faryabi (NIH/NCI) [F]" <babak.faryabi at="" nih.gov=""> > To: bioconductor at r-project.org > Sent: Monday, July 21, 2014 9:45:34 AM > Subject: [BioC] error in SRAdb > > Hello list, > > I'm having problem with SRAdb package. Any suggestion is appreciated. > I'm getting the following error after trying to update my sqlite file > using getSRAdbFile() command. > > > getSRAdbFile() > trying URL 'http://dl.dropbox.com/u/51653511/SRAmetadb.sqlite.gz' > Error in download.file(url_sra, destfile = localfile, mode = "wb", > method = method) : > cannot open URL > 'http://dl.dropbox.com/u/51653511/SRAmetadb.sqlite.gz' > > > sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] SRAdb_1.18.0 RCurl_1.95-4.1 bitops_1.0-6 graph_1.42.0 > RSQLite_0.11.4 > [6] DBI_0.2-7 > > loaded via a namespace (and not attached): > [1] Biobase_2.24.0 BiocGenerics_0.10.0 GEOquery_2.30.1 > [4] XML_3.98-1.1 parallel_3.1.0 stats4_3.1.0 > [7] tools_3.1.0 > > Best, > Robert > > Robert Babak Faryabi, PhD > > Laboratory of Genome Integrity > NCI/NIH > Building 37, Room 1108 > 37 Convent Drive > Bethesda, MD 20892 > Tel: (301)594-6485 > Fax: (301)402-0711 > URL: http://ccr.cancer.gov/labs/lab.asp?labid=920 > > _______________________________________________ > 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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Hi Robert and Dan, Out server was down during the weekend and it looks Dropbox has blocked downloading files programmatically. Anyway our server is back. Please try again. Sorry for the inconvenience. Jack ---- Yuelin Jack Zhu Biologist (Bioinformatics) Genetics Branch/CCR/NCI/NIH Tel: (301)496-4527 FAX: (301) 402-3241 E-mail: zhujack at mail.nih.gov On Mon, Jul 21, 2014 at 12:55 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > CC'ing the maintainer of SRAdb. > Dan > > > ----- Original Message ----- >> From: "Robert Faryabi (NIH/NCI) [F]" <babak.faryabi at="" nih.gov=""> >> To: bioconductor at r-project.org >> Sent: Monday, July 21, 2014 9:45:34 AM >> Subject: [BioC] error in SRAdb >> >> Hello list, >> >> I'm having problem with SRAdb package. Any suggestion is appreciated. >> I'm getting the following error after trying to update my sqlite file >> using getSRAdbFile() command. >> >> > getSRAdbFile() >> trying URL 'http://dl.dropbox.com/u/51653511/SRAmetadb.sqlite.gz' >> Error in download.file(url_sra, destfile = localfile, mode = "wb", >> method = method) : >> cannot open URL >> 'http://dl.dropbox.com/u/51653511/SRAmetadb.sqlite.gz' >> >> > sessionInfo() >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] SRAdb_1.18.0 RCurl_1.95-4.1 bitops_1.0-6 graph_1.42.0 >> RSQLite_0.11.4 >> [6] DBI_0.2-7 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.24.0 BiocGenerics_0.10.0 GEOquery_2.30.1 >> [4] XML_3.98-1.1 parallel_3.1.0 stats4_3.1.0 >> [7] tools_3.1.0 >> >> Best, >> Robert >> >> Robert Babak Faryabi, PhD >> >> Laboratory of Genome Integrity >> NCI/NIH >> Building 37, Room 1108 >> 37 Convent Drive >> Bethesda, MD 20892 >> Tel: (301)594-6485 >> Fax: (301)402-0711 >> URL: http://ccr.cancer.gov/labs/lab.asp?labid=920 >> >> _______________________________________________ >> 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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tdaley • 0
@tdaley-9681
Last seen 8.2 years ago

Getting the same error.  The file is not available from Dropbox.
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I am having this same problem and think it is due to my employer blocking dropbox for data security reasons.   Is there any alternative download site?

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I am having the same problem. Did you manage to solve it somehow?

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djlemas • 0
@djlemas-14033
Last seen 6.6 years ago

I am having the same problem. I was able to download last week but unable to download this week.

> sqlfile <- 'SRAmetadb.sqlite'
> if(!file.exists('SRAmetadb.sqlite')) sqlfile <<- getSRAdbFile()
trying URL 'http://dl.dropbox.com/u/51653511/SRAmetadb.sqlite.gz'
Error in download.file(url_sra, destfile = localfile, mode = "wb", method = method) : 
  cannot open URL 'http://dl.dropbox.com/u/51653511/SRAmetadb.sqlite.gz'
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I am having the same problem too. By modifying the getSRAdbFile() function a bit, I've noticed that none of the 3 SQLite backup GZ files are available. I will email the maintainers.

 

By the way: the previous SRAdb version returned ByExp FTP addresses for the SRA files, however the NCBI SRA's "ByExp" arborescence no longer seems to exist as of recently (though ByRun and ByStudy still do: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/). I don't know why this has happened but it might be an issue.

 

-- A

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I received a reply from Jack Zhu for SRAdb and from Rick Lapoint for the SRA. I'm copying the essence of those answers here:

  • this error is common when the SRAdb package version is out-of-date.
    (in my case this is because my R version is out-of-date, which is in turn due to my operating system being too old for the latest R version)
  • the SRA has changed its file hierarchy, essentially retiring the "ByExp" arboresence. The FTP addresses provided in SRAdb have not yet been updated to reflect this.
  • Jack provided a download link for the latest version of the SRAdb database: https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz

 

Hope this helps,

 

-- A

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