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Question: GEOmetadb: problem with SQLite database download
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gravatar for Axel Klenk
7.9 years ago by
Axel Klenk810
Switzerland
Axel Klenk810 wrote:
Dear BioC list, I have tried updating my GEOmetadb SQLite database today using the code below (which has worked for me about a month ago) and received the following error message: > library("GEOmetadb") Loading required package: GEOquery Loading required package: RCurl Loading required package: bitops Loading required package: RSQLite Loading required package: DBI > getSQLiteFile() trying URL 'http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz' Error in download.file(" http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz", : cannot open URL 'http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz' In addition: Warning message: In download.file("http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz", : cannot open: HTTP status was '404 Not Found' In addition, the package website at http://gbnci.abcc.ncifcrf.gov/geo/ reports a funny size and date for this file -- and the link to that file also gives an HTTP 404. So I assume there's a problem on the server side or am I going wrong somewhere? Thanks in advance, - axel > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu 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=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 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] GEOmetadb_1.6.0 RSQLite_0.7-3 DBI_0.2-4 [4] GEOquery_2.11.2 RCurl_1.3-0 bitops_1.0-4.1 [7] limma_3.2.1 sfsmisc_1.0-9 geneplotter_1.24.0 [10] lattice_0.17-26 annotate_1.24.0 AnnotationDbi_1.8.1 [13] Biobase_2.6.1 MASS_7.3-3 gmodels_2.15.0 [16] fortunes_1.3-6 loaded via a namespace (and not attached): [1] gdata_2.6.1 grid_2.10.1 gtools_2.6.1 RColorBrewer_1.0-2 [5] tools_2.10.1 xtable_1.5-6 Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com
ADD COMMENTlink modified 7.9 years ago • written 7.9 years ago by Axel Klenk810
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gravatar for Axel Klenk
7.9 years ago by
Axel Klenk810
Switzerland
Axel Klenk810 wrote:
Hi Jack and Sean, yep, it works again -- thanks a lot for your quick help, - axel Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland Jack Zhu <zhujack at="" mail.nih.gov=""> Sent by: yuelin at gmail.com 12/16/2009 04:42 PM To axel.klenk at actelion.com cc "Davis, Sean (NCI)" <seandavi at="" gmail.com=""> Subject Re: [BioC] GEOmetadb: problem with SQLite database download Hi Axel, GEOmetadb.sqlite.gz was not available due to one of our servers was down. It has been fixed. Thanks for the message. Jack On Wed, Dec 16, 2009 at 10:19 AM, Davis, Sean (NCI) <seandavi at="" gmail.com=""> wrote: > I assume this was due to Alps being down. Can you trigger a build? > > Thanks, > Sean > > > ---------- Forwarded message ---------- > From: <axel.klenk at="" actelion.com=""> > Date: Wed, Dec 16, 2009 at 9:43 AM > Subject: [BioC] GEOmetadb: problem with SQLite database download > To: bioconductor at stat.math.ethz.ch > > > Dear BioC list, > > I have tried updating my GEOmetadb SQLite database today > using the code below (which has worked for me about a month > ago) and received the following error message: > >> library("GEOmetadb") > Loading required package: GEOquery > Loading required package: RCurl > Loading required package: bitops > Loading required package: RSQLite > Loading required package: DBI > >> getSQLiteFile() > trying URL 'http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz' > Error in download.file(" > http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz", : > cannot open URL 'http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz' > In addition: Warning message: > In download.file("http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz ", > : > cannot open: HTTP status was '404 Not Found' > > > In addition, the package website at http://gbnci.abcc.ncifcrf.gov/geo/ > reports a funny size and date for this file -- and the link to that file > also > gives an HTTP 404. So I assume there's a problem on the server side > or am I going wrong somewhere? > > Thanks in advance, > > - axel > > >> sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-pc-linux-gnu > > 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=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 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] GEOmetadb_1.6.0 RSQLite_0.7-3 DBI_0.2-4 > [4] GEOquery_2.11.2 RCurl_1.3-0 bitops_1.0-4.1 > [7] limma_3.2.1 sfsmisc_1.0-9 geneplotter_1.24.0 > [10] lattice_0.17-26 annotate_1.24.0 AnnotationDbi_1.8.1 > [13] Biobase_2.6.1 MASS_7.3-3 gmodels_2.15.0 > [16] fortunes_1.3-6 > > loaded via a namespace (and not attached): > [1] gdata_2.6.1 grid_2.10.1 gtools_2.6.1 RColorBrewer_1.0-2 > [5] tools_2.10.1 xtable_1.5-6 > > > Axel Klenk > Research Informatician > Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / > Switzerland > > > > The information of this email and in any file transmitted with it is > strictly confidential and may be legally privileged. > It is intended solely for the addressee. If you are not the intended > recipient, any copying, distribution or any other use of this email is > prohibited and may be unlawful. In such case, you should please notify > the sender immediately and destroy this email. > The content of this email is not legally binding unless confirmed by letter. > Any views expressed in this message are those of the individual > sender, except where the message states otherwise and the sender is > authorised to state them to be the views of the sender's company. For > further information about Actelion please see our website at > http://www.actelion.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com
ADD COMMENTlink written 7.9 years ago by Axel Klenk810
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