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Question: rsqlite for windows from fhcrc
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gravatar for Kasper Daniel Hansen
3.3 years ago by
United States
Kasper Daniel Hansen6.3k wrote:
I have had an off-list email exchange with a user about installing minfi and therefore RSQLite for Windows. Now, there has been quite a few emails back and forth and I am not sure the user is doing everything by the book, but based on the log message it appears that you can run BiocInstaller 1.14.2 R 3.1.0 (Windows) and then do biocLite("RSQLite") which fetches version 0.11.4 from cran.fhcrc.org and still get R> library(RSQLite) Error: package 'RSQlite' was built before R 3.0.0: please reinstall it. (details being transcribed from a PNG screenshot so there may be typing mistakes; I am happy to send screen shot). My initial reaction is that this sound wrong (on the user side), but I now have a session transcription and it looks a bit fishy. Can anyone check this? Best, Kasper [[alternative HTML version deleted]]
ADD COMMENTlink modified 3.3 years ago by Martin Morgan ♦♦ 20k • written 3.3 years ago by Kasper Daniel Hansen6.3k
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gravatar for Martin Morgan
3.3 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:
Hi Kasper -- On 08/21/2014 07:08 PM, Kasper Daniel Hansen wrote: > I have had an off-list email exchange with a user about installing minfi > and therefore RSQLite for Windows. Now, there has been quite a few emails > back and forth and I am not sure the user is doing everything by the book, > but based on the log message it appears that you can run > BiocInstaller 1.14.2 > R 3.1.0 (Windows) > and then do > biocLite("RSQLite") > which fetches version 0.11.4 from cran.fhcrc.org and still get > R> library(RSQLite) > Error: package 'RSQlite' was built before R 3.0.0: please reinstall it. > > (details being transcribed from a PNG screenshot so there may be typing > mistakes; I am happy to send screen shot). > > My initial reaction is that this sound wrong (on the user side), but I now > have a session transcription and it looks a bit fishy. Can anyone check > this? The binary was built under 3.1.1, and installing under 3.1.0 generates a _warning_ about the mis-match between 3.1.0 and 3.1.1. It seems like biocLite() (if it's successful?) is writing to one library, and library() is reading from another. Perhaps .libPaths() in addition to information about permissions on each directory would help, e.g., if the user writeable library comes second, and there is already a version in the system library??. One can provide a 'lib' argument to both biocLite and to library to ensure that the both reference the same location. Martin > > Best, > Kasper > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > -- 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 3.3 years ago by Martin Morgan ♦♦ 20k
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