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Question: sva package
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gravatar for S T
7.9 years ago by
S T60
S T60 wrote:
Dear users, I am having some trouble installing the SVA package for surrogate variable analysis > source("http://bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). > biocLite("sva") Using R version 2.11.1, biocinstall version 2.6.9. Installing Bioconductor version 2.6 packages: [1] "sva" Please wait... Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘sva’ is not available Can anyone help? Thanks very much. E.N.S [[alternative HTML version deleted]]
sva
ADD COMMENTlink modified 7.9 years ago by Sean Davis21k • written 7.9 years ago by S T60
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gravatar for Sean Davis
7.9 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Tue, Nov 23, 2010 at 7:07 AM, S T <elengss@gmail.com> wrote: > Dear users, > > I am having some trouble installing the SVA package for surrogate variable > analysis > > > source("http://bioconductor.org/biocLite.R") > BioC_mirror = http://www.bioconductor.org > Change using chooseBioCmirror(). > > biocLite("sva") > Using R version 2.11.1, biocinstall version 2.6.9. > Installing Bioconductor version 2.6 packages: > [1] "sva" > Please wait... > > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ‘sva’ is not available > > Can anyone help? > > I do not think that sva is a bioconductor package and it is not available via CRAN. Therefore, biocLite() won't find it. The URL appears to be: http://www.biostat.jhsph.edu/~jleek/sva/index.html Sean > Thanks very much. > > E.N.S > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 7.9 years ago by Sean Davis21k
Dear Sean, Thanks very much. I downloaded from there and installed it. However, the error message states > utils:::menuInstallLocal() package 'sva' successfully unpacked and MD5 sums checked > library(sva) Error: package 'sva' was built before R 2.10.0: please re-install it Does this mean that I would have to use it on an older version of R (I'm currently using 2.11)? Thanks again. E.N.S On Tue, Nov 23, 2010 at 8:38 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > > On Tue, Nov 23, 2010 at 7:07 AM, S T <elengss@gmail.com> wrote: > >> Dear users, >> >> I am having some trouble installing the SVA package for surrogate variable >> analysis >> >> > source("http://bioconductor.org/biocLite.R") >> BioC_mirror = http://www.bioconductor.org >> Change using chooseBioCmirror(). >> > biocLite("sva") >> Using R version 2.11.1, biocinstall version 2.6.9. >> Installing Bioconductor version 2.6 packages: >> [1] "sva" >> Please wait... >> >> Warning message: >> In getDependencies(pkgs, dependencies, available, lib) : >> package ‘sva’ is not available >> >> Can anyone help? >> >> > I do not think that sva is a bioconductor package and it is not available > via CRAN. Therefore, biocLite() won't find it. The URL appears to be: > > http://www.biostat.jhsph.edu/~jleek/sva/index.html > > Sean > > >> Thanks very much. >> >> E.N.S >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 7.9 years ago by S T60
On Tue, Nov 23, 2010 at 7:55 AM, S T <elengss@gmail.com> wrote: > Dear Sean, > > Thanks very much. > I downloaded from there and installed it. > However, the error message states > > > utils:::menuInstallLocal() > package 'sva' successfully unpacked and MD5 sums checked > > library(sva) > Error: package 'sva' was built before R 2.10.0: please re-install it > > You could ask the author to build the package for another version of R or you could install from source. In any case, it is probably best to contact the author directly, as he may have thought of these situations already. Sean > Does this mean that I would have to use it on an older version of R (I'm > currently using 2.11)? > > Thanks again. > > E.N.S > > On Tue, Nov 23, 2010 at 8:38 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > >> >> >> On Tue, Nov 23, 2010 at 7:07 AM, S T <elengss@gmail.com> wrote: >> >>> Dear users, >>> >>> I am having some trouble installing the SVA package for surrogate >>> variable >>> analysis >>> >>> > source("http://bioconductor.org/biocLite.R") >>> BioC_mirror = http://www.bioconductor.org >>> Change using chooseBioCmirror(). >>> > biocLite("sva") >>> Using R version 2.11.1, biocinstall version 2.6.9. >>> Installing Bioconductor version 2.6 packages: >>> [1] "sva" >>> Please wait... >>> >>> Warning message: >>> In getDependencies(pkgs, dependencies, available, lib) : >>> package ‘sva’ is not available >>> >>> Can anyone help? >>> >>> >> I do not think that sva is a bioconductor package and it is not available >> via CRAN. Therefore, biocLite() won't find it. The URL appears to be: >> >> http://www.biostat.jhsph.edu/~jleek/sva/index.html >> >> Sean >> >> >>> Thanks very much. >>> >>> E.N.S >>> >>> [[alternative HTML version deleted]] >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > [[alternative HTML version deleted]]
ADD REPLYlink written 7.9 years ago by Sean Davis21k
My impression is that the author is considering putting it on Bioconductor. Any additional pressure (besides me) might expedite the process; I highly recommend bugging him about it. Kasper On Tue, Nov 23, 2010 at 8:08 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Tue, Nov 23, 2010 at 7:55 AM, S T <elengss at="" gmail.com=""> wrote: > >> Dear Sean, >> >> Thanks very much. >> I downloaded from there and installed it. >> However, the error message states >> >> > utils:::menuInstallLocal() >> package 'sva' successfully unpacked and MD5 sums checked >> > library(sva) >> Error: package 'sva' was built before R 2.10.0: please re-install it >> >> > You could ask the author to build the package for another version of R or > you could install from source. ?In any case, it is probably best to contact > the author directly, as he may have thought of these situations already. > > Sean > > > >> Does this mean that I would have to use it on an older version of R (I'm >> currently using 2.11)? >> >> Thanks again. >> >> E.N.S >> >> On Tue, Nov 23, 2010 at 8:38 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> >>> >>> >>> On Tue, Nov 23, 2010 at 7:07 AM, S T <elengss at="" gmail.com=""> wrote: >>> >>>> Dear users, >>>> >>>> I am having some trouble installing the SVA package for surrogate >>>> variable >>>> analysis >>>> >>>> > source("http://bioconductor.org/biocLite.R") >>>> BioC_mirror = http://www.bioconductor.org >>>> Change using chooseBioCmirror(). >>>> > biocLite("sva") >>>> Using R version 2.11.1, biocinstall version 2.6.9. >>>> Installing Bioconductor version 2.6 packages: >>>> [1] "sva" >>>> Please wait... >>>> >>>> Warning message: >>>> In getDependencies(pkgs, dependencies, available, lib) : >>>> ?package ?sva? is not available >>>> >>>> Can anyone help? >>>> >>>> >>> I do not think that sva is a bioconductor package and it is not available >>> via CRAN. ?Therefore, biocLite() won't find it. ?The URL appears to be: >>> >>> http://www.biostat.jhsph.edu/~jleek/sva/index.html >>> >>> Sean >>> >>> >>>> Thanks very much. >>>> >>>> E.N.S >>>> >>>> ? ? ? ?[[alternative HTML version deleted]] >>>> >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >>> >> > > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > 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 >
ADD REPLYlink written 7.9 years ago by Kasper Daniel Hansen6.4k
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