Question: Windows binary for GEOquery (R 2.10.0)
0
gravatar for Scott Markel
10.0 years ago by
Scott Markel50
Canada
Scott Markel50 wrote:
I attempted to use GEOquery in R 2.10.0 today. I'm running Windows XP. ====================== > source("http://bioconductor.org/biocLite.R") > biocLite("GEOquery") Using R version 2.10.0, biocinstall version 2.5.8. Installing Bioconductor version 2.5 packages: [1] "GEOquery" Please wait... Warning message: In getDependencies(pkgs, dependencies, available, lib) : package 'GEOquery' is not available ====================== Checking the GEOquery package page (http://bioconductor.org/packages/2.5/bioc/html/GEOquery.html) I see that the Windows binary is indeed listed as "Not available". Checking the vignette, mailing list, and a Google search didn't provide any 2.10.0-specific information that I saw. Are there plans for releasing a new Windows binary for GEOquery? Scott > sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.10.0 Scott Markel, Ph.D. Principal Bioinformatics Architect email: smarkel at accelrys.com Accelrys (SciTegic R&D) mobile: +1 858 205 3653 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 San Diego, CA 92121 fax: +1 858 799 5222 USA web: http://www.accelrys.com http://www.linkedin.com/in/smarkel Vice President, Board of Directors: International Society for Computational Biology Chair: ISCB Publications Committee Associate Editor: PLoS Computational Biology Editorial Board: Briefings in Bioinformatics
geoquery • 706 views
ADD COMMENTlink modified 10.0 years ago by Keith Satterley450 • written 10.0 years ago by Scott Markel50
Answer: Windows binary for GEOquery (R 2.10.0)
0
gravatar for Keith Satterley
10.0 years ago by
Australia
Keith Satterley450 wrote:
Hi Scott, Sean Davis responded to me on Bioc-devel about this problem. However the Bioc-devel archives report his email as " "An embedded and charset-unspecified text was scrubbed..." so I guess that is why google doesn't find it. His response on Nov-25-2009 was: On Mon, Nov 23, 2009 at 6:33 PM, Keith Satterley <keith at="" wehi.edu.au="" <mailto:keith="" at="" wehi.edu.au="">> wrote: Hi Sean, I was reading your response to Amit Mandal's query re normalization of affy data and it prompted me to check my installation of GEOquery on R-2.10.0 on my Windows box and of course you know that it is not available at the moment. Wondering if it maybe come available soon as I generally work on Windows and have used your package very successfully on R-2.9.2, I've made some changes to the vignette in the hopes that it will build fast enough to become available again. I don't have any idea why the Windows build is slower than that on Linux or MacOS, but that appears to be the case, resulting in a timeout in the vignette build process. In the meantime, the package can almost certainly be installed from source on Windows IF you have the capability of doing that. Sean Hope that helps, cheers, Keith ======================== Keith Satterley Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville, Melbourne, Victoria, Australia email:keith at wehi.edu.au ======================= Scott Markel wrote: > I attempted to use GEOquery in R 2.10.0 today. I'm running Windows XP. > > ====================== > >> source("http://bioconductor.org/biocLite.R") >> biocLite("GEOquery") >> > Using R version 2.10.0, biocinstall version 2.5.8. > Installing Bioconductor version 2.5 packages: > [1] "GEOquery" > Please wait... > > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package 'GEOquery' is not available > ====================== > > Checking the GEOquery package page > (http://bioconductor.org/packages/2.5/bioc/html/GEOquery.html) > I see that the Windows binary is indeed listed as "Not available". > Checking the vignette, mailing list, and a Google search didn't > provide any 2.10.0-specific information that I saw. > > Are there plans for releasing a new Windows binary for GEOquery? > > Scott > > >> sessionInfo() >> > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.10.0 > > > Scott Markel, Ph.D. > Principal Bioinformatics Architect email: smarkel at accelrys.com > Accelrys (SciTegic R&D) mobile: +1 858 205 3653 > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > San Diego, CA 92121 fax: +1 858 799 5222 > USA web: http://www.accelrys.com > > http://www.linkedin.com/in/smarkel > Vice President, Board of Directors: > International Society for Computational Biology > Chair: ISCB Publications Committee > Associate Editor: PLoS Computational Biology > Editorial Board: Briefings in Bioinformatics > > _______________________________________________ > 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 in this email is confidential and intend...{{dropped:4}}
ADD COMMENTlink written 10.0 years ago by Keith Satterley450
Keith Satterley wrote: > Hi Scott, > > Sean Davis responded to me on Bioc-devel about this problem. However the > Bioc-devel archives report his email as " > > "An embedded and charset-unspecified text was scrubbed..." > > so I guess that is why google doesn't find it. His response on > Nov-25-2009 was: > > On Mon, Nov 23, 2009 at 6:33 PM, Keith Satterley <keith at="" wehi.edu.au=""> <mailto:keith at="" wehi.edu.au="">> wrote: > > Hi Sean, > > I was reading your response to Amit Mandal's query re normalization > of affy data and it prompted me to check my installation of GEOquery > on R-2.10.0 on my Windows box and of course you know that it is not > available at the moment. > > Wondering if it maybe come available soon as I generally work on > Windows and have used your package very successfully on R-2.9.2, > > > I've made some changes to the vignette in the hopes that it will build > fast enough to become available again. I don't have any idea why the > Windows build is slower than that on Linux or MacOS, but that appears to > be the case, resulting in a timeout in the vignette build process. In > the meantime, the package can almost certainly be installed from source > on Windows IF you have the capability of doing that. And having the capability to build packages on Windows is now almost trivial. See http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install- packages-into-libraries-in-this-version_003f for more information. Best, Jim > > Sean > > Hope that helps, > > cheers, > > Keith > > ======================== > Keith Satterley > Bioinformatics Division > The Walter and Eliza Hall Institute of Medical Research > Parkville, Melbourne, > Victoria, Australia > email:keith at wehi.edu.au > ======================= > > > > Scott Markel wrote: >> I attempted to use GEOquery in R 2.10.0 today. I'm running Windows XP. >> >> ====================== >> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("GEOquery") >>> >> Using R version 2.10.0, biocinstall version 2.5.8. >> Installing Bioconductor version 2.5 packages: >> [1] "GEOquery" >> Please wait... >> >> Warning message: >> In getDependencies(pkgs, dependencies, available, lib) : >> package 'GEOquery' is not available >> ====================== >> >> Checking the GEOquery package page >> (http://bioconductor.org/packages/2.5/bioc/html/GEOquery.html) >> I see that the Windows binary is indeed listed as "Not available". >> Checking the vignette, mailing list, and a Google search didn't >> provide any 2.10.0-specific information that I saw. >> >> Are there plans for releasing a new Windows binary for GEOquery? >> >> Scott >> >> >>> sessionInfo() >>> >> R version 2.10.0 (2009-10-26) i386-pc-mingw32 >> locale: >> [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United >> States.1252 [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C [5] LC_TIME=English_United >> States.1252 >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> loaded via a namespace (and not attached): >> [1] tools_2.10.0 >> >> >> Scott Markel, Ph.D. >> Principal Bioinformatics Architect email: smarkel at accelrys.com >> Accelrys (SciTegic R&D) mobile: +1 858 205 3653 >> 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 >> San Diego, CA 92121 fax: +1 858 799 5222 >> USA web: http://www.accelrys.com >> >> http://www.linkedin.com/in/smarkel >> Vice President, Board of Directors: >> International Society for Computational Biology >> Chair: ISCB Publications Committee >> Associate Editor: PLoS Computational Biology >> Editorial Board: Briefings in Bioinformatics >> >> _______________________________________________ >> 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 in this email is confidential and intend...{{dropped:4}} > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD REPLYlink written 10.0 years ago by James W. MacDonald52k
On 12/8/09 10:23 AM, James W. MacDonald wrote: >> I've made some changes to the vignette in the hopes that it will build >> fast enough to become available again. I don't have any idea why the >> Windows build is slower than that on Linux or MacOS, but that appears >> to be the case, resulting in a timeout in the vignette build process. >> In the meantime, the package can almost certainly be installed from >> source on Windows IF you have the capability of doing that. > > And having the capability to build packages on Windows is now almost > trivial. See > > http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I -install-packages-into-libraries-in-this-version_003f We believe we have now identified the cause of the problem for GEOquery on Windows. At issue is the use of base::seek which is not reliable on Windows. So while installing on Windows from source will work, not all package functionality will work as desired. We are working with Sean to fix things by avoiding seek. + seth -- Seth Falcon Program in Computational Biology | Fred Hutchinson Cancer Research Center
ADD REPLYlink written 10.0 years ago by Seth Falcon7.4k
On Tue, Dec 8, 2009 at 1:39 PM, Seth Falcon <sfalcon at="" fhcrc.org=""> wrote: > On 12/8/09 10:23 AM, James W. MacDonald wrote: >>> >>> I've made some changes to the vignette in the hopes that it will build >>> fast enough to become available again. I don't have any idea why the >>> Windows build is slower than that on Linux or MacOS, but that appears >>> to be the case, resulting in a timeout in the vignette build process. >>> In the meantime, the package can almost certainly be installed from >>> source on Windows IF you have the capability of doing that. >> >> And having the capability to build packages on Windows is now almost >> trivial. See >> >> >> http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I -install-packages-into-libraries-in-this-version_003f > > We believe we have now identified the cause of the problem for GEOquery on > Windows. ?At issue is the use of base::seek which is not reliable on > Windows. ?So while installing on Windows from source will work, not all > package functionality will work as desired. > > We are working with Sean to fix things by avoiding seek. As far as I know, I have fixed these issues. Thanks to Martin and the folks in Seattle for identifying the source of the problem. A new version of GEOquery is now available. Sorry for the inconvenience. Sean
ADD REPLYlink written 10.0 years ago by Sean Davis21k
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