Installation of ath1121501cdf
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@delphine-fleury-414
Last seen 10.2 years ago
Dear all, I tried to install the package ath1121501cdf without success. When BioConductor needs the environment I got this error message: Environment ath1121501cdf is not available. This environment contains needed probe location information. We will try to download and install the ath1121501cdf package. Note: No specified download type, defaulting to Source [1] "Attempting to download ath1121501cdf from BIOCcdf/" Error in download.file(fileURL, destFile, mode = "wb", quiet = TRUE, method = method) : unsupported URL scheme I tried several other things that didn't work. Could you give me hints? Thank you, Philippe -- ================================================================== Delphine Fleury DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium Vlaams Interuniversitair Instituut voor Biotechnologie VIB mailto:defle@psb.ugent.be http://www.psb.ugent.be
cdf probe cdf probe • 1.6k views
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@james-w-macdonald-5106
Last seen 1 hour ago
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The simplest way to get the package is to use your browser to go to the bioconductor website, download, and then use R CMD INSTALL <pkgname> (well, second easiest way, but the easiest way is not working for you...). Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> defle@psb.ugent.be 08/19/03 07:25AM >>> Dear all, I tried to install the package ath1121501cdf without success. When BioConductor needs the environment I got this error message: Environment ath1121501cdf is not available. This environment contains needed probe location information. We will try to download and install the ath1121501cdf package. Note: No specified download type, defaulting to Source [1] "Attempting to download ath1121501cdf from BIOCcdf/" Error in download.file(fileURL, destFile, mode = "wb", quiet = TRUE, method = method) : unsupported URL scheme I tried several other things that didn't work. Could you give me hints? Thank you, Philippe -- ================================================================== Delphine Fleury DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium Vlaams Interuniversitair Instituut voor Biotechnologie VIB mailto:defle@psb.ugent.be http://www.psb.ugent.be _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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Jeff Gentry ★ 3.9k
@jeff-gentry-12
Last seen 10.2 years ago
> I tried to install the package ath1121501cdf without success. When > BioConductor needs > the environment I got this error message: What are you doing to cause it to download the package? I'm not sure what it means when you say "When BioConductor needs the environment"
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The manual installation worked fine for me yesterday on linux RH9 after I had the same download error. This occurred when I tried to use justRMA() on some ATH1 .cel files when the ath1121501cdf had not been installed privously. Other packages (e.g. getBioC() ) do download fine on my system so there may be a problem with the ath1121501cdf source link in this case. Justin http://naturalvariation.org -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of James MacDonald Sent: Tuesday, August 19, 2003 5:46 AM To: defle@psb.ugent.be; delphine.fleury@psb.ugent.be; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Installation of ath1121501cdf The simplest way to get the package is to use your browser to go to the bioconductor website, download, and then use R CMD INSTALL <pkgname> (well, second easiest way, but the easiest way is not working for you...). Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> defle@psb.ugent.be 08/19/03 07:25AM >>> Dear all, I tried to install the package ath1121501cdf without success. When BioConductor needs the environment I got this error message: Environment ath1121501cdf is not available. This environment contains needed probe location information. We will try to download and install the ath1121501cdf package. Note: No specified download type, defaulting to Source [1] "Attempting to download ath1121501cdf from BIOCcdf/" Error in download.file(fileURL, destFile, mode = "wb", quiet = TRUE, method = method) : unsupported URL scheme I tried several other things that didn't work. Could you give me hints? Thank you, Philippe -- ================================================================== Delphine Fleury DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium Vlaams Interuniversitair Instituut voor Biotechnologie VIB mailto:defle@psb.ugent.be http://www.psb.ugent.be _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Justin http://naturalvariation.org -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Jeff Gentry Sent: Tuesday, August 19, 2003 8:15 AM To: delphine.fleury@psb.ugent.be Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Installation of ath1121501cdf > I tried to install the package ath1121501cdf without success. When > BioConductor needs > the environment I got this error message: What are you doing to cause it to download the package? I'm not sure what it means when you say "When BioConductor needs the environment" _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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> The manual installation worked fine for me yesterday on linux RH9 after I > had the same download error. This occurred when I tried to use justRMA() on > some ATH1 .cel files when the ath1121501cdf had not been installed > privously. Other packages (e.g. getBioC() ) do download fine on my system so > there may be a problem with the ath1121501cdf source link in this case. I am fairly certain that the affy code just uses a call in to install.packages2() from reposTools. Using reposTool I just ran 'install.packages2("ath1121501cdf") and it worked. Perhaps Laurent/Rafa might be able to shed some light. -J
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@delphine-fleury-414
Last seen 10.2 years ago
by this way it works now thanks Philippe James MacDonald wrote: > The simplest way to get the package is to use your browser to go to the > bioconductor website, download, and then use R CMD INSTALL <pkgname> > (well, second easiest way, but the easiest way is not working for > you...). > > Jim > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>> defle@psb.ugent.be 08/19/03 07:25AM >>> > Dear all, > > I tried to install the package ath1121501cdf without success. When > BioConductor needs > the environment I got this error message: > > Environment ath1121501cdf is not available. > This environment contains needed probe location information. > We will try to download and install the ath1121501cdf package. > > Note: No specified download type, defaulting to Source > [1] "Attempting to download ath1121501cdf from BIOCcdf/" > Error in download.file(fileURL, destFile, mode = "wb", quiet = TRUE, > method = method) : > unsupported URL scheme > > I tried several other things that didn't work. Could you give me > hints? > > Thank you, > Philippe > -- > ================================================================== > Delphine Fleury > DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 > GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium > Vlaams Interuniversitair Instituut voor Biotechnologie VIB > mailto:defle@psb.ugent.be http://www.psb.ugent.be > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- ================================================================== Delphine Fleury DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium Vlaams Interuniversitair Instituut voor Biotechnologie VIB mailto:defle@psb.ugent.be http://www.psb.ugent.be
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