Can't get RCurl...
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Jenny Drnevich ★ 2.2k
@jenny-drnevich-382
Last seen 10.2 years ago
HI, I'm helping someone install the affycoretools package, but there seems to be a problem getting RCurl that's needed for biomaRt and hence affycoretools. Here's what was done and the sessionInfo(): I just uninstalled everything and re-installed R and Bioconductor packages using > source("http://bioconductor.org/biocLite.R") > biocLite() After that I installed afyycoretools by: > biocLite("affycoretools") It gave the following message: > biocLite("affycoretools") Running biocinstall version 1.9.9 with R version 2.4.1 Your version of R requires version 1.9 of Bioconductor. trying URL 'http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/aff ycoretools_1.6.1.zip' Content type 'application/zip' length 6867656 bytes opened URL downloaded 6706Kb package 'affycoretools' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\Hoyer Lab\Local Settings\Temp\RtmpDLCJrb\downloaded_packages updating HTML package descriptions It seems the installation is successful. However, when I tried to load affycoretools by: >library(affycoretools) It gave the fowllowings: > library(affycoretools) Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Loading required package: affyio Loading required package: limma Loading required package: GOstats Loading required package: graph Loading required package: GO Loading required package: annotate Loading required package: RBGL Loading required package: Category Loading required package: KEGG Loading required package: genefilter Loading required package: survival Loading required package: splines Loading required package: biomaRt Loading required package: XML Attaching package: 'XML' The following object(s) are masked from package:graph : addNode Loading required package: RCurl Error: package 'RCurl' could not be loaded In addition: Warning message: there is no package called 'RCurl' in: library(pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc) > sessionInfo() R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: XML GOstats Category genefilter survival KEGG RBGL "1.6-0" "2.0.4" "2.0.3" "1.12.0" "2.30" "1.14.1" "1.10.0" annotate GO graph limma affy affyio Biobase "1.12.1" "1.14.1" "1.12.1" "2.9.17" "1.12.2" "1.2.0" "1.12.2" > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
GO Survival annotate genefilter affy graph limma GOstats biomaRt Category affycoretools • 2.0k views
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@james-w-macdonald-5106
Last seen 1 day ago
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Hi Jenny, Seems odd that biocLite() didn't install all dependencies, but what do you get with biocLite("RCurl")? You might also add RMySQL, which is much faster if you need to annotate lots of genes. Best, Jim Jenny Drnevich wrote: > HI, > > I'm helping someone install the affycoretools package, but there > seems to be a problem getting RCurl that's needed for biomaRt and > hence affycoretools. Here's what was done and the sessionInfo(): > > I just uninstalled everything and re-installed R and Bioconductor > packages using > > > source("http://bioconductor.org/biocLite.R") > > biocLite() > > After that I installed afyycoretools by: > > biocLite("affycoretools") > > It gave the following message: > > > biocLite("affycoretools") > > Running biocinstall version 1.9.9 with R version 2.4.1 > Your version of R requires version 1.9 of Bioconductor. > trying URL > 'http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/a ffycoretools_1.6.1.zip' > Content type 'application/zip' length 6867656 bytes > opened URL > downloaded 6706Kb > > package 'affycoretools' successfully unpacked and MD5 sums checked > > The downloaded packages are in > C:\Documents and Settings\Hoyer Lab\Local > Settings\Temp\RtmpDLCJrb\downloaded_packages > updating HTML package descriptions > > It seems the installation is successful. > > However, when I tried to load affycoretools by: > >library(affycoretools) > > It gave the fowllowings: > > library(affycoretools) > > Loading required package: affy > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > > Loading required package: affyio > Loading required package: limma > Loading required package: GOstats > Loading required package: graph > Loading required package: GO > Loading required package: annotate > Loading required package: RBGL > Loading required package: Category > Loading required package: KEGG > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Loading required package: biomaRt > Loading required package: XML > > Attaching package: 'XML' > > > The following object(s) are masked from package:graph : > > addNode > > Loading required package: RCurl > Error: package 'RCurl' could not be loaded > In addition: Warning message: > there is no package called 'RCurl' in: library(pkg, character.only = > TRUE, logical = TRUE, lib.loc = lib.loc) > > > sessionInfo() > > R version 2.4.1 (2006-12-18) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "methods" "base" > > other attached packages: > XML GOstats Category genefilter survival KEGG RBGL > "1.6-0" "2.0.4" "2.0.3" "1.12.0" "2.30" "1.14.1" "1.10.0" > annotate GO graph limma affy affyio Biobase > "1.12.1" "1.14.1" "1.12.1" "2.9.17" "1.12.2" "1.2.0" "1.12.2" > > > > > > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > _______________________________________________ > 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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Hi Jim, biocLite("RCurl") did work. I'm not sure what went wrong before... The person I was helping had tried to download packages on his own before, and I don't think he was using biocLite. What may have happened is that he installed biomaRt via a local zip file, but then didn't remove it before doing biocLite("affycoretools"). Perhaps biocLite stopped because it saw he had biomaRt, which is a dependency of affycoretools, whereas RCurl is not a direct dependency of affycoretools. Thanks, Jenny At 03:42 PM 4/5/2007, James W. MacDonald wrote: >Hi Jenny, > >Seems odd that biocLite() didn't install all dependencies, but what >do you get with biocLite("RCurl")? > >You might also add RMySQL, which is much faster if you need to >annotate lots of genes. > >Best, > >Jim > >Jenny Drnevich wrote: >>HI, >>I'm helping someone install the affycoretools package, but there >>seems to be a problem getting RCurl that's needed for biomaRt and >>hence affycoretools. Here's what was done and the sessionInfo(): >>I just uninstalled everything and re-installed R and Bioconductor >>packages using >> > source("http://bioconductor.org/biocLite.R") >> > biocLite() >>After that I installed afyycoretools by: >> > biocLite("affycoretools") >>It gave the following message: >> > biocLite("affycoretools") >>Running biocinstall version 1.9.9 with R version 2.4.1 >>Your version of R requires version 1.9 of Bioconductor. >>trying URL >>'http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/a ffycoretools_1.6.1.zip' >>Content type 'application/zip' length 6867656 bytes >>opened URL >>downloaded 6706Kb >>package 'affycoretools' successfully unpacked and MD5 sums checked >>The downloaded packages are in >> C:\Documents and Settings\Hoyer Lab\Local >> Settings\Temp\RtmpDLCJrb\downloaded_packages >>updating HTML package descriptions >>It seems the installation is successful. >>However, when I tried to load affycoretools by: >> >library(affycoretools) >>It gave the fowllowings: >> > library(affycoretools) >>Loading required package: affy >>Loading required package: Biobase >>Loading required package: tools >>Welcome to Bioconductor >> Vignettes contain introductory material. To view, type >> 'openVignette()' or start with 'help(Biobase)'. For details >> on reading vignettes, see the openVignette help page. >>Loading required package: affyio >>Loading required package: limma >>Loading required package: GOstats >>Loading required package: graph >>Loading required package: GO >>Loading required package: annotate >>Loading required package: RBGL >>Loading required package: Category >>Loading required package: KEGG >>Loading required package: genefilter >>Loading required package: survival >>Loading required package: splines >>Loading required package: biomaRt >>Loading required package: XML >>Attaching package: 'XML' >> >> The following object(s) are masked from package:graph : >> addNode >>Loading required package: RCurl >>Error: package 'RCurl' could not be loaded >>In addition: Warning message: >>there is no package called 'RCurl' in: library(pkg, character.only >>= TRUE, logical = TRUE, lib.loc = lib.loc) >> > sessionInfo() >>R version 2.4.1 (2006-12-18) >>i386-pc-mingw32 >>locale: >>LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>States.1252;LC_MONETARY=English_United >>States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>attached base packages: >>[1] "splines" "tools" "stats" "graphics" "grDevices" "utils" >>[7] "datasets" "methods" "base" >>other attached packages: >> XML GOstats Category >> genefilter survival KEGG RBGL >> "1.6-0" "2.0.4" "2.0.3" "1.12.0" "2.30" "1.14.1" >> "1.10.0" >> annotate GO graph limma affy affyio >> Biobase >> "1.12.1" "1.14.1" "1.12.1" "2.9.17" "1.12.2" "1.2.0" >> "1.12.2" >> > >> >>Jenny Drnevich, Ph.D. >>Functional Genomics Bioinformatics Specialist >>W.M. Keck Center for Comparative and Functional Genomics >>Roy J. Carver Biotechnology Center >>University of Illinois, Urbana-Champaign >>330 ERML >>1201 W. Gregory Dr. >>Urbana, IL 61801 >>USA >>ph: 217-244-7355 >>fax: 217-265-5066 >>e-mail: drnevich at uiuc.edu >>_______________________________________________ >>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 >Affymetrix and cDNA Microarray Core >University of Michigan Cancer Center >1500 E. Medical Center Drive >7410 CCGC >Ann Arbor MI 48109 >734-647-5623 > > >********************************************************** >Electronic Mail is not secure, may not be read every day, and should >not be used for urgent or sensitive issues. Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
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RCurl is available from the Omegahat site: http://www.omegahat.org/RCurl/RCurl_0.8-0.tar.gz -Christos Christos Hatzis, Ph.D. Nuvera Biosciences, Inc. 400 West Cummings Park Suite 5350 Woburn, MA 01801 Tel: 781-938-3830 www.nuverabio.com > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Jenny Drnevich > Sent: Thursday, April 05, 2007 5:21 PM > To: James W. MacDonald > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Can't get RCurl... > > Hi Jim, > > biocLite("RCurl") did work. I'm not sure what went wrong > before... The person I was helping had tried to download > packages on his own before, and I don't think he was using > biocLite. What may have happened is that he installed biomaRt > via a local zip file, but then didn't remove it before doing > biocLite("affycoretools"). Perhaps biocLite stopped because > it saw he had biomaRt, which is a dependency of > affycoretools, whereas RCurl is not a direct dependency of > affycoretools. > > Thanks, > Jenny > > > At 03:42 PM 4/5/2007, James W. MacDonald wrote: > >Hi Jenny, > > > >Seems odd that biocLite() didn't install all dependencies, > but what do > >you get with biocLite("RCurl")? > > > >You might also add RMySQL, which is much faster if you need > to annotate > >lots of genes. > > > >Best, > > > >Jim > > > >Jenny Drnevich wrote: > >>HI, > >>I'm helping someone install the affycoretools package, but > there seems > >>to be a problem getting RCurl that's needed for biomaRt and hence > >>affycoretools. Here's what was done and the sessionInfo(): > >>I just uninstalled everything and re-installed R and Bioconductor > >>packages using > >> > source("http://bioconductor.org/biocLite.R") > >> > biocLite() > >>After that I installed afyycoretools by: > >> > biocLite("affycoretools") > >>It gave the following message: > >> > biocLite("affycoretools") > >>Running biocinstall version 1.9.9 with R version 2.4.1 Your > version of > >>R requires version 1.9 of Bioconductor. > >>trying URL > >>'http://bioconductor.org/packages/1.9/bioc/bin/windows/contr > ib/2.4/affycoretools_1.6.1.zip' > >>Content type 'application/zip' length 6867656 bytes opened URL > >>downloaded 6706Kb package 'affycoretools' successfully unpacked and > >>MD5 sums checked The downloaded packages are in > >> C:\Documents and Settings\Hoyer Lab\Local > >>Settings\Temp\RtmpDLCJrb\downloaded_packages > >>updating HTML package descriptions > >>It seems the installation is successful. > >>However, when I tried to load affycoretools by: > >> >library(affycoretools) > >>It gave the fowllowings: > >> > library(affycoretools) > >>Loading required package: affy > >>Loading required package: Biobase > >>Loading required package: tools > >>Welcome to Bioconductor > >> Vignettes contain introductory material. To view, type > >> 'openVignette()' or start with 'help(Biobase)'. For details > >> on reading vignettes, see the openVignette help page. > >>Loading required package: affyio > >>Loading required package: limma > >>Loading required package: GOstats > >>Loading required package: graph > >>Loading required package: GO > >>Loading required package: annotate > >>Loading required package: RBGL > >>Loading required package: Category > >>Loading required package: KEGG > >>Loading required package: genefilter > >>Loading required package: survival > >>Loading required package: splines > >>Loading required package: biomaRt > >>Loading required package: XML > >>Attaching package: 'XML' > >> > >> The following object(s) are masked from package:graph : > >> addNode > >>Loading required package: RCurl > >>Error: package 'RCurl' could not be loaded In addition: Warning > >>message: > >>there is no package called 'RCurl' in: library(pkg, > character.only = > >>TRUE, logical = TRUE, lib.loc = lib.loc) > >> > sessionInfo() > >>R version 2.4.1 (2006-12-18) > >>i386-pc-mingw32 > >>locale: > >>LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > >>States.1252;LC_MONETARY=English_United > >>States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > attached > >>base packages: > >>[1] "splines" "tools" "stats" "graphics" > "grDevices" "utils" > >>[7] "datasets" "methods" "base" > >>other attached packages: > >> XML GOstats Category > >> genefilter survival KEGG RBGL > >> "1.6-0" "2.0.4" "2.0.3" "1.12.0" "2.30" "1.14.1" > >> "1.10.0" > >> annotate GO graph limma affy affyio > >> Biobase > >> "1.12.1" "1.14.1" "1.12.1" "2.9.17" "1.12.2" "1.2.0" > >> "1.12.2" > >> > > >> > >>Jenny Drnevich, Ph.D. > >>Functional Genomics Bioinformatics Specialist W.M. Keck Center for > >>Comparative and Functional Genomics Roy J. Carver > Biotechnology Center > >>University of Illinois, Urbana-Champaign 330 ERML > >>1201 W. Gregory Dr. > >>Urbana, IL 61801 > >>USA > >>ph: 217-244-7355 > >>fax: 217-265-5066 > >>e-mail: drnevich at uiuc.edu > >>_______________________________________________ > >>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 > >Affymetrix and cDNA Microarray Core > >University of Michigan Cancer Center > >1500 E. Medical Center Drive > >7410 CCGC > >Ann Arbor MI 48109 > >734-647-5623 > > > > > >********************************************************** > >Electronic Mail is not secure, may not be read every day, and should > >not be used for urgent or sensitive issues. > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > _______________________________________________ > 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 > >
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