int.geneint.db package installation
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.9 years ago
Hi, I was trying to install the int.geneint.db package, but was getting errors: > source("http://bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). Warning messages: 1: In safeSource() : Redefining ‘biocinstall’ 2: In safeSource() : Redefining ‘biocinstallPkgGroups’ 3: In safeSource() : Redefining ‘biocinstallRepos’ > biocLite("int.geneint.db") Using R version 2.11.1, biocinstall version 2.6.8. Installing Bioconductor version 2.6 packages: [1] "int.geneint.db" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument 'lib' is missing: using '/Users/nj/Library/R/2.11/library' Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘int.geneint.db’ is not available > library("int.geneint.db") Error in library("int.geneint.db") : there is no package called 'int.geneint.db' > My sessionInfo(): > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] colorRamps_2.3 org.Hs.eg.db_2.4.1 lumiHumanIDMapping_1.6.2 [4] lumi_1.14.0 preprocessCore_1.10.0 mgcv_1.6-2 [7] affy_1.26.1 annotate_1.26.1 methylumi_1.3.3 [10] GOstats_2.14.0 RSQLite_0.9-1 DBI_0.2-5 [13] graph_1.26.0 Category_2.14.0 AnnotationDbi_1.10.1 [16] Biobase_2.8.0 biclust_0.9.1 vcd_1.2-8 [19] colorspace_1.0-1 MASS_7.3-6 isa2_0.2.1 [22] gplots_2.8.0 caTools_1.10 bitops_1.0-4.1 [25] gdata_2.7.2 gtools_2.6.2 heatmap.plus_1.3 loaded via a namespace (and not attached): [1] affyio_1.16.0 genefilter_1.30.0 GO.db_2.4.1 GSEABase_1.10.0 [5] lattice_0.18-8 Matrix_0.999375-39 nlme_3.1-96 RBGL_1.24.0 [9] splines_2.11.1 survival_2.35-8 tools_2.11.1 XML_3.1-0 [13] xtable_1.5-6 [[alternative HTML version deleted]]
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Heidi Dvinge ★ 2.0k
@heidi-dvinge-2195
Last seen 7.9 years ago
Hello Tim, it looks like this package has been deprecated and is no longer available in R 2.6. Cheers \Heidi > Hi, > > I was trying to install the int.geneint.db package, but was getting > errors: > > >> source("http://bioconductor.org/biocLite.R") > BioC_mirror = http://www.bioconductor.org > Change using chooseBioCmirror(). > Warning messages: > 1: In safeSource() : Redefining ???biocinstall??? > 2: In safeSource() : Redefining ???biocinstallPkgGroups??? > 3: In safeSource() : Redefining ???biocinstallRepos??? >> biocLite("int.geneint.db") > Using R version 2.11.1, biocinstall version 2.6.8. > Installing Bioconductor version 2.6 packages: > [1] "int.geneint.db" > Please wait... > > Warning in install.packages(pkgs = pkgs, repos = repos, ...) : > argument 'lib' is missing: using '/Users/nj/Library/R/2.11/library' > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ???int.geneint.db??? is not available >> library("int.geneint.db") > Error in library("int.geneint.db") : > there is no package called 'int.geneint.db' >> > > My sessionInfo(): > >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > base > > > other attached packages: > [1] colorRamps_2.3 org.Hs.eg.db_2.4.1 > lumiHumanIDMapping_1.6.2 > [4] lumi_1.14.0 preprocessCore_1.10.0 mgcv_1.6-2 > [7] affy_1.26.1 annotate_1.26.1 methylumi_1.3.3 > [10] GOstats_2.14.0 RSQLite_0.9-1 DBI_0.2-5 > [13] graph_1.26.0 Category_2.14.0 > AnnotationDbi_1.10.1 > [16] Biobase_2.8.0 biclust_0.9.1 vcd_1.2-8 > [19] colorspace_1.0-1 MASS_7.3-6 isa2_0.2.1 > [22] gplots_2.8.0 caTools_1.10 bitops_1.0-4.1 > [25] gdata_2.7.2 gtools_2.6.2 heatmap.plus_1.3 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 genefilter_1.30.0 GO.db_2.4.1 > GSEABase_1.10.0 > [5] lattice_0.18-8 Matrix_0.999375-39 nlme_3.1-96 RBGL_1.24.0 > [9] splines_2.11.1 survival_2.35-8 tools_2.11.1 XML_3.1-0 > [13] xtable_1.5-6 > > > > > [[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
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Thanks Heidi. Do you know of any other package that would provide gene gene interactions? take care, ________________________________ From: Heidi Dvinge <heidi@ebi.ac.uk> Cc: bioc <bioconductor@stat.math.ethz.ch> Sent: Sun, September 5, 2010 12:05:46 PM Subject: Re: [BioC] int.geneint.db package installation Hello Tim, it looks like this package has been deprecated and is no longer available in R 2.6. Cheers \Heidi > Hi, > > I was trying to install the int.geneint.db package, but was getting > errors: > > >> source("http://bioconductor.org/biocLite.R") > BioC_mirror = http://www.bioconductor.org > Change using chooseBioCmirror(). > Warning messages: > 1: In safeSource() : Redefining ‘biocinstall’ > 2: In safeSource() : Redefining ‘biocinstallPkgGroups’ > 3: In safeSource() : Redefining ‘biocinstallRepos’ >> biocLite("int.geneint.db") > Using R version 2.11.1, biocinstall version 2.6.8. > Installing Bioconductor version 2.6 packages: > [1] "int.geneint.db" > Please wait... > > Warning in install.packages(pkgs = pkgs, repos = repos, ...) : > argument 'lib' is missing: using '/Users/nj/Library/R/2.11/library' > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ‘int.geneint.db’ is not available >> library("int.geneint.db") > Error in library("int.geneint.db") : > there is no package called 'int.geneint.db' >> > > My sessionInfo(): > >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > base > > > other attached packages: > [1] colorRamps_2.3 org.Hs.eg.db_2.4.1 > lumiHumanIDMapping_1.6.2 > [4] lumi_1.14.0 preprocessCore_1.10.0 mgcv_1.6-2 > [7] affy_1.26.1 annotate_1.26.1 methylumi_1.3.3 > [10] GOstats_2.14.0 RSQLite_0.9-1 DBI_0.2-5 > [13] graph_1.26.0 Category_2.14.0 > AnnotationDbi_1.10.1 > [16] Biobase_2.8.0 biclust_0.9.1 vcd_1.2-8 > [19] colorspace_1.0-1 MASS_7.3-6 isa2_0.2.1 > [22] gplots_2.8.0 caTools_1.10 bitops_1.0-4.1 > [25] gdata_2.7.2 gtools_2.6.2 heatmap.plus_1.3 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 genefilter_1.30.0 GO.db_2.4.1 > GSEABase_1.10.0 > [5] lattice_0.18-8 Matrix_0.999375-39 nlme_3.1-96 RBGL_1.24.0 > [9] splines_2.11.1 survival_2.35-8 tools_2.11.1 XML_3.1-0 > [13] xtable_1.5-6 > > > > > [[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]]
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