Unable to install KEGGgraph
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anupam sinha ▴ 270
@anupam-sinha-3207
Last seen 8.2 years ago
Hi all, I am unable to install "KEGGgraph" packages> It gives the following error : *> source("http://bioconductor.org/biocLite.R") Warning messages: 1: In safeSource() : Redefining ‘biocinstall’ 2: In safeSource() : Redefining ‘biocinstallPkgGroups’ 3: In safeSource() : Redefining ‘biocinstallRepos’ > biocLite("KEGGgraph") Running biocinstall version 2.1.11 with R version 2.6.1 Your version of R requires version 2.1 of BioConductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/anupam/R/i686-redhat-linux-gnu-library/2.6' Warning message: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : package ‘KEGGgraph’ is not available * *> sessionInfo() R version 2.6.1 (2007-11-26) i686-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] ppiStats_1.4.1 ppiData_0.1.10 Rgraphviz_1.16.0 [4] YEAST_2.0.1 GOstats_2.4.0 Category_2.4.0 [7] genefilter_1.16.0 survival_2.34 RBGL_1.16.0 [10] annotate_1.16.1 xtable_1.5-2 GO.db_2.0.2 [13] AnnotationDbi_1.0.6 RSQLite_0.6-9 DBI_0.2-4 [16] Biobase_1.16.3 graph_1.20.0 GO_2.0.1 loaded via a namespace (and not attached): [1] cluster_1.11.9 rcompgen_0.1-17 * Can anyone help me out please ? Regards, Anupam Sinha [[alternative HTML version deleted]]
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@wolfgang-huber-3550
Last seen 10 weeks ago
EMBL European Molecular Biology Laborat…
Dear Anupam Sinha you need a more recent version of R, e.g. version 2.9, which you can get from here: http://www.r-project.org Then try again with source("http://bioconductor.org/biocLite.R") biocLite("KEGGgraph") Best wishes Wolfgang ------------------------------------------------ Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber anupam sinha ha scritto: > Hi all, > I am unable to install "KEGGgraph" packages> It gives the > following error : > > *> source("http://bioconductor.org/biocLite.R") > Warning messages: > 1: In safeSource() : Redefining ?biocinstall? > 2: In safeSource() : Redefining ?biocinstallPkgGroups? > 3: In safeSource() : Redefining ?biocinstallRepos? >> biocLite("KEGGgraph") > Running biocinstall version 2.1.11 with R version 2.6.1 > Your version of R requires version 2.1 of BioConductor. > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > argument 'lib' is missing: using > '/home/anupam/R/i686-redhat-linux-gnu-library/2.6' > Warning message: > In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > package ?KEGGgraph? is not available > * > *> sessionInfo() > R version 2.6.1 (2007-11-26) > i686-redhat-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] ppiStats_1.4.1 ppiData_0.1.10 Rgraphviz_1.16.0 > [4] YEAST_2.0.1 GOstats_2.4.0 Category_2.4.0 > [7] genefilter_1.16.0 survival_2.34 RBGL_1.16.0 > [10] annotate_1.16.1 xtable_1.5-2 GO.db_2.0.2 > [13] AnnotationDbi_1.0.6 RSQLite_0.6-9 DBI_0.2-4 > [16] Biobase_1.16.3 graph_1.20.0 GO_2.0.1 > > loaded via a namespace (and not attached): > [1] cluster_1.11.9 rcompgen_0.1-17 > * > Can anyone help me out please ? > > Regards, > > Anupam Sinha > > [[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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