Help in installing affycoretools

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Sunny Srivastava ▴ 350

@sunny-srivastava-3793

Last seen 9.6 years ago

Dear Bioconductor Helpers, I was trying to install affycoretools package on my computer but it gives a series of errors and doesn't install following are the messages: ## I think the error is related to this warning at the time I use biocLite("affycoretools") Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/baba/R/x86_64-pc-linux-gnu-library/2.8' also installing the dependencies GSEABase, Category, XML, RCurl, GOstats, biomaRt ## These are the series of errors in between downloads and other gcc checks ERROR: configuration failed for package 'XML' ERROR: configuration failed for package 'RCurl' Error in loadNamespace(i[[1]], c(lib.loc, .libPaths())) : ERROR: lazy loading failed for package 'GSEABase' Error in loadNamespace(i, c(lib.loc, .libPaths())) : ERROR: lazy loading failed for package 'biomaRt' ERROR: lazy loading failed for package 'Category' ERROR: lazy loading failed for package 'GOstats' ---------------------------------------------------------------------- ---------------------------------------------------------------------- ------------------------------- I also tried >biocLite("XML") But I get the same set of warnings again. Any help is appreciated. Following is my sessionInfo() output: > sessionInfo() R version 2.8.1 (2008-12-22) x86_64-pc-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=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] mdssgpexprcdf_1.20.0 limma_2.16.5 simpleaffy_2.18.0 [4] genefilter_1.22.0 survival_2.34-1 affyPLM_1.18.1 [7] preprocessCore_1.4.0 gcrma_2.14.1 matchprobes_1.14.1 [10] affy_1.20.2 Biobase_2.2.2 loaded via a namespace (and not attached): [1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.3 [4] DBI_0.2-4 RSQLite_0.7-3 [[alternative HTML version deleted]]

affycoretools affycoretools • 1.6k views

ADD COMMENT • link updated 14.4 years ago by Martin Morgan 25k • written 14.4 years ago by Sunny Srivastava ▴ 350

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Martin Morgan 25k

@martin-morgan-1513

Last seen 7 hours ago

United States

Sunny Srivastava <research.baba at="" gmail.com=""> writes: > Dear Bioconductor Helpers, > I was trying to install affycoretools package on my computer but it gives a > series of errors and doesn't install following are the messages: > > ## I think the error is related to this warning at the time I use > biocLite("affycoretools") > > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > argument 'lib' is missing: using > '/home/baba/R/x86_64-pc-linux-gnu-library/2.8' > also installing the dependencies ?GSEABase?, ?Category?, ?XML?, ?RCurl?, > ?GOstats?, ?biomaRt? > > ## These are the series of errors in between downloads and other gcc checks > > ERROR: configuration failed for package 'XML' > > ERROR: configuration failed for package 'RCurl' XML and RCurl have external operating system dependencies, likely you need to install libxml2 and libcurl into your system. Martin > Error in loadNamespace(i[[1]], c(lib.loc, .libPaths())) : > > ERROR: lazy loading failed for package 'GSEABase' > > Error in loadNamespace(i, c(lib.loc, .libPaths())) : > > ERROR: lazy loading failed for package 'biomaRt' > > ERROR: lazy loading failed for package 'Category' > > ERROR: lazy loading failed for package 'GOstats' > -------------------------------------------------------------------- ---------------------------------------------------------------------- --------------------------------- > I also tried >>biocLite("XML") > > But I get the same set of warnings again. > > Any help is appreciated. > > > Following is my sessionInfo() output: >> sessionInfo() > R version 2.8.1 (2008-12-22) > x86_64-pc-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=C;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_IDEN TIFICATION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] mdssgpexprcdf_1.20.0 limma_2.16.5 simpleaffy_2.18.0 > [4] genefilter_1.22.0 survival_2.34-1 affyPLM_1.18.1 > [7] preprocessCore_1.4.0 gcrma_2.14.1 matchprobes_1.14.1 > [10] affy_1.20.2 Biobase_2.2.2 > > loaded via a namespace (and not attached): > [1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.3 > [4] DBI_0.2-4 RSQLite_0.7-3 > > [[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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

ADD COMMENT • link 14.4 years ago Martin Morgan 25k

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Thanks Martin for the reply. I am using ubuntu 9.04 and libxml2 was already installed on it. I installed libcurl3 (could not find libcurl). Still I am not able to install affycoretools or XML. --- > sessionInfo() R version 2.8.1 (2008-12-22) x86_64-pc-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=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.8.1 ----- Thanks for any help. Regards, S. On Sat, Nov 21, 2009 at 12:19 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > Sunny Srivastava <research.baba@gmail.com> writes: > > > Dear Bioconductor Helpers, > > I was trying to install affycoretools package on my computer but it gives > a > > series of errors and doesn't install following are the messages: > > > > ## I think the error is related to this warning at the time I use > > biocLite("affycoretools") > > > > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > > dependencies, : > > argument 'lib' is missing: using > > '/home/baba/R/x86_64-pc-linux-gnu-library/2.8' > > also installing the dependencies GSEABase, Category, XML, RCurl, > > GOstats, biomaRt > > > > ## These are the series of errors in between downloads and other gcc > checks > > > > ERROR: configuration failed for package 'XML' > > > > ERROR: configuration failed for package 'RCurl' > > XML and RCurl have external operating system dependencies, likely you > need to install libxml2 and libcurl into your system. > > Martin > > > Error in loadNamespace(i[[1]], c(lib.loc, .libPaths())) : > > > > ERROR: lazy loading failed for package 'GSEABase' > > > > Error in loadNamespace(i, c(lib.loc, .libPaths())) : > > > > ERROR: lazy loading failed for package 'biomaRt' > > > > ERROR: lazy loading failed for package 'Category' > > > > ERROR: lazy loading failed for package 'GOstats' > > > -------------------------------------------------------------------- ---------------------------------------------------------------------- --------------------------------- > > I also tried > >>biocLite("XML") > > > > But I get the same set of warnings again. > > > > Any help is appreciated. > > > > > > Following is my sessionInfo() output: > >> sessionInfo() > > R version 2.8.1 (2008-12-22) > > x86_64-pc-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=C;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_IDEN TIFICATION=C > > > > attached base packages: > > [1] splines tools stats graphics grDevices utils datasets > > [8] methods base > > > > other attached packages: > > [1] mdssgpexprcdf_1.20.0 limma_2.16.5 simpleaffy_2.18.0 > > [4] genefilter_1.22.0 survival_2.34-1 affyPLM_1.18.1 > > [7] preprocessCore_1.4.0 gcrma_2.14.1 matchprobes_1.14.1 > > [10] affy_1.20.2 Biobase_2.2.2 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.3 > > [4] DBI_0.2-4 RSQLite_0.7-3 > > > > [[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 > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]

ADD REPLY • link 14.4 years ago Sunny Srivastava ▴ 350

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Entering edit mode

Sunny Srivastava wrote: > Thanks Martin for the reply. > > I am using ubuntu 9.04 and libxml2 was already installed on it. I > installed libcurl3 (could not find libcurl). I am not using ubuntu; you require the 'devel' versions, for me these are libxml2-devel, libcurl-devel > > Still I am not able to install affycoretools or XML. > --- > > sessionInfo() > R version 2.8.1 (2008-12-22) > x86_64-pc-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=C;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_IDEN TIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.8.1 > ----- > > Thanks for any help. > > Regards, > S. > > On Sat, Nov 21, 2009 at 12:19 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> <mailto:mtmorgan at="" fhcrc.org="">> wrote: > > Sunny Srivastava <research.baba at="" gmail.com=""> <mailto:research.baba at="" gmail.com="">> writes: > > > Dear Bioconductor Helpers, > > I was trying to install affycoretools package on my computer but > it gives a > > series of errors and doesn't install following are the messages: > > > > ## I think the error is related to this warning at the time I use > > biocLite("affycoretools") > > > > Warning in install.packages(pkgs = pkgs, repos = repos, > dependencies = > > dependencies, : > > argument 'lib' is missing: using > > '/home/baba/R/x86_64-pc-linux-gnu-library/2.8' > > also installing the dependencies ?GSEABase?, ?Category?, ?XML?, > ?RCurl?, > > ?GOstats?, ?biomaRt? > > > > ## These are the series of errors in between downloads and other > gcc checks > > > > ERROR: configuration failed for package 'XML' > > > > ERROR: configuration failed for package 'RCurl' > > XML and RCurl have external operating system dependencies, likely you > need to install libxml2 and libcurl into your system. > > Martin > > > Error in loadNamespace(i[[1]], c(lib.loc, .libPaths())) : > > > > ERROR: lazy loading failed for package 'GSEABase' > > > > Error in loadNamespace(i, c(lib.loc, .libPaths())) : > > > > ERROR: lazy loading failed for package 'biomaRt' > > > > ERROR: lazy loading failed for package 'Category' > > > > ERROR: lazy loading failed for package 'GOstats' > > > ---------------------------------------------------------------- ---------------------------------------------------------------------- ------------------------------------- > > I also tried > >>biocLite("XML") > > > > But I get the same set of warnings again. > > > > Any help is appreciated. > > > > > > Following is my sessionInfo() output: > >> sessionInfo() > > R version 2.8.1 (2008-12-22) > > x86_64-pc-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=C;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] mdssgpexprcdf_1.20.0 limma_2.16.5 simpleaffy_2.18.0 > > [4] genefilter_1.22.0 survival_2.34-1 affyPLM_1.18.1 > > [7] preprocessCore_1.4.0 gcrma_2.14.1 matchprobes_1.14.1 > > [10] affy_1.20.2 Biobase_2.2.2 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.3 > > [4] DBI_0.2-4 RSQLite_0.7-3 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > <mailto: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 > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

ADD REPLY • link 14.4 years ago Martin Morgan 25k

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