i met such error > library(affycoretools); Error in loadNamespace(imp[[1L]], c(lib.loc, .libPaths())) : there is no package called ‘graph’ Error: package/namespace load failed for ‘affycoretools’ coding: *source*('http://Bioconductor.org/biocLite.R')<http: bioconductor.org="" bioclite.r')=""> ; *biocLite*("gcrma"); *biocLite*("graph"); *biocLite*("affycoretools"); library (CLL); *library* (gcrma); *library*(affycoretools); sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 [4] LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu95av2probe_2.10.0 hgu95av2cdf_2.10.0 KEGG.db_2.7.1 GO.db_2.7.1 [5] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.18.4 gcrma_2.28.0 [9] BiocInstaller_1.4.9 CLL_1.2.12 affy_1.34.0 Biobase_2.16.0 [13] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 annaffy_1.28.0 annotate_1.34.1 biomaRt_2.12.0 [5] Biostrings_2.24.1 IRanges_1.14.4 limma_3.12.3 preprocessCore_1.18.0 [9] RCurl_1.95-4.1 splines_2.15.1 stats4_2.15.1 tools_2.15.1 [13] XML_3.96-1.1 xtable_1.7-1 zlibbioc_1.2.0 -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute for Plant Research Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839@cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253 [[alternative HTML version deleted]]

On Tue, Jun 11, 2013 at 10:03 PM, Wang Peter <wng.peter at="" gmail.com=""> wrote: > i met such error >> library(affycoretools); > Error in loadNamespace(imp[[1L]], c(lib.loc, .libPaths())) : > there is no package called ?graph? > Error: package/namespace load failed for ?affycoretools? > > > coding: > > *source*('http://Bioconductor.org/biocLite.R')<http: bioconductor.o="" rg="" bioclite.r')=""> > ; > > *biocLite*("gcrma"); > > *biocLite*("graph"); Hi, Shan. And what was the output of biocLite("graph")? Sean > *biocLite*("affycoretools"); > > library (CLL); > > *library* (gcrma); > > *library*(affycoretools); > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > locale: > [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 > [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 > [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 > [4] LC_NUMERIC=C > [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] hgu95av2probe_2.10.0 hgu95av2cdf_2.10.0 KEGG.db_2.7.1 > GO.db_2.7.1 > [5] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.18.4 > gcrma_2.28.0 > [9] BiocInstaller_1.4.9 CLL_1.2.12 affy_1.34.0 > Biobase_2.16.0 > [13] BiocGenerics_0.2.0 > loaded via a namespace (and not attached): > [1] affyio_1.24.0 annaffy_1.28.0 annotate_1.34.1 > biomaRt_2.12.0 > [5] Biostrings_2.24.1 IRanges_1.14.4 limma_3.12.3 > preprocessCore_1.18.0 > [9] RCurl_1.95-4.1 splines_2.15.1 stats4_2.15.1 > tools_2.15.1 > [13] XML_3.96-1.1 xtable_1.7-1 zlibbioc_1.2.0 > -- > shan gao > Room 231(Dr.Fei lab) > Boyce Thompson Institute for Plant Research > Cornell University > Tower Road, Ithaca, NY 14853-1801 > Office phone: 1-607-254-1267(day) > Official email:sg839 at cornell.edu > Facebook:http://www.facebook.com/profile.php?id=100001986532253 > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor