############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf ChAMP.buildbin-libdir && mkdir ChAMP.buildbin-libdir && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=ChAMP.buildbin-libdir ChAMP_2.26.0.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'ChAMP' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: replacing previous import 'matrixStats::rowMedians' by 'Biobase::rowMedians' when loading 'DSS' 2: replacing previous import 'matrixStats::anyMissing' by 'Biobase::anyMissing' when loading 'DSS' No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP' Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP' Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP' Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP' Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP' Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP' Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP' Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP' Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP' Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP' Note: possible error in 'dmrcate(myannotation, ': unused argument (mc.cores = cores) ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'matrixStats::rowMedians' by 'Biobase::rowMedians' when loading 'DSS' Warning: replacing previous import 'matrixStats::anyMissing' by 'Biobase::anyMissing' when loading 'DSS' No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP' Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP' Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP' Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP' Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP' Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP' Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP' Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP' Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP' Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP' ** testing if installed package can be loaded from final location Warning: replacing previous import 'matrixStats::rowMedians' by 'Biobase::rowMedians' when loading 'DSS' Warning: replacing previous import 'matrixStats::anyMissing' by 'Biobase::anyMissing' when loading 'DSS' No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP' Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP' Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP' Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP' Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP' Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP' Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP' Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP' Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP' Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP' ** testing if installed package keeps a record of temporary installation path * MD5 sums packaged installation of 'ChAMP' as ChAMP_2.26.0.zip * DONE (ChAMP)