I want to update my Bioconductor packages. I am running R 3.6.0 on an updated Windows 10 machine. I have updated the BiocInstaller package, as well as all of my packages installed from the Global (CDN) - RStudio CRAN repository. When I then run biocLite, it wants to update many, many packages that are, according to old.packages(), already up to date, but which biocLite thinks are 'old.' How can I limit the update search only to Bioconductor packages without having to go through the whole list to choose? Thanks for any help or clarification. Larry Hunsicker

> > old.packages() NULL
> > BiocInstaller::biocLite() BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.6.0 (2019-04-26).
> Old packages: 'BH', 'bibtex', 'bigalgebra', 'biganalytics',
> 'biglasso',   'biglm', 'bigmemory', 'bigmemory.sri', 'bigtabulate',
> 'bindr', 'bindrcpp',   'binom', 'BiocInstaller', 'BiocParallel',
> 'bit', 'bit64', 'bitops',   'blavaan', 'blob', 'BMA', 'boot', 'brew',
> 'bridgesampling', 'brms',   'Brobdingnag', 'broom', 'c060', 'Cairo',
> 'cairoDevice', 'callr', 'car',   'carData', 'caTools', 'cellranger',
> 'chron', 'CircStats', 'class',   'classInt', 'cli', 'clipr',
> 'clisymbols', 'cmprsk', 'coda', 'codetools',   'colorspace',
> 'colourpicker', 'combinat', 'commonmark', 'CompQuadForm',  
> 'compute.es', 'config', 'corpcor', 'corrplot', 'cowplot', 'coxme',  
> 'cramer', 'crayon', 'crosstalk', 'curl', 'data.table', 'DBI',
> 'dbplyr',   'debugme', 'DEoptimR', 'desc', 'deSolve', 'devtools',
> 'dichromat',   'digest', 'doParallel', 'drat', 'dtplyr', 'dunn.test',
> 'dygraphs',   'e1071', 'effects', 'ellipse', 'estimability',
> 'evaluate', 'evd', 'Exact',   'exact2x2', 'exactci', 'expm', 'ez',
> 'FactoMineR', 'fansi', 'ff',   'flashClust', 'flexsurv', 'forcats',
> 'foreach', 'foreign', 'forge',   'formatR', 'Formula',
> 'futile.logger', 'futile.options', 'fuzzyjoin',   'gam', 'gamm4',
> 'gdata', 'gendata', 'generics', 'geoR', 'geoRglm',   'geosphere',
> 'GGally', 'ggfortify', 'ggplot2', 'ggpubr', 'ggridges',   'ggsci',
> 'ggsignif', 'ggstance', 'ggvis', 'gh', 'git2r', 'glmmLasso',  
> 'glmnet', 'globals', 'glue', 'gmodels', 'GO.db', 'GPArotation',
> 'gplots',   'gridExtra', 'grplasso', 'gsl', 'gsubfn', 'gtable',
> 'gtools', 'gWidgets',   'gWidgetsRGtk2', 'haven', 'hflights', 'highr',
> 'Hmisc', 'hms', 'HSAUR',   'HSAUR3', 'htmlTable', 'htmltools',
> 'htmlwidgets', 'httpuv', 'httr',   'hunspell', 'igraph', 'ini',
> 'inline', 'irlba', 'ISOcodes', 'iterators',   'jagsUI', 'janeaustenr',
> 'JM', 'JMbayes', 'joineR', 'jomo', 'jsonlite',   'KernSmooth',
> 'km.ci', 'KMsurv', 'knitr', 'labeling', 'laeken',   'lambda.r',
> 'LaplacesDemon', 'later', 'lattice', 'latticeExtra', 'lavaan',  
> 'lazyeval', 'leaps', 'lhs', 'listenv', 'lme4', 'lmerTest', 'loo',  
> 'lubridate', 'lvplot', 'magrittr', 'manipulate', 'manipulateWidget',  
> 'mapproj', 'maps', 'maptools', 'maptree', 'markdown', 'MASS',
> 'matlib',   'Matrix', 'matrixcalc', 'MatrixModels', 'matrixStats',
> 'maxLik',   'maxstat', 'mcmc', 'MCMCpack', 'memoise', 'mgcv', 'mi',
> 'microbenchmark',   'mime', 'miniUI', 'minqa', 'miscTools', 'mitml',
> 'mitools', 'mlegp',   'mnormt', 'modelr', 'mstate', 'muhaz',
> 'multcomp', 'multcompView',   'MuMIn', 'munsell', 'mvtnorm', 'ncvreg',
> 'nleqslv', 'nloptr', 'nnet',   'nonnest2', 'nortest', 'numDeriv',
> 'nycflights13', 'openssl', 'openxlsx',   'ordinal', 'osmar',
> 'packrat', 'pan', 'pander', 'pbivnorm', 'pbkrtest',   'pcaPP',
> 'penalizedSVM', 'peperr', 'permute', 'pkgbuild', 'pkgconfig',  
> 'pkgload', 'pkgmaker', 'PKI', 'plogr', 'plotly', 'pls', 'plyr',  
> 'polspline', 'polynom', 'pracma', 'praise', 'prettyunits', 'projpred',
> 'promises', 'proto', 'pryr', 'ps', 'pspearman', 'psych', 'purrr',  
> 'quantmod', 'quantreg', 'R.methodsS3', 'R.oo', 'R.utils', 'r2d3',  
> 'R2jags', 'R2WinBUGS', 'R6', 'RandomFields', 'RandomFieldsUtils',  
> 'randomForest', 'ranger', 'rappdirs', 'rARPACK', 'rattle',
> 'rbenchmark',   'RCA', 'RcmdrMisc', 'RColorBrewer', 'Rcpp', 'RcppDE',
> 'RcppEigen',   'RcppGSL', 'RcppParallel', 'readr', 'readstata13',
> 'readxl', 'registry',   'relimp', 'rematch', 'remotes', 'reprex',
> 'reshape', 'reshape2',   'rgenoud', 'rgeos', 'rgl', 'Rglpk',
> 'RGraphics', 'RGtk2', 'rio', 'rjags',   'rJava', 'RLRsim',
> 'rmarkdown', 'rms', 'RMySQL', 'roxygen2', 'rpart',   'rpart.plot',
> 'RPostgreSQL', 'rprojroot', 'rrcov', 'rsconnect',   'RSpectra',
> 'RSQLite', 'rstan', 'rstanarm', 'rstantools', 'rstudioapi',   'RUnit',
> 'runjags', 'RVAideMemoire', 'rvest', 'RWiener', 'sandwich',  
> 'sas7bdat', 'scales', 'scatterplot3d', 'SDMTools', 'selectr', 'sem',  
> 'sessioninfo', 'sf', 'shiny', 'shinyBS', 'shinyjs', 'shinystan',  
> 'shinythemes', 'slam', 'snow', 'SnowballC', 'snowfall', 'softImpute', 
> 'sourcetools', 'sp', 'sparklyr', 'SparseM', 'spatial', 'spData',  
> 'splancs', 'sqldf', 'SqlRender', 'ssanv', 'StanHeaders', 'statmod',  
> 'stopwords', 'stringi', 'stringr', 'SuppDists', 'survey', 'survival', 
> 'survminer', 'survMisc', 'sys', 'tcltk2', 'testit', 'testthat', 'tgp',
> 'TH.data', 'threejs', 'tidyselect', 'tidytext', 'tidyverse', 'tigris',
> 'tokenizers', 'TTR', 'ucminf', 'udunits2', 'USAboundaries',  
> 'UScensus2010', 'usethis', 'utf8', 'uuid', 'vcd', 'VIM', 'viridis',  
> 'viridisLite', 'webshot', 'whisker', 'withr', 'XML', 'xml2', 'xopen', 
> 'xtable', 'xts', 'yaml', 'zoo' Update all/some/none? [a/s/n]:  n
> > sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build
> 17763)
> 
> Matrix products: default
> 
> Random number generation:  RNG:     Mersenne-Twister   Normal: 
> Inversion   Sample:  Rounding    locale: [1] LC_COLLATE=English_United
> States.1252  [2] LC_CTYPE=English_United States.1252    [3]
> LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C               
> [5] LC_TIME=English_United States.1252    
> 
> attached base packages: [1] stats     graphics  grDevices utils    
> datasets  methods   base     
> 
> loaded via a namespace (and not attached): [1] BiocManager_1.30.4  
> compiler_3.6.0       rsconnect_0.8.13     [4] BiocInstaller_1.30.0
> htmltools_0.3.6      tools_3.6.0          [7] Rcpp_1.0.1          
> digest_0.6.18        packrat_0.5.0