Question: biocLite() wants to update current packages
0
gravatar for lghunsicker
5 months ago by
lghunsicker0 wrote:

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
biocinstaller • 168 views
ADD COMMENTlink written 5 months ago by lghunsicker0

Firstly For R 3.6.0 The current Bioconductor release is Bioc 3.9. BiocInstaller has been removed from Bioconductor. To update and install Bioconductor package please use the functions in BiocManager.

install.packages("BiocManager")
library(BiocManager)
BiocManager::valid()
ADD REPLYlink written 5 months ago by shepherl ♦♦ 1.6k

Thanks, shepherl:

I deleted BiocInstaller and loaded BiocManager, etc., as above. I am happy to have got up to date with Bioconductor with this update. But BiocManager::valid() still marks 387 packages as out_of_date. Virtually all of these are packages installed from CRAN. As previously noted, update.packages() considers all the installed packages to be up to date. Why does BiocManager consider these 387 packages to be outofdate? Is it possible that BiocManager is marking these packages as out_of_date simply because they were installed under R 3.5.3, rather than 3.6.0? If so, is this appropriate? The packages all seem to work correctly, so far as I have been able to check. Note the following output for the first "out-of-date" package. The installed and ReposVer of the version is identical. Sorry for the bad formatting. I can't get the quotation function to work in a Reply.

> unk <- BiocManager::valid()$out_of_date Warning message: 387 packages
> out-of-date; 5 packages too new 
> > class(junk) [1] "matrix"
> > names(matrix) NULL
> > junk[1,]
>                                Package 
>                                   "BH" 
>                                LibPath 
>           "C:/Larry/R/win-library/3.6" 
>                              Installed 
>                             "1.69.0-1" 
>                                  Built 
>                                "3.5.2" 
>                               ReposVer 
>                             "1.69.0-1" 
>                             Repository  "https://cran.rstudio.com/src/contrib"
ADD REPLYlink modified 5 months ago by Martin Morgan ♦♦ 23k • written 5 months ago by lghunsicker0

Yes, the current version of BiocManager uses checkBuilt = TRUE when asking about validity. The default will be changed when BiocManager version 1.30.6 makes it to CRAN, and can be controlled via BiocManager::valid(checkBuilt = ...).

ADD REPLYlink written 5 months ago by Martin Morgan ♦♦ 23k
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