agriutilities check lacks asreml (in Enhances)

[tdhock]

asreml is in Enhances which I believe we do not install

[tdhock]

from check_one.R:

install.time <- system.time({
  install.packages(rev.dep, dep=TRUE)
})

doc ?install.packages says TRUE implies only Depends/LinkingTo/Imports/Suggests (not Enhances)

dependencies: logical indicating whether to also install uninstalled
          packages which these packages depend on/link
          to/import/suggest (and so on recursively).  Not used if
          ‘repos = NULL’.  Can also be a character vector, a subset of
          ‘c("Depends", "Imports", "LinkingTo", "Suggests",
          "Enhances")’.

[tdhock]

should be fixed by https://github.com/tdhock/data.table-revdeps/commit/0cd2013888f52d88ab1e86c19f59dcf6cffe99a3

[tdhock]

actually this makes the checks take way too long. Instead of installing Enhances in check_one.R (now removed), now I try to put those in popular_deps.csv.. if that works TODO add docs about that in the "not available dependent packages" section.

[tdhock]

params.teeout has the following output, which indicates that some packages were not able to install.

The downloaded source packages are in
    ‘/tmp/th798/7337297/Rtmp1o07js/downloaded_packages’
Warning messages:
1: packages ‘rkward’, ‘ffbase’, ‘sl3’, ‘asreml’ are not available for this version of R

Versions of these packages for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages 
2: In install.packages(some) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
3: In install.packages(some) :
  installation of package ‘Biostrings’ had non-zero exit status
4: In install.packages(some) :
  installation of package ‘KEGGREST’ had non-zero exit status
5: In install.packages(some) :
  installation of package ‘AnnotationDbi’ had non-zero exit status
6: In install.packages(some) :
  installation of package ‘WGCNA’ had non-zero exit status

[tdhock]

https://cran.r-project.org/web/packages/asremlPlus/index.html says that asreml is a commercial package. ffbase was archived from CRAN sl3 seems to be on GitHub not CRAN, https://github.com/tlverse/sl3 https://github.com/KDE/rkward is nor on CRAN packages with non-zero exit status are from bioc, but we are able to download from bioc, since it is in repos, see below.

> dep <- read.csv("~/genomic-ml/data.table-revdeps/popular_deps.csv")$dep;ins <- rownames(installed.packages());print(some <- dep[!dep %in% ins]);install.packages(some)
  [1] "rkward"          "chron"           "AER"             "betareg"        
  [5] "ordinal"         "survey"          "eha"             "simex"          
  [9] "leaflet"         "aod"             "biglm"           "brglm"          
 [13] "caret"           "crch"            "earth"           "ff"             
 [17] "ffbase"          "gam"             "gee"             "glmx"           
 [21] "mclogit"         "mda"             "mlogit"          "MNP"            
 [25] "plm"             "pscl"            "sampleSelection" "speedglm"       
 [29] "survey"          "vegalite"        "spacyr"          "geojsonio"      
 [33] "sl3"             "truncreg"        "VGAM"            "tis"            
 [37] "vdiffr"          "ggdendro"        "dendroextras"    "WGCNA"          
 [41] "moduleColor"     "distory"         "phangorn"        "cleaner"        
 [45] "janitor"         "skimr"           "tsibble"         "asreml"         
 [49] "polyclip"        "clock"           "hardhat"         "caTools"        
 [53] "recipes"         "lpSolve"         "lgr"             "xgboost"        
 [57] "dotCall64"       "spam"            "RhpcBLASctl"     "reticulate"     
 [61] "pROC"            "TH.data"         "multcomp"        "RcppProgress"   
 [65] "rbibutils"       "ipred"           "Rdpack"          "gower"          
 [69] "crul"            "rcmdcheck"       "urlchecker"      "devtools"       
 [73] "patchwork"       "kernlab"         "kableExtra"      "RcppTOML"       
 [77] "anytime"         "ape"             "ranger"          "RSQLite"        
 [81] "rstatix"         "prodlim"         "ggsignif"        "ggpubr"         
 [85] "mnormt"          "spelling"        "httpcode"        "xopen"          
 [89] "profvis"         "rversions"       "fastmatch"       "ggsci"          
 [93] "timeDate"        "lava"            "RCurl"           "diagram"        
 [97] "sessioninfo"     "polynom"         "x13binary"       "V8"             
[101] "downlit"         "here"            "FNN"             "corrplot"       
[105] "triebeard"       "urltools"        "plogr"           "SQUAREM"        
[109] "hunspell"        "pkgdown"         "R.cache"         "rstanarm"       
[113] "hesim"           "ctmm"            "disk.frame"      "nc"             
[117] "data.table"      "magrittr"        "glue"            "rlang"          
[121] "R6"              "jsonlite"        "cli"             "lifecycle"      
[125] "pkgconfig"       "digest"          "vctrs"           "withr"          
[129] "utf8"            "fansi"           "pillar"          "tibble"         
[133] "evaluate"        "fs"              "stringi"         "stringr"        
[137] "ellipsis"        "yaml"            "Rcpp"            "crayon"         
[141] "fastmap"         "base64enc"       "xfun"            "highr"          
[145] "knitr"           "htmltools"       "ps"              "processx"       
[149] "callr"           "rprojroot"       "cachem"          "memoise"        
[153] "desc"            "rematch2"        "rappdirs"        "pkgload"        
[157] "diffobj"         "brio"            "praise"          "waldo"          
[161] "testthat"        "jquerylib"       "sass"            "bslib"          
[165] "tinytex"         "rmarkdown"       "RColorBrewer"    "viridisLite"    
[169] "colorspace"      "farver"          "labeling"        "munsell"        
[173] "scales"          "gtable"          "isoband"         "ggplot2"        
[177] "generics"        "mime"            "cpp11"           "tidyselect"     
[181] "curl"            "dplyr"           "purrr"           "sys"            
[185] "askpass"         "openssl"         "httr"            "tidyr"          
[189] "lazyeval"        "htmlwidgets"     "xml2"            "backports"      
[193] "RcppEigen"       "commonmark"      "gridExtra"       "prettyunits"    
[197] "plyr"            "hms"             "bit"             "rstudioapi"     
[201] "later"           "promises"        "bit64"           "progress"       
[205] "xtable"          "zoo"             "clipr"           "rex"            
[209] "RcppArmadillo"   "iterators"       "tzdb"            "foreach"        
[213] "httpuv"          "png"             "timechange"      "lubridate"      
[217] "numDeriv"        "viridis"         "DBI"             "fontawesome"    
[221] "sourcetools"     "shiny"           "covr"            "checkmate"      
[225] "vroom"           "proxy"           "readr"           "crosstalk"      
[229] "BH"              "e1071"           "reshape2"        "abind"          
[233] "mvtnorm"         "sp"              "broom"           "igraph"         
[237] "minqa"           "parallelly"      "assertthat"      "nloptr"         
[241] "globals"         "listenv"         "future"          "systemfonts"    
[245] "Formula"         "jpeg"            "lme4"            "zip"            
[249] "deldir"          "doParallel"      "SparseM"         "MatrixModels"   
[253] "uuid"            "quantreg"        "whisker"         "forcats"        
[257] "future.apply"    "classInt"        "units"           "interp"         
[261] "bitops"          "R.oo"            "R.methodsS3"     "R.utils"        
[265] "brew"            "wk"              "latticeExtra"    "markdown"       
[269] "selectr"         "s2"              "sf"              "rvest"          
[273] "ggrepel"         "htmlTable"       "rematch"         "plotly"         
[277] "miniUI"          "raster"          "Hmisc"           "cellranger"     
[281] "sandwich"        "XML"             "blob"            "readxl"         
[285] "pbkrtest"        "RcppParallel"    "carData"         "DT"             
[289] "car"             "roxygen2"        "shape"           "remotes"        
[293] "progressr"       "gtools"          "cowplot"         "quadprog"       
[297] "haven"           "xts"             "webshot"         "matrixStats"    
[301] "credentials"     "gitcreds"        "ini"             "gert"           
[305] "gh"              "usethis"         "pbapply"         "lmtest"         
[309] "coda"            "maps"            "svglite"         "textshaping"    
[313] "ragg"            "pkgbuild"        "glmnet"         
Warning: dependencies ‘GO.db’, ‘GenomeInfoDbData’ are not available
also installing the dependencies ‘zlibbioc’, ‘XVector’, ‘GenomeInfoDb’, ‘Biostrings’, ‘bbmle’, ‘fastGHQuad’, ‘gmp’, ‘DEoptimR’, ‘plotrix’, ‘protolite’, ‘geometries’, ‘jsonify’, ‘rapidjsonr’, ‘sfheaders’, ‘BiocGenerics’, ‘Biobase’, ‘IRanges’, ‘S4Vectors’, ‘KEGGREST’, ‘ggridges’, ‘tensorA’, ‘distributional’, ‘inline’, ‘QuickJSR’, ‘colourpicker’, ‘dygraphs’, ‘shinyjs’, ‘shinythemes’, ‘threejs’, ‘deSolve’, ‘mstate’, ‘muhaz’, ‘rstpm2’, ‘Rmpfr’, ‘RSpectra’, ‘robustbase’, ‘lobstr’, ‘fstcore’, ‘bigassertr’, ‘benchmarkmeData’, ‘flexmix’, ‘modeltools’, ‘ucminf’, ‘mitools’, ‘leaflet.providers’, ‘profileModel’, ‘ModelMetrics’, ‘scoringRules’, ‘plotmo’, ‘TeachingDemos’, ‘memisc’, ‘dfidx’, ‘statmod’, ‘bdsmatrix’, ‘collapse’, ‘maxLik’, ‘miscTools’, ‘systemfit’, ‘base64’, ‘geojson’, ‘geojsonsf’, ‘jqr’, ‘dynamicTreeCut’, ‘fastcluster’, ‘impute’, ‘preprocessCore’, ‘AnnotationDbi’, ‘snakecase’, ‘repr’, ‘bayesplot’, ‘loo’, ‘posterior’, ‘rstan’, ‘rstantools’, ‘shinystan’, ‘StanHeaders’, ‘flexsurv’, ‘msm’, ‘Bessel’, ‘expm’, ‘fasttime’, ‘Gmedian’, ‘gsl’, ‘manipulate’, ‘parsedate’, ‘pbivnorm’, ‘pracma’, ‘terra’, ‘pryr’, ‘fst’, ‘bigreadr’, ‘benchmarkme’, ‘arrow’, ‘httr2’

trying URL 'http://www.bioconductor.org/packages/release/bioc/src/contrib/zlibbioc_1.48.0.tar.gz'
Content type 'application/x-gzip' length 163378 bytes (159 KB)
==================================================
downloaded 159 KB

Why are GO.db and GenomeInfoDbData not available? they are not in the bioc release repository. bioc now uses a bunch of different repos,

> BiocManager:::.repositories(character(), version = BiocManager::version())
                                                BioCsoft 
           "https://bioconductor.org/packages/3.18/bioc" 
                                                 BioCann 
"https://bioconductor.org/packages/3.18/data/annotation" 
                                                 BioCexp 
"https://bioconductor.org/packages/3.18/data/experiment" 
                                           BioCworkflows 
      "https://bioconductor.org/packages/3.18/workflows" 
                                               BioCbooks 
          "https://bioconductor.org/packages/3.18/books" 

     "http://www.bioconductor.org/packages/release/bioc" 

on https://bioconductor.org/packages/release/data/annotation/html/GO.db.html they recommend installing via code below,

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("GO.db")

[tdhock]

https://github.com/tdhock/data.table-revdeps/commit/2ba778ab2eb765602ec7aef6082d0aa1b260a099 should fix the GO.db issue at least.