anchor.diff:    x = c(.fail.cran, .fail.bioc)
     cat("Writing 00check.log for",length(x),"packages to",fnam,":\n")
     cat(paste(x,collapse=" "), "\n")
  -  cat(capture.output(sessionInfo()), "\n\n", file=fnam, sep="\n")
  +  cat(capture.output(sessionInfo()), "\n", file=fnam, sep="\n")
  +  cat("> BiocManager::install()\n", file=fnam, append=TRUE)
  +  capture.output(BiocManager::install(), type="message", file=fnam, append=TRUE)
  +  cat("> BiocManager::valid()\n", file=fnam, append=TRUE)
  +  capture.output(ans<-BiocManager::valid(), type="message", file=fnam, append=TRUE)
  +  cat(ans, "\n", file=fnam, append=TRUE, sep="\n")
     for (i in x) {
  +    system(paste0("ls | grep '",i,".*tar.gz' >> ",fnam))
       system(paste0("grep -H . ./",i,".Rcheck/00check.log >> ",fnam))
       cat("\n\n", file=fnam, append=TRUE)
     }
  
positive.code: install.packages("<pkg>", repos="http://cran.stat.ucla.edu/")
  update.packages(ask=FALSE)   # a repeat sometimes does more, keep repeating until none
  
  # Follow: https://bioconductor.org/install/#troubleshoot-biocinstaller
  # Ensure no library() call in .Rprofile, such as library(bit64)
  source("http://bioconductor.org/biocLite.R")
  biocLite()   # keep repeating until returns with nothing left to do.   Note: huge number of updates under R-devel (I assume that's false)
  # biocLite("BiocUpgrade")
  # This error means it's up to date: "Bioconductor version 3.4 cannot be upgraded with R version 3.3.2"
  
  avail = available.packages(repos=biocinstallRepos())   # includes CRAN at the end from getOption("repos")
  deps = tools::package_dependencies("data.table", db=avail, which="most", reverse=TRUE, recursive=FALSE)[[1]]
  exclude = c("TCGAbiolinks", # takes loo long: https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/240
              "facopy")       # fails for over a year and isn't getting fixed:  Error : object ‘setting.graph.attributes’ is not exported by 'namespace:DOSE'
  deps = deps[-match(exclude, deps)]
  table(avail[deps,"Repository"])
  length(deps)
  
negative.code: }
  cat("New downloaded:",new," Already had latest:", old, " TOTAL:", length(deps), "\n")
  length(deps)
  update.packages(repos=BiocManager::repositories())  # double-check all dependencies are latest too
  
  # Remove the tar.gz no longer needed :
  system("ls *.tar.gz | wc -l")
  