Why is apt-get telling me to remove packages that I need? And how do I tell it to shut up?

I'm running an EC2 with Ubuntu 14.04 and R 3.1.2 and Rstudio-server. I just ran apt-get update and upgrade and now apt-get is telling me:

The following packages were automatically installed and are no longer required:
  icu-devtools libicu-dev r-cran-assertthat r-cran-bh r-cran-bibtex
  r-cran-bitops r-cran-chron r-cran-colorspace r-cran-data.table r-cran-dbi
  r-cran-devtools r-cran-dichromat r-cran-digest r-cran-dplyr r-cran-evaluate
  r-cran-formatr r-cran-gdata r-cran-gender r-cran-ggplot2 r-cran-gridextra
  r-cran-gtable r-cran-gtools r-cran-highr r-cran-httr r-cran-igraph
  r-cran-jsonlite r-cran-knitcitations r-cran-knitr r-cran-labeling
  r-cran-lazyeval r-cran-lubridate r-cran-magrittr r-cran-markdown
  r-cran-memoise r-cran-mime r-cran-munsell r-cran-nlp r-cran-opennlp
  r-cran-opennlpdata r-cran-plotrix r-cran-plyr r-cran-proto
  r-cran-qdapdictionaries r-cran-qdapregex r-cran-qdaptools r-cran-r6
  r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-refmanager
  r-cran-reports r-cran-reshape2 r-cran-rjsonio r-cran-rstudioapi
  r-cran-scales r-cran-slam r-cran-stringdist r-cran-stringi r-cran-stringr
  r-cran-tm r-cran-venneuler r-cran-whisker r-cran-wordcloud r-cran-xlsx
  r-cran-xlsxjars r-cran-xml
Use 'apt-get autoremove' to remove them.

But I need those libraries. In fact I ran apt-get autoremove and it broke stuff -- there were other libraries (qdap) that depended on these. Of course I made a snapshot first.

Previously, I installed the R library qdap which requires the R library rjava which requires Java jdk. I posted the steps I took here: https://stackoverflow.com/questions/17019405/rjava-installation-in-r-on-debian/27109120#27109120

Everything seems to be working fine. But is it? I'm disturbed by the apt-get message repeating itself again and again for every action. How can Apt be wrong??


This situation resolved itself. Though previously repeated with each and every individual update, the most recent batch of updates did not display that suggestion. All the R libraries are working and up-to-date.

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