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??