Subject: 25.0.91; Deleting dependency package and reinstalling overwrites custom file

From: Joost Kremers <[email-masked]>
Date: Wed, 24 Feb 2016 14:54:53 +0100

- Given the following init file:

```
(setq custom-file "~/.emacs.d/custom.el")

(require 'package)
;; (add-to-list 'package-archives '("melpa" . "http://melpa.org/packages/"))
(setq package-enable-at-startup nil)
(package-initialize)

(load custom-file)
```

- Customize some option (e.g., `fill-column') with `M-x
  customize-option'. (This is not an essential step, it just serves to
  illustrate the problem.)

- Install a package that has some dependency, e.g., ace-window, which
  has avy as a dependency.

    M-x package-install RET ace-window RET

- Close Emacs and do (from a shell):

    $ rm -rf ~/.emacs.d/elpa/avy-*

- Restart Emacs (this will give an error about not being able to load
  ace-window, because its dependency avy is not met.)

- Install avy:

    M-x package-install RET avy RET

At this point, the custom file ~/.emacs.d/custom.el is overwritten: the
custom setting for `fill-column' is gone.

The bug is dependent on `package-enable-at-startup' being set to nil and
`custom-file' being set. If either of these conditions isn't met, the
bug doesn't occur.

In GNU Emacs 25.0.91.1 (x86_64-unknown-linux-gnu, GTK+ Version 2.24.23)
 of 2016-02-24 built on IdeaPad
Repository revision: e01c72f8f4987f9de71130b8b6d8224999fc6c6f
Windowing system distributor 'The X.Org Foundation', version 11.0.11600000
System Description:	elementary OS Freya

Configured using:
 'configure --with-x-toolkit=gtk2'

Configured features:
XPM JPEG TIFF GIF PNG RSVG IMAGEMAGICK SOUND GPM DBUS GCONF GSETTINGS
NOTIFY LIBSELINUX GNUTLS LIBXML2 FREETYPE M17N_FLT LIBOTF XFT ZLIB
TOOLKIT_SCROLL_BARS GTK2 X11

Important settings:
  value of $LC_MONETARY: en_GB.UTF-8
  value of $LC_NUMERIC: en_GB.UTF-8
  value of $LC_TIME: en_GB.UTF-8
  value of $LANG: en_GB.UTF-8
  value of $XMODIFIERS: @im=ibus
  locale-coding-system: utf-8-unix

Major mode: Fundamental

Minor modes in effect:
  tooltip-mode: t
  global-eldoc-mode: t
  electric-indent-mode: t
  mouse-wheel-mode: t
  tool-bar-mode: t
  menu-bar-mode: t
  file-name-shadow-mode: t
  global-font-lock-mode: t
  blink-cursor-mode: t
  auto-composition-mode: t
  auto-encryption-mode: t
  auto-compression-mode: t
  buffer-read-only: t
  line-number-mode: t
  transient-mark-mode: t

Recent messages:
Loading /home/joost/.emacs.d/custom.el (source)...done
For information about GNU Emacs and the GNU system, type C-h C-a.

Load-path shadows:
None found.

Features:
(shadow sort mail-extr emacsbug message dired format-spec rfc822 mml
mml-sec epg gnus-util mm-decode mm-bodies mm-encode mail-parse rfc2231
mailabbrev gmm-utils mailheader sendmail rfc2047 rfc2045 ietf-drums
mm-util help-fns help-mode cl-loaddefs pcase cl-lib mail-prsvr
mail-utils finder-inf package easymenu epg-config time-date mule-util
tooltip eldoc electric uniquify ediff-hook vc-hooks lisp-float-type
mwheel x-win term/common-win x-dnd tool-bar dnd fontset image regexp-opt
fringe tabulated-list newcomment elisp-mode lisp-mode prog-mode register
page menu-bar rfn-eshadow timer select scroll-bar mouse jit-lock
font-lock syntax facemenu font-core frame cl-generic cham georgian
utf-8-lang misc-lang vietnamese tibetan thai tai-viet lao korean
japanese eucjp-ms cp51932 hebrew greek romanian slovak czech european
ethiopic indian cyrillic chinese charscript case-table epa-hook
jka-cmpr-hook help simple abbrev minibuffer cl-preloaded nadvice
loaddefs button faces cus-face macroexp files text-properties overlay
sha1 md5 base64 format env code-pages mule custom widget
hashtable-print-readable backquote dbusbind inotify dynamic-setting
system-font-setting font-render-setting move-toolbar gtk x-toolkit x
multi-tty make-network-process emacs)

Memory information:
((conses 16 95208 5746)
 (symbols 48 20534 0)
 (miscs 40 86 96)
 (strings 32 17037 5159)
 (string-bytes 1 488155)
 (vectors 16 12781)
 (vector-slots 8 433765 4260)
 (floats 8 174 15)
 (intervals 56 236 0)
 (buffers 976 12)
 (heap 1024 37336 913))

-- 
Joost Kremers
Life has its moments