This is a bug that has been around for over a year now. On a package upgrade (either by -S or -U) a new directory could overwrite any file. This is caused by the filelist difference calculation ignoring all directories and thus no new directories were checked for conflicting files on the filesystem. Signed-off-by: Allan McRae <allan@archlinux.org> --- I saw the comment was added to that code in 2011, but I think this issue has been around for a very long time before that. Please look at the patch and give it an ack somewhat urgently. I intend to backport to the Arch Linux pacman package. lib/libalpm/filelist.c | 22 ++++++++-------------- 1 file changed, 8 insertions(+), 14 deletions(-) diff --git a/lib/libalpm/filelist.c b/lib/libalpm/filelist.c index bf7645b..f8a5258 100644 --- a/lib/libalpm/filelist.c +++ b/lib/libalpm/filelist.c @@ -228,23 +228,17 @@ alpm_list_t *_alpm_filelist_difference(alpm_filelist_t *filesA, alpm_file_t *fileA = filesA->files + ctrA; const char *strA = filesA->resolved_path[ctrA]; const char *strB = filesB->resolved_path[ctrB]; - /* skip directories, we don't care about them */ - if(strA[strlen(strA)-1] == '/') { + + int cmp = strcmp(strA, strB); + if(cmp < 0) { + /* item only in filesA, qualifies as a difference */ + ret = alpm_list_add(ret, fileA); ctrA++; - } else if(strB[strlen(strB)-1] == '/') { + } else if(cmp > 0) { ctrB++; } else { - int cmp = strcmp(strA, strB); - if(cmp < 0) { - /* item only in filesA, qualifies as a difference */ - ret = alpm_list_add(ret, fileA); - ctrA++; - } else if(cmp > 0) { - ctrB++; - } else { - ctrA++; - ctrB++; - } + ctrA++; + ctrB++; } } -- 1.8.0.1