Mistakenly overwrote some *.dylib files in /usr/lib

Hello all. I made a foolish mistake while working on my iMac remotely (via SSH). I realized how stupid I was right as I did it--but, of course, it was already too late. So now I have to figure out what to do to get things back in working order.
Here's what I did... I copied the following three *.dylib files into /usr/lib/:
i386_libstdc++.6.dylib
libgcc_s.1.dylib
libstdc++.6.dylib
I am not 100% sure if I overwrote existing files (as I don't have access to another Mac at the moment to see if these files exist by default) but I think that is the case. After I did it, the most simple of commands no longer worked. "ls" gave me this:
dyld: Symbol not found: dyld_stub_binder
  Referenced from: /usr/lib/libSystem.B.dylib
  Expected in: /usr/lib/libSystem.B.dylib
in /usr/lib/libSystem.B.dylib
Trace/BPT trap: 5
I do not yet know if this has made the GUI non-functional as well (like I said, I was doing this remotely). But as soon as someone is availble on the other end I will have them check. If the GUI is funcitonal, would it be possible to just delete the offending files via Finder, and copy over versions (if another version of these files indeed exists by default) from another Lion machine? (Unfortunately, I don't have a Time Machine backup for this Mac so that is not an option).
If the GUI is not functional and/or this will not work for some other reason, I suppose I will need to use Target Disk Mode to retrieve my data from the machine and rebuild it from scratch?
At any rate, if anyone can give me any troubleshooting steps or other suggestions for how to tackel this issue, that would be very appreciated.

Do you think a restore is necessary? Is there a reason removing/replacing the offending files will not work? (I did verify that I have normal access via the GUI, by the way--so far these librarie seem to only affect CLI commands, though I wouldn't be surprised if other odd things popped up too).
If I *do* have to do a restore, would it be possible for me to set up Time Machine, back up the machine as-is right now, restore the machine to a factory state, then use Time Machine to just recover my user data? Or maybe kist clone the disk to an external drive? Or is just a plain old copy to an external drive the best option? Just want to make sure I have an understanding of the best route here so that I can save the data (which is mainly just Applicaitons and iMovie projects and events).
As for "mucking" with it remotely--if I couldn't do that, it would ruin all my fun, now wouldn't it?! :-) I'm a linux admin for a living so thus why the Terminal is very comfortable (perhaps TOO comfortable in this case!) for me, yet I am less familiar with things like Time Machine. I'm definitely about to learn though! If I had Time Machine it would make recovering the proper versions of these files very simple, no?

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    ldconfig: File /usr/lib/libspeexdsp.so.1 is empty, not checked.
    ldconfig: File /usr/lib/libfftw3f.so.3.3.2 is empty, not checked.
    ldconfig: File /usr/lib/libfftw3l_threads.so.3 is empty, not checked.
    ldconfig: File /usr/lib/libwebrtc_audio_processing.so.0.0.0 is empty, not checked.
    ldconfig: File /usr/lib/libfftw3l_threads.so.3.3.2 is empty, not checked.
    ldconfig: File /usr/lib/libasyncns.so.0 is empty, not checked.
    ldconfig: File /usr/lib/libasyncns.so.0.3.1 is empty, not checked.
    ldconfig: File /usr/lib/libfftw3l.so.3 is empty, not checked.
    ldconfig: File /usr/lib/libpulse-mainloop-glib.so is empty, not checked.
    ldconfig: File /usr/lib/libsbc.so is empty, not checked.
    ldconfig: File /usr/lib/libasyncns.so is empty, not checked.
    ldconfig: File /usr/lib/libfftw3f_threads.so is empty, not checked.
    ldconfig: File /usr/lib/libfftw3f.so is empty, not checked.
    ldconfig: File /usr/lib/libjson-c.so.2.0.1 is empty, not checked.
    ldconfig: File /usr/lib/libjson.so.0 is empty, not checked.
    ldconfig: File /usr/lib/libpulse.so.0 is empty, not checked.
    ldconfig: File /usr/lib/libfftw3_threads.so.3 is empty, not checked.
    ldconfig: File /usr/lib/libfftw3l.so is empty, not checked.
    ldconfig: File /usr/lib/libpulse-simple.so.0.0.4 is empty, not checked.
    ldconfig: File /usr/lib/libtdb.so is empty, not checked.
    ldconfig: File /usr/lib/libjson-c.so is empty, not checked.
    ldconfig: File /usr/lib/libfftw3f.so.3 is empty, not checked.
    ldconfig: File /usr/lib/libfftw3f_threads.so.3 is empty, not checked.
    ldconfig: File /usr/lib/libfftw3.so is empty, not checked.
    ldconfig: File /usr/lib/libspeexdsp.so.1.5.0 is empty, not checked.
    ldconfig: File /usr/lib/libspeex.so.1.5.0 is empty, not checked.
    ldconfig: File /usr/lib/libfftw3.so.3.3.2 is empty, not checked.
    ldconfig: File /usr/lib/libfftw3l.so.3.3.2 is empty, not checked.
    ldconfig: File /usr/lib/libpulse-simple.so.0 is empty, not checked.
    ldconfig: File /usr/lib/libjson.so.0.1.0 is empty, not checked.
    ldconfig: File /usr/lib/libspeex.so is empty, not checked.
    ldconfig: File /usr/lib/libfftw3f_threads.so.3.3.2 is empty, not checked.
    ldconfig: File /usr/lib/libpulsecore-4.0.so is empty, not checked.
    ldconfig: File /usr/lib/libjson.so is empty, not checked.
    ldconfig: File /usr/lib/libpulse-mainloop-glib.so.0 is empty, not checked.
    ldconfig: File /usr/lib/libfftw3.so.3 is empty, not checked.
    ldconfig: File /usr/lib/libwebrtc_audio_processing.so is empty, not checked.
    ldconfig: File /usr/lib/libjson-c.so.2 is empty, not checked.
    ldconfig: File /usr/lib/libsbc.so.1.1.0 is empty, not checked.
    ldconfig: File /usr/lib/libtdb.so.1.2.11 is empty, not checked.
    ldconfig: File /usr/lib/libfftw3l_threads.so is empty, not checked.
    ldconfig: File /usr/lib/libpulse-simple.so is empty, not checked.
    ldconfig: File /usr/lib/libspeex.so.1 is empty, not checked.
    ldconfig: File /usr/lib/libpulse-mainloop-glib.so.0.0.4 is empty, not checked.
    ldconfig: File /usr/lib/libwebrtc_audio_processing.so.0 is empty, not checked.
    ldconfig: File /usr/lib/libsbc.so.1 is empty, not checked.
    ldconfig: File /usr/lib/libfftw3_threads.so is empty, not checked.
    ldconfig: File /usr/lib/libtdb.so.1 is empty, not checked.
    ldconfig: File /usr/lib/libpulse.so.0.16.2 is empty, not checked.
    ldconfig: File /usr/lib/libspeexdsp.so is empty, not checked.
    ldconfig: File /usr/lib/libfftw3_threads.so.3.3.2 is empty, not checked.
    ldconfig: File /usr/lib/libpulse.so is empty, not checked.
    Running findbrokenpkgs returns the following advice:
    Recompile these packages:
    avahi colord flac glib2 gnupg iproute2 libproxy lm_sensors python2 qt4 systemd tumbler
    Is that the best way? If it is, how do I do it?
    I tried moving all the empty files from /usr/lib to /usr/lib/0size and then I tried simply pacmatic -S avahi colord flac glib2 gnupg iproute2 libproxy lm_sensors python2 qt4 systemd tumbler and the same using pacman, but that didn't work. Since I moved all the empty files, I'm not getting the errors about empty libraries, but lots of stuff still doesn't work.
    Last edited by colinkeenan (2013-06-13 10:26:46)

    A couple of packages wouldn't build. I tried clearing the cache and installing those with pacman, but that didn't work. Now findbrokenpkgs wants me to recompile the following:
    boost cups-filters rrdtool vlc xmms
    I tried clearing the cache again and installing those with pacman, but it didn't work. I've already recompiled boost. Before continuing, I double checked that findbrokenpkgs wasn't adding even more stuff to recompile, and it's not. I'm sure everybody reading this thinks I should just start over with a clean install of Arch, but I want to see if this last round of recompiling will work. But, if findbrokenpkgs finds more stuff to recompile, I'll definitely start over.

  • [SOLVED] Error "libpng12: /usr/lib/libpng.so.3 exists in filesystem".

    I've just tried to install the stable "google-chrome" package from AUR with the command.  I have all of the dependencies already installed except for these two:
    - libjpeg6 (building from AUR)
    - libpng12 (package found)
    When the package manage tries to install "libpng12-1.2.43-1", I get the following error:
    error: failed to commit transaction (conflicting files)
    libpng12: /usr/lib/libpng.so.3 exists in filesystem
    Errors occurred, no packages were upgraded.
    According to the file manager (Thunar), the file /usr/lib/libpng.so.3 is a link to /usr/lib/libpng.so.
    This is probably a silly question (as I'm a clueless newbie!) but... can I just delete this link and expect the installation of libpng12 to replace it so that everything will still work...?
    Thanks in advance :-)
    Last edited by esuhl (2011-01-21 02:46:19)

    $ pacman -Ql libpng|grep /lib/
    libpng /usr/lib/
    libpng /usr/lib/libpng.a
    libpng /usr/lib/libpng.so
    libpng /usr/lib/libpng14.a
    libpng /usr/lib/libpng14.so
    libpng /usr/lib/libpng14.so.14
    libpng /usr/lib/libpng14.so.14.5.0
    libpng /usr/lib/pkgconfig/
    libpng /usr/lib/pkgconfig/libpng.pc
    libpng /usr/lib/pkgconfig/libpng14.pc
    A tip: run pacman -Qo on the file in question, either you put that symlink there yourself or strange things are happening on your system.

  • Having issues with /usr/lib/libfreeimageplus.so.3 exists in filesystem

    Hello!
    On sunday I did a pamcan -Suy and it fails showing:
    error: failed to commit transaction (conflicting files)
    freeimage: /usr/lib/libfreeimageplus.so.3 exists in filesystem
    It is trying to install: Packages (9): farstream-0.1-0.1.2-4  freeimage-3.16.0-2  gnome-desktop-sharp-2.26.0-10
                  gtkhtml-sharp-2.26.0-9 [removal]  gtksourceview2-sharp-2.26.0-10
                  libgnome-desktop-sharp-2.26.0-10  rsvg2-sharp-2.26.0-10  vte-sharp-2.26.0-10
                  wnck-sharp-2.26.0-10
    And I did this:
    pacman -Qo /usr/lib/libfreeimageplus.so.3
    error: No package owns /usr/lib/libfreeimageplus.so.3
    Any idea? what to do?

    Luuuciano:
    So, I'm having the same problem.  I'm relatively new to Arch: I've  just been using  it a month or two, and I'm not entirely sure what the wiki is telling me to do when it says to "rename" the file.  Would you please elaborate for me?  I would really appreciate your help. 
    Thank you,
    Corey Goettsch

  • Gpm: /usr/lib/libgpm.so.1 exists in filesystem

    Hi all,
    Ran pacman -Syu today and I get the following error: -
    error: could not prepare transaction
    error: failed to commit transaction (conflicting files)
    gpm: /usr/lib/libgpm.so.1 exists in filesystem
    Errors occurred, no packages were upgraded.
    I tried a google search and a search of this forum but no results.
    Any ideas?
    Cheers
    EmyrB

    toofishes wrote:
    dolby wrote:force the upgrade
    man pacman
    I hate blanket advice like this without explanation. Forcing is not usually a good idea. Why not something more like this:
    Since there is only one file that is conflicting, you can manually delete it and then try the upgrade again. If there were quite a few files that conflicted, you should be sure you know what you are doing and then pacman -Sf just that one package, and then your normal -Sy will work fine.
    i just rephrased what the maintainer of the package said on the mailing list http://archlinux.org/pipermail/arch-dev … 05907.html giving the two imo crucial pointers. users are responsible for maintaining their own system.

  • Pacman upgrade error with /usr/lib/libgmp.so.1

    /media # pacup
    Password:
    :: Synchronizing package databases...
    core is up to date
    extra is up to date
    error: failed retrieving file 'community.db.tar.gz' from ftp.archlinux.org : Connection reset by peer
    error: failed retrieving file 'community.db.tar.gz' from locke.suu.edu : Connection timed out
    community is up to date
    :: Starting full system upgrade...
    resolving dependencies...
    looking for inter-conflicts...
    Targets: autoconf-2.62-1 cairomm-1.6.0-1 hspell-1.0-2 enchant-1.4.1-1 exempi-2.0.1-2 gnome-screensaver-2.22.2-1 gpm-1.20.3-1 gstreamer0.10-good-0.10.8-1
    gstreamer0.10-good-plugins-0.10.8-1 gtk-engines-2.14.1-1 gtkmm-2.12.7-1 iso-codes-2.0-1 libisofs-0.6.4-1 libxml2-2.6.32-1 libxslt-1.1.23-1
    poppler-0.8.2-1 poppler-glib-0.8.2-1 wine-0.9.60-1
    Total Download Size: 0.00 MB
    Total Installed Size: 31.11 MB
    Proceed with installation? [Y/n] y
    checking package integrity...
    (18/18) checking for file conflicts [########################################################################################################] 100%
    error: could not prepare transaction
    error: failed to commit transaction (conflicting files)
    gpm: /usr/lib/libgpm.so.1 exists in filesystem
    Errors occurred, no packages were upgraded.
    /media #
    IIRC, I had to make a symbolic link with libgmp.so.1 a long time ago, but not too sure. Any help appreciated, thanks

    hi, take a look at:
    http://bbs.archlinux.org/viewtopic.php?id=47981

  • [SOLVED] freeimage: /usr/lib/libfreeimage.so.3 exists in filesystem

    Issue:
    I can't upgrade.
    $ pacman -Syu
    error: failed to commit transaction (conflicting files)
    freeimage: /usr/lib/libfreeimage.so.3 exists in filesystem
    Errors occurred, no packages were upgraded
    I check whether a package, possibly from AUR, is responsible:
    # pacman -Qo
    error: No package owns /usr/lib/libfreeimage.so.3
    No.
    Apparently this happened to other users as well. I was recommended the following solution:
    $ pacman -Sf freeimage
    Thanks to jelly1, Hattara-pilvi and Tucos of #archlinux!
    Last edited by qubodup (2012-03-22 15:07:46)

    $ pacman -Ql libpng|grep /lib/
    libpng /usr/lib/
    libpng /usr/lib/libpng.a
    libpng /usr/lib/libpng.so
    libpng /usr/lib/libpng14.a
    libpng /usr/lib/libpng14.so
    libpng /usr/lib/libpng14.so.14
    libpng /usr/lib/libpng14.so.14.5.0
    libpng /usr/lib/pkgconfig/
    libpng /usr/lib/pkgconfig/libpng.pc
    libpng /usr/lib/pkgconfig/libpng14.pc
    A tip: run pacman -Qo on the file in question, either you put that symlink there yourself or strange things are happening on your system.

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