Screw you too, Github

ERROR: We're doing an SSH key audit. 

Reason: legacy key automatically unverified

I could generate a new key ... or I could just stop using Github. Those projects are all unpaid, anyways.

brittleR

Apparently the current crop of R developers was never told the standard policy of never break backwards compatibility on a minor version increment.

Put simply, packages available for 3.3 do not work in 3.4. I'm sure there is some perfectly justifiable reason for making the release 3.4 instead of 4.0, while breaking all existing packages (until manually updated by the maintainers), but guess what: it's bollocks. 

Anyways, to forestall a long rant about disregarding long-held policy due to historical ignorance (*cough* Uber), here is how to downgrade 3.4 to 3.3 on Debian:

1. add stretch to /etc/apt/sources.list
        deb http://ftp.us.debian.org/debian/ stretch main non-free contrib
        deb-src http://ftp.us.debian.org/debian/ stretch main non-free contrib
 2.  apt-get update
     apt-cache showpkg r-base should show version 3.3.3-1
 3. apt-get remove r-base r-base-core r-base-html r-base-dev
 4. go to https://packages.debian.org/stretch/r-base-html to get version number (3.3.3-1)
     also https://packages.debian.org/stretch/r-recommended for version numbers for dependencies
  5. now do the big install:
    sudo apt-get install r-base=3.3.3-1 r-base-core=3.3.3-1 \
         r-recommended=3.3.3-1 r-base-dev=3.3.3-1 r-base-html=3.3.3-1 \
         r-cran-boot=1.3-18-2 r-cran-class=7.3-14-1 r-cran-cluster=2.0.5-1 \
         r-cran-codetools=0.2-15-1 r-cran-foreign=0.8.67-1 \
         r-cran-kernsmooth=2.23-15-2 r-cran-lattice=0.20-34-1 \
         r-cran-mass=7.3-45-1 r-cran-matrix=1.2-7.1-1 r-cran-mgcv=1.8-16-1 \
         r-cran-nlme=3.1.129-1 r-cran-nnet=7.3-12-1 r-cran-rpart=4.1-10-2 \
         r-cran-spatial=7.3-11-1 r-cran-survival=2.40-1-1
  6. prevent R from updating again, because its developers obviously cannot be trusted:
         sudo sudo apt-mark hold r-base r-base-core
  7. comment out the lines in sources.list for step 1

In related news, here is how to downgrade an R package to a specific version number. The example uninstalls the package 'BH' and replaces it with version 1.62.0. As with most package management in R these days, you need the devtools package installed.

remove.packages('BH')
library(devtools)
install_version('BH', '1.62.0')

RIP inittab

Your getty configs are all in /lib/systemd/system/getty@.service now.

[Service]
# the VT is cleared by TTYVTDisallocate
ExecStart=-/sbin/agetty --noclear %I $TERM                                      
Type=idle
Restart=always
RestartSec=0
UtmpIdentifier=%I
TTYPath=/dev/%I
TTYReset=yes
TTYVHangup=yes
TTYVTDisallocate=yes
KillMode=process
IgnoreSIGPIPE=no
SendSIGHUP=yes

Control via /etc/systemd/logind.conf -- see man 5 logind.conf for more info.

Dispatches from the X1 front

The first-gen Thinkpad X1: possibly the best laptop I've ever owned. Lasted three years, compared to the usual 12-18 months. It still runs, but the battery is down to about 40 minutes, and the (second!) keyboard is starting to lose keys.

The third-gen Thinkpad X1 Carbon: a little annoying at first: no SD slot, no h/w kill switch for the wireless, no spill-through keyboard (wtf guys, that was brilliant!). About 6 months in, the video glitches started: there is a short which corrupts video memory while using wifi. The fix, of course, is a replacement system board, which is great if you have a spare third-gen X1 Thinkpad Carbon lying around and can just up and change workstations like it's no big. Workaround: rfkill block wifi, or just get used to the strobe effect.

The latest: Thinkpad X1 Yoga. And let's just put it out there: this doesn't work out of the box like the previous two did. Lenovo and Intel seem to have backed off of their Linux commitment, though that's probably half their users these days (errybody else on the mobile, right?)

Here's the rundown on getting the X1 Yoga up and running with a Linux install.


Basic Linux

Debian 8.3.0 AMD64 netinst ISO if you were wise enough to buy the OneLink+ RJ45 ethernet adapter; otherwise, use the regular (non-netinst) ISO.

Use unetbootin to make a USB flash drive image for this. Go into the BIOS on the X1 Yoga, enable F12 for boot device selection (just because), turn off secure boot, maybe enable diagnostic boot as well. No need to allow legacy BIOS installs, Debian will work just fine with uEFI (unlike FreeBSD where you need to use the 10.3-Beta or 11 memstick). Go through the install like you usually do. Your ethernet (if you have it) will be detected (again, unlike in FreeBSD).

Sound, APCI (suspend, hibernate, and battery status) and video card should all be working out of the box.


Wireless

Upgrade your kernel to 4.4.1 from the ubuntu PPA:
  http://kernel.ubuntu.com/~kernel-ppa/mainline/v4.4.1-wily/
This is per notes about a typo in the iwlwifi driver at
 https://bbs.archlinux.org/viewtopic.php?id=206831
Looking at the kernel source, 4.2.7 has the fix as well, but might as well go with the latest stable release of the kernel if we're upgrading.

You'll also need to upgrade the firmware, or your Wifi will not be recognized. There is a debian package in backports for this:
 https://packages.debian.org/jessie-backports/firmware-iwlwifi


Skylake P-State Fix

If you rebooted excitedly into your new kernel without following the rest of these steps, you're likely looking at a blank screen. That's because of a skylake p-state bug reported here:
 https://www.reddit.com/r/thinkpad/comments/410haw/yoga_260_wont_boot_ubuntu_with_kernel_4244_but/

This is because the kernel needs a command line parameter to not totally crap itself when it encounters Skylake's poor implementation of pstate.

To fix this, change the cmdline in /etc/default/grub to:
  GRUB_CMDLINE_LINUX_DEFAULT='intel_pstate=no_hwp quiet'

Don't forget to run update-grub when you're done.

Hopefully this will go away in 4.5; according to a commenter, that's what the kernel guys are trying for.


i915 Xorg Video fix

Of course, the fancy new kernel hosed your X windows, didn't it?

Not sure why there's such a tight coupling there, but never mind. This one's an easy fix, per http://comments.gmane.org/gmane.linux.debian.user/508779 . Download (and install) a new version of the xserver-xorg-video-intel package from backports:

https://packages.debian.org/jessie-backports/xserver-xorg-video-intel


Touchscreen

The touchscreen is recognized and configurable in X Windows, but does not respond to touch or stylus events. A bug report is open at the linuxwacom project.

The touchscreen (+ stylus) works out of the box once the firmware update is installed (via windows, sadly,so don't pave the drive until you've updated firmware). Make sure to perform a hard reset (60 sec with a paperclip in the bottom of the laptop) after the upgrade.

To disable the touchpad when entering tablet mode (note: the keyboard will be disabled by  the BIOS), create the file /etc/acpi/events/thinkpad-tablet-touchpad-off with the following contents:

event=ibm/hotkey LEN0068:00 00000080 000060f0
action=/usr/local/bin/touchpad_disable.sh

You can verify the hotkey parameter by running acpi_listen and folding the display back to tablet position.

Next, create the file /usr/local/bin/touchpad_disable.sh with the following contents:

export XAUTHORITY=`ls -1 /home/*/.Xauthority | head -n 1`

export DISPLAY=":`ls -1 /tmp/.X11-unix/ | sed -e s/^X//g | head -n 1`"

tp_dev='SynPS/2 Synaptics TouchPad'

state=`xinput list-props "$tp_dev" | grep 'Device Enabled' | cut -d':' -f2 | tr -d '\t '`

if [ $state -eq 1 ]

then

  xinput disable "$tp_dev"

else

  xinput enable "$tp_dev"

fi

You will need to give root access to the X server session for this. The quickhack version is to add xhost + & to ~/.xsessionrc, but it's better to do something like +root@localhost..

The Acer BMA150 accelerometer is detected as a joystick device, so various /sys/bus/iio -based screen orientation scripts like thinkpad-yoga-scripts won't work. An alternative is to define a Window Manager screen edge event that invokes a script to cycle through screen orientation rotations:

#!/bin/sh
# script to rotate screen (counter-clockwise) based on current orientation

conn_line=`xrandr | grep ' connected'`
dev=`echo "$conn_line" | cut -d' ' -f 1`
orient=`echo "$conn_line" | cut -d' ' -f 5`

case $orient in
  '(normal' )
    xrandr --output $dev --rotate left
    ;;
  'left' )
    xrandr --output $dev --rotate inverted
    ;;
  'inverted' )
    xrandr --output $dev --rotate right
    ;;
  'right' )
    xrandr --output $dev --rotate normal
    ;;
  * )
    xrandr --output $dev --rotate normal
    ;;
esac

Some other approaches are discussed in this Manjaro Linux post.

Fingerprint reader

Is not supported by fprint. USB ID: 138a:0090 (Validity, no product string in usb-devices).


Camera

Works out of the box. Driver is uvcvideo. VLC mirrors it without any problems:

vlc v4l:// :v4l-dev="/dev/video0" :v4l-adev="/dev/audio"


FreeBSD

You need to use a 10.3 (BETA3 or more current) UEFI memstick image to do the install with, of course, the OneLink ethernet adapter connected. Presently, no support for wifi or Xorg support (perhaps in 11?). To boot, add an entry in /etc/grub.d/40_custom as follows:

menuentry "FreeBSD 10.3-BETA3" {
  insmod chain
  set root=(hd0,gpt10)
  chainloader (hd0,gpt10)/boot/loader.efi
}

...replacing gpt10 with the partition number where FreeBSD was installed. This starts counting from 1, so the example here is the tenth partition on the first hard drive (hd0).

Note that for update-grub to correctly recognize the FreeBSD partition (and therefore find loader.efi), you should provide an fstab entry to specify the UFS partition type:

/dev/sda10      /home/bsd       ufs    ro,noauto,ufstype=ufs2       0       0

"losetup -e blowfish" broken across distributions

Apparently this has been an issue for a long time:

  1. create an encrypted disk image with "losetup -e blowfish"
  2. ...years pass...
  3. move the encrypted disk image to a machine with a
      different distribution of Linux
     -or-
     upgrade the installed version of Linux
  4. discover that all access to the encrypted data is lost!

This apparently has to do the hash being used in blowfish changing, usually for security reasons and usually without a backwards-compatibility option, as documented in loop-AES.README.

This is very bad news if you've been backing up your encrypted disk image. Better stick with a losetup-mount-tar-pgp backup procedure instead:

# to backup:
bash$ cd /media/encrypted_fs
bash$ tar cf - * | gpg --output /home/backup/encrypted_fs.gpg -r you@email.address -e - 
# to restore:
bash$ cd /media/encrypted_fs
bash$ gpg -d /home/backup/encrypted_fs.gp | tar xf -

Returning to Pre-Framebuffer console fonts

At some point in time, the various Linuxes out there decided that the large, blocky, easy-to-read console (as in Virtual Console, not Terminal Emulator) fonts should be replaced with tiny, hard-to-read fonts that make it a chore to edit standard 80-column scripts/source/config files in vim.

Experimenting with various grub and kernel options to change the resolution, fix i915.modeset, and so forth make for a lot of rebooting to get things just right.

Enter the Debian console-setup package. This provides a wizard that ultimately calls setfont and stty to configure the Linux Virtual Consoles.

The dialog-based wizard is invoked via sudo dpkg-reconfigure console-setup .  Each screen is simple enough to navigate on its own; however, the following selections will configure the consoles to display an old, 90s-to-early-oughts style of font:

1. UTF-8 [default, just press ENTER]
2. Combined - Latin; Slavic Cyrillic; Greek [default]
3. VGA
4. 28x16

The result should produce a nice 80 column x 25 row vim display that is visible from halfway across the room (and to old geezers a few inches away). Chuck it on a Macbook air to really get some double-takes from passers by.

Ubuntu, you're fired.

Attempted to upgrade a workstation (dual-xeon, sata3 ssd for /; sata 3 hdd for /usr, /var, /opt, /usr/local; sata2 mirrored raid (via dmraid) for /home) from 10.04 to 11.04 via do-release-upgrade (in update-manager-core) last night. Why do that? Because Ubuntu only updates software packages for its newest release, so if you need, say, Python 2.7 in order to work on a project, you're SOL unless you upgrade.

Everything went well until the final reboot, which left the machine at:


error: the symbol 'grub_xputs' not found.

Verified that the grub software is all present:

grub rescue> ls (hd0,1)/boot
... lots of modules and such...

Everything seemed to be there, so attempted to boot manually, under the assumption it was all due to misconfiguration:

grub rescue> set root=(hd0,1)
grub rescue> set kernel=/boot/vmlinuz-2.6.32-33-generic
grub rescue> set initrd=/boot/initrd.img-2.6.32-33-generic
grub rescue> boot
error: no loaded kernel

Second attempt, loading the grub modules manually (per Ubuntu Grub2 Docs and this thread):

grub rescue> set prefix=(hd0,1)/boot/grub
grub rescue> insmod normal
error: the symbol 'grub_xputs' not found.
grub rescue> insmod linuxgrub
error: the symbol 'grub_xputs' not found.

For some reason, the symbols in the grub2 bootstrap code do not match the ones expected by the modules. One of them is the wrong version. Looks to be a reported bug.

The solution, per Ubuntu Grub2 Docs and this fix, is to boot a LiveCD (which must be the same version as the newly-installed-but-broken Ubuntu) and run grub-install. This turns out to be a huge delay, as the upgrade took place without a LiveCD, so an ISO must be downloaded. It is also a huge pain when one is out of blank CDs, and has to press a usbstick into service (accomplished per Ubuntu Install Docs).

It also doesn't work. The new error on reboot is

error: file not found

grub rescue> insmod linux

ELF header smaller than expected

It turns out that 10.04 upgrades to 10.10, NOT 11.04, so the LiveCD contained the wrong version of grub!

Fortunately, there is a guide to purging and reinstalling grub once booted from any LiveCD.

The steps are (details such as hdd devices and mount points are specific to this workstation):

bash$ sudo bash

bash# mount /dev/sdk1 /mnt

bash# mount /dev/sdf3 /usr

bash# mount /dev/sdf4 /var

bash# mount --bind /dev /mnt/dev

bash# mount --bind /dev/pts /mnt/dev/pts

bash# mount --bind /proc /mnt/proc

bash# mount --bind /sys /mnt/sys

bash# chroot /mnt

bash-chroot# apt-get update

bash-chroot# apt-get purge grub grub-common grub-pc

bash-chroot# apt-get install grub-common grub-pc

bash-chroot# #NOTE: Be sure to select /dev/sdk for Grub2 install location

bash-chroot# exit

bash# umount /mnt/dev/pts

bash# umount /mnt/dev 

bash# umount /dev/sys

bash# umount /mnt/proc

bash# umount /mnt/var

bash# umount /mnt/usr

bash# umount /mnt

bash# reboot

That does the trick.

But you know what would really be nice? A way to upgrade the OS, including the kernel and all packages, WITHOUT TOUCHING THE GODDAMN BOOT-LOADER. Seriously, it's an upgrade, the bootloader already works -- don't mess with it!

Ubuntu getting crappier and crappier

Stupidly made the decision to upgrade to 10.10 (for a single package!) on the main laptop (mbpro 5,5) and poof! No wireless!

Seriously, it's been three releases since an ethernet cable was required to do an upgrade.

Piece.
Of.
Shit.

Only question now is how many hours of productivity are going to be lost fixing what *was* a perfectly working system before the upgrade.

The sad fact is that os x and windows are just as unreliable for upgrades (while being less usable), and FreeBSD refuses to even glance at this hardware.

A decade ago, this shit used to *work*!

Running log of the fixes:

* apt-get install gnome-icon-theme to get NetworkManager running again. There is no fix for Wicd; it has apparently "stopped working".

* apt-get install gnome-alsa-mixer to un-mute the sound. Kmixer has been reduced from 7 or so channels to 1 (without a mute option).

* uninstall ruby 1.9 via apt-get. Download and install rvm (system-wide as this is a workstation), then do 'sudo rvm --default use 1.9.2' to make 1.9 the system-wide default (might roll that back later).

* reinstall all 1.9 gems.

* rebuild the passenger apache module ('sudo passenger-install-apache2-module') and update the config files to point to the new location.

* fix all rack-based webapps to include the line
    $: << File.dirname(__FILE__)
in config.ru and in each Sinatra::Base application file, as something got screwed in the ruby-passenger-rack environment, and PassengerRoot is no longer in the Ruby module path.

See? A smooth, seamless upgrade! You almost don't even notice that it happened!

Insipid Ibex

Finally upgraded (K)Ubuntu to 8.10. Thanks for breaking my xorg config, guys, by assuming that HAL could actually do a better job that my hand-picked settings. This is easily fixed by uncommenting all of the lines commented out by HAL, but it's amazing that it had to be done at all, since the HAL change made X flat-out stop working. Also, for some reason, ~/.xsession no longer works -- one has to use ~/.xsessionrc instead. Those wacky Ubuntites.

Upgraded E17 shortly afterwards, using the packages at

deb http://greenie.sk/ubuntu intrepid e17

The new version of E has compiz support (which has to almost entirely be disabled for it to run at E17's proper speed) and looks nice. The modules all seem to work, for once.

But it crashes!

The first one came immediately, and was fixed by wiping ~/.e, which contained all of my old config settings. Apparently E17 can't reliably be upgraded with an existing config. Thanks for moving to a binary config file, guys, so that this is actually a far larger problem than it should be. Really, how hard is it to use the binary config only at runtime, and compile from text to binary whenever a config change is made?

Some of the other crashes appear to be from the OpenGeu inclusion of compiz. After removing the calls to emerald and ecomorph from enlightenment_startup.sh, and stripping out the -evil command line option (which, along with -good and -psychotic, did not seem to make things stable), it's become pretty stable, if a little buggy. Dialog boxes occasionally do not disappear when closed, requiring a restart of E17.

Also, some E17 idiocies remain -- things that seemed to be oversights before, but now (having been a pretty stable WM for the past three years) appear to be truly asinine design decisions.

Specifically:

* There is no way to modify the properties of an application (short of adding it to iBar, or modifying the desktop file directly). A dialog exists for this (it's used by ibar and when creating a new application), so it can't be much extra work.

* One cannot cut/copy/paste between E17 widgets and X. This is nice to be able to do when, say, setting an icon file path (since the desktop files for KDE applications do not seem to be handled correctly by E17, and therefore have no icon files). Hope you like typing.

* The binary only config, mentioned above. Really, there is no excuse for this -- the rest of the industry learned that lesson in the 90s. Even Windows allows its abhorred registry to be read from and written to text files.

Aside from that, Ibex works well, and the upgrade was generally painless. The only sticky points were the Xorg conf file (their mistake), E17 (my fault for running it), and the patch I needed to add to get toshset supported by the latest kernel (the maintainer's fault, for not getting it merged after 2 years of reliable performance).