Mittwoch, 13. August 2014

How to install Ubuntu 14.04 on an old Macbook 2.1 EFI.

UPDATE on 13/3/2015: this instruction method is no longer valid for newer Ubuntu versions > 14.04 (e.g. 14.10)! I will write a follow up soon on this you can find here. There are lots of instructions and tutorials out there on how to install Ubuntu on Mac computers. Most dont work as stated (mostly because it is not easy to make a bootable ubuntu usb boot stick with a mac), so I wrote this tutorial which I think is the most easy one out there!

This post is basically just a short reminder for myself on how to install Ubuntu 14.04 on Macbook 2.1 EFI. Maybe it is useful for other people as well.


Macbook with Mac Os X >=10.6, the full harddisk is occupied by Mac Os X.

1. start Mac Os X, open Disk utility, shrink Mac Os X partition so much that you can create another two partitions, one for Linux root with at least 30 gb and another one for swap, rule of thumb: available RAM memory equals two. For me it was 2 gb * 2 = 4 gb. Choose Mac Os X journaling as filesystem for the new two partitions.
2. After partitioning you should now have three partitions, my setup was 65 gb total (SSD): 30 gb for Mac Os X, 30 gb for Linux (root paritions), 4 gb for the swap partition
3. Install rEFIt, power off computer (do not just restart) to see if rEFIt logo is booting up, if not try again powering off.
4. Boot back into Mac Os X and download Ubuntu 14.04 64 bit AMD for Mac ISO
5. download ISO2USB-Efi-Loader and prepare an USB stick with the ISO from step 3 (details here: here (in german) use the boot64bit efi file on the stick. Use google translate if you cannot understand German.
6. reboot and use the Mac ´ALT´ key during startup and choose the usb-efi stick
7. install ubuntu, choose ´something else´ as the installation type, then use the linux root partition from step 1. (mine is called /dev/sda4) and format it as ext4 and select root (/). Also define the swap partition from step 1. Most importantly in this step is to select the root parititon for the boot loader (e.g. /dev/sda4) but never NEVER use the whole disk for installation of it!!! (never use the full disk e.g. /dev/sda use a partition e.g. /dev/sda4)
8. at the end of the installation the installer says it cant install the bootloader at /dev/sda4, click on ´ignore this and continue installation´ (dont install on /dev/sda - the full disk etc.)
9. after successfully install ubuntu, click on ´test live system´
10. prepare a boot-repair-disk on your usb stick, install boot-repair as stated here (on a usb stick!, you can download the iso and use it similar to step 5 here), reboot and start the stick than click on ´Recommended repair´
11. done! reboot. now a tux symbol will appear at the rEFIt boot menue. Click on it to start ubuntu!

Dienstag, 11. Februar 2014

Fixing package installation problems 'failed to install' in Architect (architect 0.9.3-10) under Ubuntu 12.04

Fixing package installation problems 'failed to install' in Architect 0.9.3-10 under Ubuntu 12.04

for a project I needed "trace into debugging" functionalities in R so I installed the architect 0.9.3-10 deb package within Ubuntu 12.04 using the following instruction which is a standalone eclipse built using the StatEt plugin

started the program, switched in the Embedded R.3.0.2 console typed

to install some additional packages I needed for debugging a specific project

got following error

The downloaded source packages are in
'biocLite.R' failed to install 'BiocInstaller', use
Warning message:
In install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) :
  installation of package ‘BiocInstaller’ had non-zero exit status

also tried out the suggested install.packages("BiocInstaller",repos="") which did not work either

someone suggested that the solution is running R in administrative mode in order to install packages, so I wrote down the R_HOME path from within R

 > R.home()
[1] "/opt/architect/stable/20131204221312/plugins/eu.openanalytics.architect.r.server.gtk.linux.x86_64_0.9.3.201310150807/R"

open a terminal and login as root

$ sudo su
# set R path  extracted from R (R.home()) for convenience 
$ export MY_R="/opt/architect/stable/20131204221312/plugins/eu.openanalytics.architect.r.server.gtk.linux.x86_64_0.9.3.201310150807/R"
$ cd $MY_R
#run the command line R
$ ./bin/R

got me the following error

./bin/R: line 236: /opt/architect/architect-stable/plugins/eu.openanalytics.architect.r.server.gtk.linux_stable/R/etc/ldpaths: No such file or directory
ERROR: R_HOME ('/opt/architect/architect-stable/plugins/eu.openanalytics.architect.r.server.gtk.linux_stable/R') not found

i opened the R shell command and saw that it sets R_HOME_DIR in line 4

$ less bin/R
# line 4: R_HOME_DIR="/opt/architect/architect-stable/plugins/eu.openanalytics.architect.r.server.gtk.linux_stable/R"

if i do a

ls  /opt/architect/architect-stable/plugins/eu.openanalytics.architect.r.server.gtk.linux_stable/

i got a

No such file or directory error

if i do a

ls -al  /opt/architect/architect-stable/plugins/eu.openanalytics.architect.r.server.gtk.linux_stable

i see that the dynamic link is misplaced

 -> /opt/architect/stable/20131204221312/plugins/eu.openanalytics.architect.r.server.gtk.linux_0.9.3.201310150807 

which does not exist!!!

the right one can be found in the directory /opt/architect/stable/20131204221312/plugins/


if you compare both, you see that the correct one has the substring 'x86_64' which the wrong one did not have, so there seems something was wrong with a command such as 'uname' (maybe they used a parameter for uname which was not available on all platforms etc. when generating the script)

to fix this remove dynamic link

rm /opt/architect/architect-stable/plugins/eu.openanalytics.architect.r.server.gtk.linux_stable 

and point to true location

ln -s /opt/architect/stable/20131204221312/plugins/eu.openanalytics.architect.r.server.gtk.linux.x86_64_0.9.3.201310150807 /opt/architect/architect-stable/plugins/eu.openanalytics.architect.r.server.gtk.linux_stable

afterwards R is running fine and I can install what I want e.g. using source("") command

$ bin/R

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> biocLite("cellHTS2")

now I can install all my needed packages from the command line using sudo rights!