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="http://www.bioconductor.org/packages/2.13/bioc") 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("http://bioconductor.org/biocLite.R") 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!