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
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
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
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
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
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
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
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)
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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
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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
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Type 'q()' to quit R.
now I can install all my needed packages from the command line using sudo rights!