SciClone installation in R version 3.3.3

Question

[mar.ark.parr]

Dear all!

I plan to use SciClone to analyze cancer metastasis, but have problems while installation it. I have Ubuntu 16.04 and R version 3.3.3.

I tried to follow instructions from https://github.com/genome/sciclone/blob/master/README.md and the error happens while installation package devtools: "Warning messages: 1: In install.packages("devtools") : installation of package ‘curl’ had non-zero exit status 2: In install.packages("devtools") : installation of package ‘openssl’ had non-zero exit status 3: In install.packages("devtools") : installation of package ‘git2r’ had non-zero exit status 4: In install.packages("devtools") : installation of package ‘httr’ had non-zero exit status 5: In install.packages("devtools") : installation of package ‘devtools’ had non-zero exit status"

When trying to build sciclone manually the problem starts just when installation IRanges and rgl. What I got for IRanges is "Warning message: package ‘IRanges’ is not available (for R version 3.3.3)"

Does anyone have experience in installation SciClone in this R version? Could anyone give any ideas how to deal with these problems?

Answer 1

[Jean-Karim Heriche]

First, according to the README file you linked, the first step is to install IRanges. The error that IRanges is not available suggests that you may be using an outdated Bioconductor so try

source("http://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")

Second, the other errors suggest that you haven't installed the required libraries on your system. For example, for openssl, you would need libssl-dev, e.g.:

sudo apt-get install libssl-dev

Check this tutorial on setting up devtools on Ubuntu 16.04.

[mar.ark.parr]

Guys, thank you very much! Now using your advice I successfully moved to the last step of installation: install_github("genome/sciClone"). Currently it seems that the main problem is with rgl package:

installing source package ‘rgl’ ... package ‘rgl’ successfully unpacked and MD5 sums checked checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for gcc... (cached) gcc -std=gnu99 checking whether we are using the GNU C compiler... (cached) yes checking whether gcc -std=gnu99 accepts -g... (cached) yes checking for gcc -std=gnu99 option to accept ISO C89... (cached) none needed checking for libpng-config... yes configure: using libpng-config configure: using libpng dynamic linkage checking for X... no configure: error: X11 not found but required, configure aborted. ERROR: configuration failed for package ‘rgl’ removing ‘/usr/local/lib/R/site-library/rgl’ Error: Command failed (1)

Interesting, that I have successfully installed this package by "sudo apt-get install r-cran-rgl" and now I am able to do "library(rgl)" in R, but SciClone installation still wants to install rgl itself...

[Santosh Anand]

It's surprising that Ubuntu 16.04 has X11 not installed by default! Anyway, try these commands and it should be fine

$ sudo apt-get update
$ sudo apt-get install x11-common

Interesting, that I have successfully installed this package by "sudo apt-get install r-cran-rgl" and now I am able to do "library(rgl)" in R, but SciClone installation still wants to install rgl itself...

Ubuntu might be installing RGL to some obscure location, which SciClone installer is not able to verify.

[mar.ark.parr]

Santosh, I apologize for late response and thank you very much again for your help! But unfortunately even if i install X11 by the way you said, SciClone still doesn't see. It still has the same error with rgl and X11... So as I understood the possible solution is to try another R version... Older one.

[Santosh Anand]

Normally, after the installation of X11, you need a reboot to make a systemwide effect. And if the other version of SciClone also depends upon X11 (check requirements from their site), then you are anyway not going to solve using different R. X11 is the GUIing/Windowing system of your OS (Linux), it doesn't depend on R.

Answer 2

[Santosh Anand]

Devtoos depend upon a host of other packages. You need to install them first before trying to install devtools. See devtools installing instructions from here

https://www.digitalocean.com/community/tutorials/how-to-install-r-packages-using-devtools-on-ubuntu-16-04

In short, you need to run this command before installing devtools

$ sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev

It will be easier to install via SciClone via devtools than manual. So try with that first. Also update bioconductor as suggested by @Jean

[mar.ark.parr]

Thank you very much! Really decided to keep manual installation as plan B :)

Answer 3

[mar.ark.parr]

For anyone who will struggle with this problem :) This is what finally helped me. Combining what guys here wrote me and advices of the colleagues from my lab: When devtools library has been already installed and "install_github("genome/bmm")" done:

sudo rm -r /tmp/*

sudo apt-get install libx11-dev

sudo apt-get install libglu1-mesa-dev

then open R and:

library(devtools)

install_github("genome/sciClone")

[Charles Plessy]

sudo rm -r /tmp/*

Be careful: on a multi-user platform, one will annoy many people with such a command, and even on your own computer you can shoot yourself in the foot if you were running other programs at the same time. I do not see this command being discussed in other answers. Are you sure you needed to delete temporary files or directories ? If yes, you should better delete them specifically instead of wiping out a lot of other files.