Need help- Installing of "DESeq2" (Bioconductor) fails

[larsLL]

Hi everybody,

I'm trying to install the package "DESeq2" from Bioconductor in R, but unfortunately ist does't work.
I'm using the newest Ubuntu Version 14.04 on a Virtual Machine in Windows.
I have the newest R version 3.1.2 and I installed the newest Bioconductor version 3.0. by typing the command:

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

I also have the newest version of the BiocInstaller 1.16.1.

When I'm trying to install the Bioconductor, the following error arises:

R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
.........
.........and so on
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
> biocLite("DESeq2")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.2.
Installing package(s) 'DESeq2'
also installing the dependencies ‘base64enc’, ‘colorspace’, ‘iterators’, ‘brew’, ‘checkmate’, ‘DBI’, ‘fail’, ‘RSQLite’, ‘sendmailR’, ‘stringr’, ‘XML’, ‘xtable’, ‘dichromat’, ‘munsell’, ‘labeling’, ‘GenomeInfoDb’, ‘XVector’, ‘foreach’, ‘BatchJobs’, ‘BBmisc’, ‘AnnotationDbi’, ‘annotate’, ‘RColorBrewer’, ‘plyr’, ‘digest’, ‘gtable’, ‘reshape2’, ‘scales’, ‘proto’, ‘Formula’, ‘latticeExtra’, ‘acepack’, ‘S4Vectors’, ‘IRanges’, ‘GenomicRanges’, ‘Rcpp’, ‘RcppArmadillo’, ‘BiocGenerics’, ‘Biobase’, ‘BiocParallel’, ‘genefilter’, ‘locfit’, ‘geneplotter’, ‘ggplot2’, ‘Hmisc’

versuche URL 'http://cran.fhcrc.org/src/contrib/base64enc_0.1-2.tar.gz'
Content type 'application/x-gzip' length 6407 bytes
URL geöffnet
==================================================
downloaded 6407 bytes

versuche URL 'http://cran.fhcrc.org/src/contrib/colorspace_1.2-4.tar.gz'
Content type 'application/x-gzip' length 242791 bytes (237 Kb)
URL geöffnet
==================================================
downloaded 237 Kb
..............
..............
..............and so on
==================================================
downloaded 594 Kb

versuche URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/DESeq2_1.6.2.tar.gz'
Content type 'application/x-gzip' length 1192621 bytes (1.1 Mb)
URL geöffnet
==================================================
downloaded 1.1 Mb


The downloaded source packages are in
‘/tmp/RtmpRgv945/downloaded_packages’
Old packages: 'spatial'
Update all/some/none? [a/s/n]: a

versuche URL 'http://cran.fhcrc.org/src/contrib/spatial_7.3-8.tar.gz'
Content type 'application/x-gzip' length 43593 bytes (42 Kb)
URL geöffnet
==================================================
downloaded 42 Kb


The downloaded source packages are in
‘/tmp/RtmpRgv945/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Es gab 50 oder mehr Warnungen (Anzeige der ersten 50 mit warnings())

> warnings()
Warnmeldungen:
1: In system2(cmd0, args, env = env, stdout = outfile, stderr = outfile) :
system call failed: Nicht genügend Hauptspeicher verfügbar
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... :
installation of package ‘base64enc’ had non-zero exit status
3: In system2(cmd0, args, env = env, stdout = outfile, stderr = outfile) :
system call failed: Nicht genügend Hauptspeicher verfügbar
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... :
installation of package ‘colorspace’ had non-zero exit status
5: In system2(cmd0, args, env = env, stdout = outfile, stderr = outfile) :
system call failed: Nicht genügend Hauptspeicher verfügbar
........
........
........ and so on
49: In system2(cmd0, args, env = env, stdout = outfile, stderr = outfile) :
system call failed: Nicht genügend Hauptspeicher verfügbar
50: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... :
installation of package ‘BBmisc’ had non-zero exit status

I read a lot about this problem in the web. Many people say that this problem is caused by not having a version of "libxml2" and "libcurl", but I have installed the newest version of libxml2 and a version of libcurl (libcurl4-openssl-dev).

Despite of having versions of libxml2 and libcurl, the installation failures.
I'm very desperate with this problem because I'm a beginner with Ubuntu
and I can't solve the problem by myself.
Im very thankful for your comments.

Sincerely

Lars

[dpryan]

The "Nicht genügend Hauptspeicher verfügbar" message suggests that /tmp is getting full and preventing R from downloading the required packages. Try cleaning /tmp out (rebooting will do that for you, though you can also do it manually).

[larsLL]

Hi dpryan,

thank you for your quick response. I made a reboot but the installation didn't work anyhow. So I guessed that my "Hauptspeicher" was to small, and that was actually the problem. The "Hauptspeicher" had only a size of 512 Mb, now it has 2048 Mb. The installation worked well.
Thank you for your help :-)

[dpryan]

You know, a terabyte disk is pretty cheap these days...

Anyway, glad that solved the problem.