[Bioc-devel] Problem on Installation of DEseq2

[Michael Love]

are you installing with:

biocLite("DESeq2")

hmm these don't look like Rcpp* version numbers. What do you get with

library(Rcpp)
library(RcppArmadillo)
sessionInfo()



On Wed, Jun 18, 2014 at 1:13 PM, jarod_v6 at libero.it <jarod_v6 at libero.it> wrote:
> Thanks for your help
> I have the 2.0 when i try to install 3.8  I have the error on version of gcc
> on Rhel5.5
>
>
>
>>----Messaggio originale----
>>Da: michaelisaiahlove at gmail.com
>>Data: 18/06/2014 17.44
>>A: "jarod_v6 at libero.it"<jarod_v6 at libero.it>
>>Cc: "bioc-devel at r-project.org"<bioc-devel at r-project.org>
>>Ogg: Re: [Bioc-devel] Problem on Installation of DEseq2
>>
>>hi Jarod,
>>
>>What version of Rcpp and RcppArmadillo is installed?
>>
>>Mike
>>
>>On Wed, Jun 18, 2014 at 11:35 AM, jarod_v6 at libero.it <jarod_v6 at libero.it>
> wrote:
>>>
>>>>    >I can't install this  DESEq2 on the RHEL 5.5 server:
>>>>    >
>>>>    >* installing *source* package ‘RcppArmadillo’ ...
>>>>    >** package ‘RcppArmadillo’ successfully unpacked and MD5 sums
>>> checked
>>>>    >* checking LAPACK_LIBS:  divide-and-conquer complex SVD unavailable
> via
>>> R-
>>>>    >supplied LAPACK
>>>>    >* divide-and-conquer algorithm for complex SVD will be redirected to
>>> default
>>>>    >** libs
>>>>    >g++ -I/illumina/software/PROG/R302/lib64/R/include -DNDEBUG  -
>>>>    >I/usr/local/include -I"
>>>>    >/illumina/software/PROG/R302/lib64/R/library/Rcpp/include"  -I..
>>> /inst/include
>>>>    -
>>>>    >fpic  -g -O2  -c RcppArmadillo.cpp -o RcppArmadillo.o
>>>>    >In file included from ../inst/include/armadillo:42,
>>>>    >                 from ../inst/include/RcppArmadilloForward.h:37,
>>>>    >                 from ../inst/include/RcppArmadillo.h:30,
>>>>    >                 from RcppArmadillo.cpp:22:
>>>>    >../inst/include/armadillo_bits/compiler_setup.hpp:119:6: error: #error
>>> "***
>>>>    >Need a newer compiler ***"
>>>>    >/illumina/software/PROG/R302/lib64/R/library/Rcpp/include/Rcpp/Date.h:
>>> In
>>>>    >member function ‘void Rcpp::Date::update_tm()’:
>>>>    >/illumina/software/PROG/R302/lib64/R/library/Rcpp/include/Rcpp/Date.h:
>>> 108:
>>>>
>>>>- Ignored:
>>>>    >warning: converting to ‘time_t’ from ‘double’
>>>>    >/illumina/software/PROG/R302/lib64/R/library/Rcpp/include/Rcpp/Date.h:
>>> In
>>>>    >function ‘Rcpp::Date Rcpp::operator+(const Rcpp::Date&, int)’:
>>>>    >/illumina/software/PROG/R302/lib64/R/library/Rcpp/include/Rcpp/Date.h:
>>> 139:
>>>>    >warning: converting to ‘time_t’ from ‘double’
>>>>    >make: *** [RcppArmadillo.o] Error 1
>>>>    >ERROR: compilation failed for package ‘RcppArmadillo’
>>>>    >* removing â
> €˜/illumina/software/PROG/R302/lib64/R/library/RcppArmadilloâ
>>> €™
>>>>    >* restoring previous
>>>>    >‘/illumina/software/PROG/R302/lib64/R/library/RcppArmadillo’
>>>>    >
>>>>    >The downloaded source packages are in
>>>>    >  ‘/tmp/Rtmp30ZzKT/downloaded_packages’
>>>>    >Updating HTML index of packages in '.Library'
>>>>    >Making 'packages.html' ... done
>>>>    >Warning messages:
>>>>    >1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>>>>    >  installation of package ‘RcppArmadillo’ had non-zero exit status
>>>>    >2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>>>>    >  installation of package ‘DESeq2’ had non-zero exit status
>>>>    >3: In install.packages(update[instlib == l, "Package"], l, contriburl
>>>>    >
>>>>    >sessionInfo()
>>>>    >R version 3.0.2 (2013-09-25)
>>>>    >Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>    >
>>>>    >locale:
>>>>    > [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>>    > [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>>    > [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>>>    > [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>>    > [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>>    >[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>    >
>>>>    >attached base packages:
>>>>    >[1] stats     graphics  grDevices utils     datasets  methods
>>> base
>>>>    >
>>>>    >other attached packages:
>>>>    >[1] BiocInstaller_1.12.1
>>>>    >
>>>>    >loaded via a namespace (and not attached):
>>>>    >[1] tools_3.0.
>>>>    >Any Idea how can resolve?
>>>>    >
>>>>    >
>>>>
>>>>
>>>>
>>>>- Done.
>>>>
>>>>
>>>
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>>
>
>