Message-ID: <CADqzidX2mVWtUare=3-wt1ukuyUX8_cpb74272s+2cN5f4vfkg@mail.gmail.com>
Date: 2014-06-18T20:05:40Z
From: Michael Love
Subject: [Bioc-devel] Problem on Installation of DEseq2
In-Reply-To: <1171560080.7524311403111604247.JavaMail.defaultUser@defaultHost>
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 ?
> ??/illumina/software/PROG/R302/lib64/R/library/RcppArmadillo?
>>> ??
>>>> >* 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.
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>