[Bioc-devel] Problem on Installation of DEseq2

[Michael Love]

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/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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