DESeq2 1.13.14
Michael Love
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DESeq2 | | Last Changed Rev: 120796 / Revision: 121152 | | Last Changed Date: 2016-09-07 18:07:40 -0700 (Wed, 07 Sep 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | [ OK ] | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL DESeq2
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* installing to library ‘/home/biocbuild/bbs-3.4-bioc/R/library’
* installing *source* package ‘DESeq2’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c DESeq2.cpp -o DESeq2.o
DESeq2.cpp: In function ‘double dlog_posterior(double, Rcpp::Matrix<14>::Row, Rcpp::Matrix<14>::Row, arma::mat, double, double, bool)’:
DESeq2.cpp:59:43: warning: ‘const arma::Op<T1, arma::op_inv> arma::Base_inv_yes<derived>::i(bool) const [with derived = arma::Mat<double>]’ is deprecated [-Wdeprecated-declarations]
double ddetb = ( det(b) * trace(b.i(true) * db) );
^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:129:0,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from DESeq2.cpp:16:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_bones.hpp:21:51: note: declared here
arma_deprecated inline const Op<derived,op_inv> i(const bool ) const; //!< kept only for compatibility with old user code
^
DESeq2.cpp: In function ‘double d2log_posterior(double, Rcpp::Matrix<14>::Row, Rcpp::Matrix<14>::Row, arma::mat, double, double, bool)’:
DESeq2.cpp:87:27: warning: ‘const arma::Op<T1, arma::op_inv> arma::Base_inv_yes<derived>::i(bool) const [with derived = arma::Mat<double>]’ is deprecated [-Wdeprecated-declarations]
arma::mat b_i = b.i(true);
^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:368:0,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from DESeq2.cpp:16:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271:1: note: declared here
Base_inv_yes<derived>::i(const bool) const // argument kept only for compatibility with old user code
^
DESeq2.cpp:90:43: warning: ‘const arma::Op<T1, arma::op_inv> arma::Base_inv_yes<derived>::i(bool) const [with derived = arma::Mat<double>]’ is deprecated [-Wdeprecated-declarations]
double ddetb = ( det(b) * trace(b.i(true) * db) );
^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:368:0,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from DESeq2.cpp:16:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271:1: note: declared here
Base_inv_yes<derived>::i(const bool) const // argument kept only for compatibility with old user code
^
DESeq2.cpp: In function ‘Rcpp::List fitBeta(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
DESeq2.cpp:348:62: warning: ‘const arma::Op<T1, arma::op_inv> arma::Base_inv_yes<derived>::i(bool) const [with derived = arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>]’ is deprecated [-Wdeprecated-declarations]
hat_matrix = sqrt(w) * x * (x.t() * w * x + ridge).i(true) * x.t() * sqrt(w);
^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:368:0,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from DESeq2.cpp:16:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271:1: note: declared here
Base_inv_yes<derived>::i(const bool) const // argument kept only for compatibility with old user code
^
DESeq2.cpp:351:43: warning: ‘const arma::Op<T1, arma::op_inv> arma::Base_inv_yes<derived>::i(bool) const [with derived = arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>]’ is deprecated [-Wdeprecated-declarations]
sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:368:0,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from DESeq2.cpp:16:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271:1: note: declared here
Base_inv_yes<derived>::i(const bool) const // argument kept only for compatibility with old user code
^
DESeq2.cpp:351:93: warning: ‘const arma::Op<T1, arma::op_inv> arma::Base_inv_yes<derived>::i(bool) const [with derived = arma::eGlue<arma::Glue<arma::Glue<arma::Op<arma::Mat<double>, arma::op_htrans>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::glue_times>, arma::Mat<double>, arma::eglue_plus>]’ is deprecated [-Wdeprecated-declarations]
sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:368:0,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from DESeq2.cpp:16:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271:1: note: declared here
Base_inv_yes<derived>::i(const bool) const // argument kept only for compatibility with old user code
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/R/library/DESeq2/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DESeq2)