DESeq2 1.12.4
Michael Love
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/DESeq2 | | Last Changed Rev: 119935 / Revision: 122332 | | Last Changed Date: 2016-08-07 07:08:50 -0700 (Sun, 07 Aug 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | [ OK ] | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf DESeq2.buildbin-libdir && mkdir DESeq2.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/DESeq2_1.12.4.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=DESeq2.buildbin-libdir --merge-multiarch DESeq2_1.12.4.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL DESeq2_1.12.4.zip && rm DESeq2_1.12.4.tar.gz DESeq2_1.12.4.zip
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install for i386
* installing *source* package 'DESeq2' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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 (declared at E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
double ddetb = ( det(b) * trace(b.i(true) * db) );
^
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 (declared at E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
arma::mat b_i = b.i(true);
^
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 (declared at E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
double ddetb = ( det(b) * trace(b.i(true) * db) );
^
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 (declared at E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
hat_matrix = sqrt(w) * x * (x.t() * w * x + ridge).i(true) * x.t() * sqrt(w);
^
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 (declared at E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
^
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 (declared at E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
^
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o DESeq2.dll tmp.def DESeq2.o RcppExports.o -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lRlapack -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/DESeq2.buildbin-libdir/DESeq2/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'DESeq2' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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 (declared at E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
double ddetb = ( det(b) * trace(b.i(true) * db) );
^
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 (declared at E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
arma::mat b_i = b.i(true);
^
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 (declared at E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
double ddetb = ( det(b) * trace(b.i(true) * db) );
^
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 (declared at E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
hat_matrix = sqrt(w) * x * (x.t() * w * x + ridge).i(true) * x.t() * sqrt(w);
^
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 (declared at E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
^
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 (declared at E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include/armadillo_bits/Base_meat.hpp:271) [-Wdeprecated-declarations]
sigma = (x.t() * w * x + ridge).i(true) * x.t() * w * x * (x.t() * w * x + ridge).i(true);
^
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o DESeq2.dll tmp.def DESeq2.o RcppExports.o -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lRlapack -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/DESeq2.buildbin-libdir/DESeq2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DESeq2' as DESeq2_1.12.4.zip
* DONE (DESeq2)
* installing to library 'E:/biocbld/bbs-3.3-bioc/R/library'
package 'DESeq2' successfully unpacked and MD5 sums checked