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BioC 3.4: INSTALL report for DESeq2 on moscato1

This page was generated on 2016-09-21 03:44:39 -0700 (Wed, 21 Sep 2016).

Package 311/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DESeq2
Version: 1.13.14
Command: rm -rf DESeq2.buildbin-libdir && mkdir DESeq2.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/DESeq2_1.13.14.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=DESeq2.buildbin-libdir --merge-multiarch DESeq2_1.13.14.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL DESeq2_1.13.14.zip && rm DESeq2_1.13.14.tar.gz DESeq2_1.13.14.zip
StartedAt: 2016-09-19 20:51:47 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 20:52:53 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 65.8 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DESeq2.buildbin-libdir && mkdir DESeq2.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/DESeq2_1.13.14.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=DESeq2.buildbin-libdir --merge-multiarch DESeq2_1.13.14.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL DESeq2_1.13.14.zip  && rm DESeq2_1.13.14.tar.gz DESeq2_1.13.14.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  717k  100  717k    0     0  34.1M      0 --:--:-- --:--:-- --:--:-- 41.2M

install for i386

* installing *source* package 'DESeq2' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lRlapack -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-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 D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lRlapack -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/DESeq2.buildbin-libdir/DESeq2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DESeq2' as DESeq2_1.13.14.zip
* DONE (DESeq2)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'DESeq2' successfully unpacked and MD5 sums checked