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BioC 3.4: INSTALL report for destiny on moscato1

This page was generated on 2016-09-21 03:47:24 -0700 (Wed, 21 Sep 2016).

Package 312/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
destiny 1.99.11
Philipp Angerer
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/destiny
Last Changed Rev: 121137 / Revision: 121152
Last Changed Date: 2016-09-19 07:05:46 -0700 (Mon, 19 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 [ OK ] ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: destiny
Version: 1.99.11
Command: rm -rf destiny.buildbin-libdir && mkdir destiny.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/destiny_1.99.11.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=destiny.buildbin-libdir --merge-multiarch destiny_1.99.11.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL destiny_1.99.11.zip && rm destiny_1.99.11.tar.gz destiny_1.99.11.zip
StartedAt: 2016-09-19 21:15:56 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 21:17:20 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 83.7 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf destiny.buildbin-libdir && mkdir destiny.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/destiny_1.99.11.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=destiny.buildbin-libdir --merge-multiarch destiny_1.99.11.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL destiny_1.99.11.zip  && rm destiny_1.99.11.tar.gz destiny_1.99.11.zip
###
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##############################################################################


  % 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 1032k  100 1032k    0     0  37.0M      0 --:--:-- --:--:-- --:--:-- 43.8M

install for i386

* installing *source* package 'destiny' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=c++0x -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/RcppEigen/include" -I"c:/local323/include"  -g   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -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/RcppEigen/include" -I"c:/local323/include"  -g   -O2 -Wall  -mtune=core2 -c censoring.cpp -o censoring.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -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/RcppEigen/include" -I"c:/local323/include"  -g   -O2 -Wall  -mtune=core2 -c no_censoring.cpp -o no_censoring.o
no_censoring.cpp: In function 'double cor(Rcpp::NumericVector, Rcpp::NumericVector)':
no_censoring.cpp:16:52: warning: operation on 'v1sqr_sum' may be undefined [-Wsequence-point]
  v1sum = v2sum = v12sum = v1sqr_sum = v1sqr_sum = 0;
                                                    ^
no_censoring.cpp:27:54: warning: 'v2sqr_sum' may be used uninitialized in this function [-Wmaybe-uninitialized]
  const double deno = (n*v1sqr_sum - v1sum*v1sum) * (n*v2sqr_sum - v2sum*v2sum);
                                                      ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o destiny.dll tmp.def RcppExports.o censoring.o no_censoring.o -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/destiny.buildbin-libdir/destiny/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'print' from package 'base' in package 'destiny'
Creating a generic function for 'plot' from package 'graphics' in package 'destiny'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'destiny' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=c++0x -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/RcppEigen/include" -I"c:/local323/include"  -g   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=c++0x -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/RcppEigen/include" -I"c:/local323/include"  -g   -O2 -Wall  -mtune=core2 -c censoring.cpp -o censoring.o
censoring.cpp: In function 'Rcpp::NumericMatrix predict_censoring_impl(Rcpp::NumericMatrix, Rcpp::NumericMatrix, double, Rcpp::NumericVector, Rcpp::NumericVector, double)':
censoring.cpp:72:17: warning: 'm1' may be used uninitialized in this function [-Wmaybe-uninitialized]
     / sqrt(m1-m0);
                 ^
censoring.cpp:55:15: note: 'm1' was declared here
    double m0, m1;
               ^
censoring.cpp:71:22: warning: 'm0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
                      ^
censoring.cpp:55:11: note: 'm0' was declared here
    double m0, m1;
           ^
censoring.cpp:66:33: warning: 'use_d' may be used uninitialized in this function [-Wmaybe-uninitialized]
    const double v = use_d ? d : c;
                                 ^
censoring.cpp:18:7: note: 'use_d' was declared here
  bool use_d;
       ^
censoring.cpp: In function 'Eigen::SparseMatrix<double, 0, int> censoring_impl(Rcpp::NumericMatrix, SEXP, SEXP, SEXP, Rcpp::NumericVector, SEXP, Rcpp::Function)':
censoring.cpp:72:17: warning: 'm1' may be used uninitialized in this function [-Wmaybe-uninitialized]
     / sqrt(m1-m0);
                 ^
censoring.cpp:55:15: note: 'm1' was declared here
    double m0, m1;
               ^
censoring.cpp:71:22: warning: 'm0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
                      ^
censoring.cpp:55:11: note: 'm0' was declared here
    double m0, m1;
           ^
censoring.cpp:66:33: warning: 'use_d' may be used uninitialized in this function [-Wmaybe-uninitialized]
    const double v = use_d ? d : c;
                                 ^
censoring.cpp:18:7: note: 'use_d' was declared here
  bool use_d;
       ^
C:/Rtools/mingw_64/bin/g++  -std=c++0x -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/RcppEigen/include" -I"c:/local323/include"  -g   -O2 -Wall  -mtune=core2 -c no_censoring.cpp -o no_censoring.o
no_censoring.cpp: In function 'double cor(Rcpp::NumericVector, Rcpp::NumericVector)':
no_censoring.cpp:16:52: warning: operation on 'v1sqr_sum' may be undefined [-Wsequence-point]
  v1sum = v2sum = v12sum = v1sqr_sum = v1sqr_sum = 0;
                                                    ^
no_censoring.cpp:27:54: warning: 'v2sqr_sum' may be used uninitialized in this function [-Wmaybe-uninitialized]
  const double deno = (n*v1sqr_sum - v1sum*v1sum) * (n*v2sqr_sum - v2sum*v2sum);
                                                      ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o destiny.dll tmp.def RcppExports.o censoring.o no_censoring.o -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/destiny.buildbin-libdir/destiny/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'destiny' as destiny_1.99.11.zip
* DONE (destiny)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'destiny' successfully unpacked and MD5 sums checked