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BioC 3.4: INSTALL report for destiny on malbec1

This page was generated on 2017-04-15 16:13:08 -0400 (Sat, 15 Apr 2017).

Package 320/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
destiny 2.0.9
Philipp Angerer
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/destiny
Last Changed Rev: 128063 / Revision: 128728
Last Changed Date: 2017-04-05 04:33:42 -0400 (Wed, 05 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64 [ OK ] OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  ERROR  OK 

Summary

Package: destiny
Version: 2.0.9
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL destiny
StartedAt: 2017-04-14 18:10:12 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 18:10:40 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 28.7 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL destiny
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.4-bioc/R/library’
* installing *source* package ‘destiny’ ...
** libs
g++ -std=c++11 -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/RcppEigen/include"  -g -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/bits/locale_classes.h:40,
                 from /usr/include/c++/5/bits/ios_base.h:41,
                 from /usr/include/c++/5/ios:42,
                 from /usr/include/c++/5/ostream:38,
                 from /usr/include/c++/5/iterator:64,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:25,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/bits/locale_classes.h:40,
                 from /usr/include/c++/5/bits/ios_base.h:41,
                 from /usr/include/c++/5/ios:42,
                 from /usr/include/c++/5/ostream:38,
                 from /usr/include/c++/5/iterator:64,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:25,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
g++ -std=c++11 -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/RcppEigen/include"  -g -fpic  -g -O2 -c censoring.cpp -o censoring.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from censoring.cpp:6:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from censoring.cpp:6:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
g++ -std=c++11 -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/RcppEigen/include"  -g -fpic  -g -O2 -c no_censoring.cpp -o no_censoring.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from no_censoring.cpp:5:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from no_censoring.cpp:4:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from no_censoring.cpp:5:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from no_censoring.cpp:4:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
g++ -std=c++11 -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o destiny.so RcppExports.o censoring.o no_censoring.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/R/library/destiny/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘destiny’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘destiny’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (destiny)