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INSTALL report for diffuStats on tokay2

This page was generated on 2020-10-17 11:56:28 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE diffuStats PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 476/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffuStats 1.8.0
Sergio Picart-Armada
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/diffuStats
Branch: RELEASE_3_11
Last Commit: a8f7c98
Last Changed Date: 2020-04-27 15:08:52 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: diffuStats
Version: 1.8.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/diffuStats_1.8.0.tar.gz && rm -rf diffuStats.buildbin-libdir && mkdir diffuStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=diffuStats.buildbin-libdir diffuStats_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL diffuStats_1.8.0.zip && rm diffuStats_1.8.0.tar.gz diffuStats_1.8.0.zip
StartedAt: 2020-10-16 17:38:12 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 17:40:34 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 142.7 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/diffuStats_1.8.0.tar.gz && rm -rf diffuStats.buildbin-libdir && mkdir diffuStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=diffuStats.buildbin-libdir diffuStats_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL diffuStats_1.8.0.zip && rm diffuStats_1.8.0.tar.gz diffuStats_1.8.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  134k  100  134k    0     0   354k      0 --:--:-- --:--:-- --:--:--  360k

install for i386

* installing *source* package 'diffuStats' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c diffuse_parallel.cpp -o diffuse_parallel.o
diffuse_parallel.cpp: In function 'arma::sp_mat convertSparse(Rcpp::S4)':
diffuse_parallel.cpp:28:84: warning: 'static eT* arma::memory::acquire_chunked(arma::uword) [with eT = double; arma::uword = unsigned int]' is deprecated [-Wdeprecated-declarations]
   arma::access::rw(res.values) = arma::memory::acquire_chunked<double>(x.size() + 1);
                                                                                    ^
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo:372,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:49,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from diffuse_parallel.cpp:1:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:1: note: declared here
 memory::acquire_chunked(const uword n_elem)
 ^~~~~~
diffuse_parallel.cpp:28:84: warning: 'static eT* arma::memory::acquire_chunked(arma::uword) [with eT = double; arma::uword = unsigned int]' is deprecated [-Wdeprecated-declarations]
   arma::access::rw(res.values) = arma::memory::acquire_chunked<double>(x.size() + 1);
                                                                                    ^
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo:372,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:49,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from diffuse_parallel.cpp:1:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:1: note: declared here
 memory::acquire_chunked(const uword n_elem)
 ^~~~~~
diffuse_parallel.cpp:32:94: warning: 'static eT* arma::memory::acquire_chunked(arma::uword) [with eT = unsigned int; arma::uword = unsigned int]' is deprecated [-Wdeprecated-declarations]
   arma::access::rw(res.row_indices) = arma::memory::acquire_chunked<arma::uword>(i.size() + 1);
                                                                                              ^
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo:372,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:49,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from diffuse_parallel.cpp:1:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:1: note: declared here
 memory::acquire_chunked(const uword n_elem)
 ^~~~~~
diffuse_parallel.cpp:32:94: warning: 'static eT* arma::memory::acquire_chunked(arma::uword) [with eT = unsigned int; arma::uword = unsigned int]' is deprecated [-Wdeprecated-declarations]
   arma::access::rw(res.row_indices) = arma::memory::acquire_chunked<arma::uword>(i.size() + 1);
                                                                                              ^
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo:372,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:49,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from diffuse_parallel.cpp:1:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:1: note: declared here
 memory::acquire_chunked(const uword n_elem)
 ^~~~~~
diffuse_parallel.cpp: In function 'arma::sp_mat sparsify2(const mat&, int, const sp_mat&)':
diffuse_parallel.cpp:69:21: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'unsigned int'} [-Wsign-compare]
   for (int i = 0; i < pos.size(); ++i) {
                   ~~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o diffuStats.dll tmp.def RcppExports.o diffuse_parallel.o init.o -LC:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/diffuStats.buildbin-libdir/00LOCK-diffuStats/00new/diffuStats/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'diffuStats'
    finding HTML links ... done
    ParallelHeatrank                        html  
    checks                                  html  
    connect_undirected_graph                html  
    convertSparse                           html  
    default_graph_param                     html  
    diffuStats                              html  
    diffuse                                 html  
    diffuse_mc                              html  
    diffuse_raw                             html  
    generate_graph                          html  
    generate_input                          html  
    graph_toy                               html  
    is_kernel                               html  
    kernels                                 html  
    largest_cc                              html  
    metric_auc                              html  
    named.list                              html  
    perf                                    html  
    perf_eval                               html  
    perf_wilcox                             html  
    scores2colours                          html  
    scores2shapes                           html  
    serialHeatrank                          html  
    sparsify2                               html  
    to_list                                 html  
    to_x_from_list                          html  
    which_format                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'diffuStats' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c diffuse_parallel.cpp -o diffuse_parallel.o
diffuse_parallel.cpp: In function 'arma::sp_mat convertSparse(Rcpp::S4)':
diffuse_parallel.cpp:28:84: warning: 'static eT* arma::memory::acquire_chunked(arma::uword) [with eT = double; arma::uword = unsigned int]' is deprecated [-Wdeprecated-declarations]
   arma::access::rw(res.values) = arma::memory::acquire_chunked<double>(x.size() + 1);
                                                                                    ^
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo:372,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:49,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from diffuse_parallel.cpp:1:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:1: note: declared here
 memory::acquire_chunked(const uword n_elem)
 ^~~~~~
diffuse_parallel.cpp:28:84: warning: 'static eT* arma::memory::acquire_chunked(arma::uword) [with eT = double; arma::uword = unsigned int]' is deprecated [-Wdeprecated-declarations]
   arma::access::rw(res.values) = arma::memory::acquire_chunked<double>(x.size() + 1);
                                                                                    ^
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo:372,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:49,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from diffuse_parallel.cpp:1:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:1: note: declared here
 memory::acquire_chunked(const uword n_elem)
 ^~~~~~
diffuse_parallel.cpp:32:94: warning: 'static eT* arma::memory::acquire_chunked(arma::uword) [with eT = unsigned int; arma::uword = unsigned int]' is deprecated [-Wdeprecated-declarations]
   arma::access::rw(res.row_indices) = arma::memory::acquire_chunked<arma::uword>(i.size() + 1);
                                                                                              ^
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo:372,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:49,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from diffuse_parallel.cpp:1:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:1: note: declared here
 memory::acquire_chunked(const uword n_elem)
 ^~~~~~
diffuse_parallel.cpp:32:94: warning: 'static eT* arma::memory::acquire_chunked(arma::uword) [with eT = unsigned int; arma::uword = unsigned int]' is deprecated [-Wdeprecated-declarations]
   arma::access::rw(res.row_indices) = arma::memory::acquire_chunked<arma::uword>(i.size() + 1);
                                                                                              ^
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo:372,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:49,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from diffuse_parallel.cpp:1:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:1: note: declared here
 memory::acquire_chunked(const uword n_elem)
 ^~~~~~
diffuse_parallel.cpp: In function 'arma::sp_mat sparsify2(const mat&, int, const sp_mat&)':
diffuse_parallel.cpp:69:21: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'unsigned int'} [-Wsign-compare]
   for (int i = 0; i < pos.size(); ++i) {
                   ~~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o diffuStats.dll tmp.def RcppExports.o diffuse_parallel.o init.o -LC:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/diffuStats.buildbin-libdir/diffuStats/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'diffuStats' as diffuStats_1.8.0.zip
* DONE (diffuStats)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'diffuStats' successfully unpacked and MD5 sums checked