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INSTALL report for Harman on tokay2

This page was generated on 2020-10-17 11:56:48 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Harman PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 801/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Harman 1.16.0
Jason Ross
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Harman
Branch: RELEASE_3_11
Last Commit: fa76ac7
Last Changed Date: 2020-04-27 14:57:16 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Harman
Version: 1.16.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Harman_1.16.0.tar.gz && rm -rf Harman.buildbin-libdir && mkdir Harman.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Harman.buildbin-libdir Harman_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Harman_1.16.0.zip && rm Harman_1.16.0.tar.gz Harman_1.16.0.zip
StartedAt: 2020-10-16 16:57:19 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 16:58:10 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 51.0 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/Harman_1.16.0.tar.gz && rm -rf Harman.buildbin-libdir && mkdir Harman.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Harman.buildbin-libdir Harman_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Harman_1.16.0.zip && rm Harman_1.16.0.tar.gz Harman_1.16.0.zip
###
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100  153k  100  153k    0     0  2635k      0 --:--:-- --:--:-- --:--:-- 3000k

install for i386

* installing *source* package 'Harman' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_ARRAYALIGNEMT=4  -D_USE_RCPP=1  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -IC:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include -std=c++0x    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Harman.cpp -o Harman.o
Harman.cpp: In function 'SEXPREC* HarmanMain(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Harman.cpp:3008:3: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
   else
   ^~~~
Harman.cpp:3022:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
     std::vector<unsigned int>    tr_std_tmp     = Rcpp::as<std::vector<unsigned int> >(tr) ;
     ^~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Harman.dll tmp.def Harman.o -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/Harman.buildbin-libdir/00LOCK-Harman/00new/Harman/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Harman'
    finding HTML links ... done
    arrowPlot                               html  
    callHarman                              html  
    detachHarman                            html  
    harman                                  html  
    harmanScores                            html  
    harmanresults                           html  
    pcaPlot                                 html  
    plot.harmanresults                      html  
    prcompPlot                              html  
    print.summary.harmanresults             html  
    reconstructData                         html  
    shiftBetas                              html  
    summary.harmanresults                   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 'Harman' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_ARRAYALIGNEMT=4  -D_USE_RCPP=1  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -IC:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include -std=c++0x    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Harman.cpp -o Harman.o
Harman.cpp: In function 'SEXPREC* HarmanMain(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Harman.cpp:3008:3: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
   else
   ^~~~
Harman.cpp:3022:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
     std::vector<unsigned int>    tr_std_tmp     = Rcpp::as<std::vector<unsigned int> >(tr) ;
     ^~~
In file included from Harman.cpp:182:
CSelectRandom.h: In instantiation of 'std::vector<unsigned int>* CSelectRandom<T>::ReturnVectOf32bitIntegersInRange_CSTDLIB(size_t, size_t, size_t, size_t) [with T = double; size_t = long long unsigned int]':
Harman.cpp:1764:117:   required from here
CSelectRandom.h:943:20: warning: comparison of integer expressions of different signedness: 'long long int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     while (currval < howManyIN)
            ~~~~~~~~^~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Harman.dll tmp.def Harman.o -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/Harman.buildbin-libdir/Harman/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Harman' as Harman_1.16.0.zip
* DONE (Harman)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Harman' successfully unpacked and MD5 sums checked