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INSTALL report for cliqueMS on tokay2

This page was generated on 2020-10-17 11:56:18 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cliqueMS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 309/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cliqueMS 1.2.1
Oriol Senan Campos
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/cliqueMS
Branch: RELEASE_3_11
Last Commit: 828442d
Last Changed Date: 2020-08-02 21:53:25 -0400 (Sun, 02 Aug 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: cliqueMS
Version: 1.2.1
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/cliqueMS_1.2.1.tar.gz && rm -rf cliqueMS.buildbin-libdir && mkdir cliqueMS.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cliqueMS.buildbin-libdir cliqueMS_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL cliqueMS_1.2.1.zip && rm cliqueMS_1.2.1.tar.gz cliqueMS_1.2.1.zip
StartedAt: 2020-10-16 18:55:22 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 18:57:59 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 156.2 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/cliqueMS_1.2.1.tar.gz && rm -rf cliqueMS.buildbin-libdir && mkdir cliqueMS.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cliqueMS.buildbin-libdir cliqueMS_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL cliqueMS_1.2.1.zip && rm cliqueMS_1.2.1.tar.gz cliqueMS_1.2.1.zip
###
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100  559k  100  559k    0     0  2655k      0 --:--:-- --:--:-- --:--:-- 2756k

install for i386

* installing *source* package 'cliqueMS' ...
** 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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c findAnnotationR.cpp -o findAnnotationR.o
In file included from findAnnotationR.cpp:1:
annotationCliqueMSR.h: In function 'std::vector<std::pair<double, double> > sortMass(annotData&, int, std::unordered_map<double, std::pair<double, double> >, int)':
annotationCliqueMSR.h:440:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<double, double> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     if(id < allM.size()) // not add more masses in case that for that feature are less than "n" top masses
        ~~~^~~~~~~~~~~~~
annotationCliqueMSR.h: In function 'std::unordered_set<double> getTopScoringMasses(annotData&, int, rawadList, int, int, double)':
annotationCliqueMSR.h:476:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<double, double> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     if(id < allM.size()) // not add more masses in case that there are less than "n" top masses
        ~~~^~~~~~~~~~~~~
annotationCliqueMSR.h: In function 'std::vector<int> sortAnnotations(std::unordered_map<int, Annotation>&, int)':
annotationCliqueMSR.h:725:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<double, int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     if(id < allAn.size() )
        ~~~^~~~~~~~~~~~~~
annotationCliqueMSR.h: In function 'double computeMaxScore(std::vector<double>&, int, double)':
annotationCliqueMSR.h:739:24: warning: 'completeroundscore' may be used uninitialized in this function [-Wmaybe-uninitialized]
     completeroundscore += *ritv;
     ~~~~~~~~~~~~~~~~~~~^~~~~~~~
"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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c findCliquesR.cpp -o findCliquesR.o
In file included from findCliquesR.cpp:2:
networkCliqueMSR.h: In function 'Edges createEdges(Rcpp::DataFrame)':
networkCliqueMSR.h:38:37: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   for(unsigned int index = 0; index < vnode1.size(); index++) {
                               ~~~~~~^~~~~~~~~~~~~~~
"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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c findIsotopesR.cpp -o findIsotopesR.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o cliqueMS.dll tmp.def RcppExports.o findAnnotationR.o findCliquesR.o findIsotopesR.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -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/cliqueMS.buildbin-libdir/00LOCK-cliqueMS/00new/cliqueMS/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cliqueMS'
    finding HTML links ... done
    anClique-class                          html  
    anClique                                html  
    cliqueMS                                html  
    computeCliques                          html  
    createNetwork                           html  
    createanClique                          html  
    ex.cliqueGroups                         html  
    getAnnotation                           html  
    getCliques                              html  
    getIsotopes                             html  
    negative.adinfo                         html  
    positive.adinfo                         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 'cliqueMS' ...
** 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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c findAnnotationR.cpp -o findAnnotationR.o
In file included from findAnnotationR.cpp:1:
annotationCliqueMSR.h: In function 'std::vector<std::pair<double, double> > sortMass(annotData&, int, std::unordered_map<double, std::pair<double, double> >, int)':
annotationCliqueMSR.h:440:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<double, double> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     if(id < allM.size()) // not add more masses in case that for that feature are less than "n" top masses
        ~~~^~~~~~~~~~~~~
annotationCliqueMSR.h: In function 'std::unordered_set<double> getTopScoringMasses(annotData&, int, rawadList, int, int, double)':
annotationCliqueMSR.h:476:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<double, double> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     if(id < allM.size()) // not add more masses in case that there are less than "n" top masses
        ~~~^~~~~~~~~~~~~
annotationCliqueMSR.h: In function 'std::vector<int> sortAnnotations(std::unordered_map<int, Annotation>&, int)':
annotationCliqueMSR.h:725:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<double, int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     if(id < allAn.size() )
        ~~~^~~~~~~~~~~~~~
annotationCliqueMSR.h: In function 'double computeMaxScore(std::vector<double>&, int, double)':
annotationCliqueMSR.h:739:24: warning: 'completeroundscore' may be used uninitialized in this function [-Wmaybe-uninitialized]
     completeroundscore += *ritv;
     ~~~~~~~~~~~~~~~~~~~^~~~~~~~
"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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c findCliquesR.cpp -o findCliquesR.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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c findIsotopesR.cpp -o findIsotopesR.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o cliqueMS.dll tmp.def RcppExports.o findAnnotationR.o findCliquesR.o findIsotopesR.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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/cliqueMS.buildbin-libdir/cliqueMS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cliqueMS' as cliqueMS_1.2.1.zip
* DONE (cliqueMS)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'cliqueMS' successfully unpacked and MD5 sums checked