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INSTALL report for ncdfFlow on tokay2

This page was generated on 2020-10-17 11:57:15 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ncdfFlow PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1176/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ncdfFlow 2.34.0
Mike Jiang , Jake Wagner
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ncdfFlow
Branch: RELEASE_3_11
Last Commit: 041c465
Last Changed Date: 2020-04-27 14:27:47 -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: ncdfFlow
Version: 2.34.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ncdfFlow_2.34.0.tar.gz && rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ncdfFlow.buildbin-libdir ncdfFlow_2.34.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ncdfFlow_2.34.0.zip && rm ncdfFlow_2.34.0.tar.gz ncdfFlow_2.34.0.zip
StartedAt: 2020-10-16 17:13:10 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 17:15:54 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 164.2 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/ncdfFlow_2.34.0.tar.gz && rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ncdfFlow.buildbin-libdir ncdfFlow_2.34.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ncdfFlow_2.34.0.zip && rm ncdfFlow_2.34.0.tar.gz ncdfFlow_2.34.0.zip
###
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100 55846  100 55846    0     0   880k      0 --:--:-- --:--:-- --:--:--  991k

install for i386

* installing *source* package 'ncdfFlow' ...
** 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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c bitOps.cpp -o bitOps.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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c hdfFlow.cpp -o hdfFlow.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from hdfFlow.cpp:2:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
hdfFlow.cpp: In function 'void readSlice_cpp(hid_t, hid_t, hid_t, std::vector<unsigned int>, unsigned int, unsigned int, double*, bool)':
hdfFlow.cpp:486:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
  herr_t      status;
              ^~~~~~
"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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c readFrame.cpp -o readFrame.o
readFrame.cpp: In function 'Rcpp::S4 readFrame(Rcpp::S4, Rcpp::RObject, Rcpp::RObject, bool)':
readFrame.cpp:98:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
    for(unsigned i = 0; i < j_val.size(); i++){
                        ~~^~~~~~~~~~~~~~
mkdir -p "C:/Users/biocbuild/bbs-3.11-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib/i386"
"C:/rtools40/mingw32/bin/"ar rs "C:/Users/biocbuild/bbs-3.11-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib/i386/libncdfFlow.a" RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o
C:\rtools40\mingw32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.11-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib/i386/libncdfFlow.a
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/library/Rhdf5lib/lib/i386 -lhdf5 -lszip -lz -lpsapi -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/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ncdfFlow'
    finding HTML links ... done
    Indices                                 html  
    as.flowSet                              html  
    clone.ncdfFlowSet                       html  
    extractFlowFrame                        html  
    finding level-2 HTML links ... done

    flowSet-accessor                        html  
    getFileName                             html  
    lapply-methods                          html  
    ncdfFlow                                html  
    ncdfFlowList-class                      html  
    ncdfFlowSet-Subset                      html  
    ncdfFlowSet-class                       html  
    ncdfFlowSet-constructor                 html  
    ncdfFlowSet-split                       html  
    ncfsApply-ncdfFlowSet-method            html  
    rbind2-method                           html  
    read.ncdfFlowSet                        html  
    replacement-method-for-ncdfFlowSet      html  
    save_ncfs                               html  
    subset-functions                        html  
    subset-methods                          html  
    unlink-ncdfFlowSet-method               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 'ncdfFlow' ...
** 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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c bitOps.cpp -o bitOps.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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c hdfFlow.cpp -o hdfFlow.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from hdfFlow.cpp:2:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
hdfFlow.cpp: In function 'void readSlice_cpp(hid_t, hid_t, hid_t, std::vector<unsigned int>, unsigned int, unsigned int, double*, bool)':
hdfFlow.cpp:486:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
  herr_t      status;
              ^~~~~~
"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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.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/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c readFrame.cpp -o readFrame.o
mkdir -p "C:/Users/biocbuild/bbs-3.11-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/x64"
"C:/rtools40/mingw64/bin/"ar rs "C:/Users/biocbuild/bbs-3.11-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/x64/libncdfFlow.a" RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o
C:\rtools40\mingw64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.11-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/x64/libncdfFlow.a
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/library/Rhdf5lib/lib/x64 -lhdf5 -lszip -lz -lpsapi -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/ncdfFlow.buildbin-libdir/ncdfFlow/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ncdfFlow' as ncdfFlow_2.34.0.zip
* DONE (ncdfFlow)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ncdfFlow' successfully unpacked and MD5 sums checked