BioC 3.5: INSTALL report for ncdfFlow on tokay2

Package: ncdfFlow

Version: 2.22.2

Command: rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/ncdfFlow_2.22.2.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=ncdfFlow.buildbin-libdir --merge-multiarch ncdfFlow_2.22.2.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL ncdfFlow_2.22.2.zip && rm ncdfFlow_2.22.2.tar.gz ncdfFlow_2.22.2.zip

StartedAt: 2017-10-17 18:30:17 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 18:35:07 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 289.5 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/ncdfFlow_2.22.2.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=ncdfFlow.buildbin-libdir --merge-multiarch ncdfFlow_2.22.2.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL ncdfFlow_2.22.2.zip  && rm ncdfFlow_2.22.2.tar.gz ncdfFlow_2.22.2.zip
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100 2819k  100 2819k    0     0  36.6M      0 --:--:-- --:--:-- --:--:-- 37.2M

install for i386

* installing *source* package 'ncdfFlow' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
cp includeWin/i386/* includeWin/
cp libwin/i386/*.dll .
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo:53:0,
                 from C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: note: #pragma message: WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+
   #pragma message ("WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+")
                                                                                                ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c bitOps.cpp -o bitOps.o
bitOps.cpp: In function 'Rcpp::LogicalVector toLogical(Rcpp::RawVector)':
bitOps.cpp:23:11: warning: unused variable 'nByte' [-Wunused-variable]
  unsigned nByte = bytes.size();
           ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c hdfFlow.c -o hdfFlow.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c readFrame.cpp -o readFrame.o
In file included from C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo:53:0,
                 from C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from readFrame.cpp:11:
C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: note: #pragma message: WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+
   #pragma message ("WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+")
                                                                                                ^
readFrame.cpp: In function 'Rcpp::NumericVector readSlice_cpp(std::string, std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, unsigned int&)':
readFrame.cpp:140:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i = 0; i < chCount; i++){
                ^
readFrame.cpp:237:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(i = 0; i < chCount; i++){
                 ^
readFrame.cpp: In function 'Rcpp::S4 readFrame(Rcpp::S4, Rcpp::RObject, Rcpp::RObject, bool)':
readFrame.cpp:379:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned i = 0; i < j_val.size(); i++){
                          ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -L. -llibhdf5ForBioC-7 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'ncdfFlow' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
cp includeWin/x64/* includeWin/
cp libwin/x64/*.dll .
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo:53:0,
                 from C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: note: #pragma message: WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+
   #pragma message ("WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+")
                                                                                                ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c bitOps.cpp -o bitOps.o
bitOps.cpp: In function 'Rcpp::LogicalVector toLogical(Rcpp::RawVector)':
bitOps.cpp:23:11: warning: unused variable 'nByte' [-Wunused-variable]
  unsigned nByte = bytes.size();
           ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c hdfFlow.c -o hdfFlow.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c readFrame.cpp -o readFrame.o
In file included from C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo:53:0,
                 from C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from readFrame.cpp:11:
C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: note: #pragma message: WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+
   #pragma message ("WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+")
                                                                                                ^
readFrame.cpp: In function 'Rcpp::NumericVector readSlice_cpp(std::string, std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, unsigned int&)':
readFrame.cpp:140:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i = 0; i < chCount; i++){
                ^
readFrame.cpp:237:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(i = 0; i < chCount; i++){
                 ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -L. -llibhdf5ForBioC-7 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ncdfFlow' as ncdfFlow_2.22.2.zip
* DONE (ncdfFlow)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'ncdfFlow' successfully unpacked and MD5 sums checked