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BioC 3.4: INSTALL report for ncdfFlow on moscato1

This page was generated on 2016-09-21 03:43:58 -0700 (Wed, 21 Sep 2016).

Package 807/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ncdfFlow 2.19.6
Mike Jiang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ncdfFlow
Last Changed Rev: 120793 / Revision: 121152
Last Changed Date: 2016-09-07 16:14:39 -0700 (Wed, 07 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ncdfFlow
Version: 2.19.6
Command: rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/ncdfFlow_2.19.6.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=ncdfFlow.buildbin-libdir --merge-multiarch ncdfFlow_2.19.6.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL ncdfFlow_2.19.6.zip && rm ncdfFlow_2.19.6.tar.gz ncdfFlow_2.19.6.zip
StartedAt: 2016-09-19 20:40:26 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 20:42:09 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 103.3 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/ncdfFlow_2.19.6.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=ncdfFlow.buildbin-libdir --merge-multiarch ncdfFlow_2.19.6.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL ncdfFlow_2.19.6.zip  && rm ncdfFlow_2.19.6.tar.gz ncdfFlow_2.19.6.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 27 2814k   27  769k    0     0  38.2M      0 --:--:-- --:--:-- --:--:-- 46.9M
100 2814k  100 2814k    0     0  72.3M      0 --:--:-- --:--:-- --:--:-- 78.5M

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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c readFrame.cpp -o readFrame.o
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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c readFrame.cpp -o readFrame.o
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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ncdfFlow' as ncdfFlow_2.19.6.zip
* DONE (ncdfFlow)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'ncdfFlow' successfully unpacked and MD5 sums checked