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BioC 3.3: INSTALL report for ncdfFlow on windows2.bioconductor.org

This page was generated on 2015-10-27 12:14:56 -0400 (Tue, 27 Oct 2015).

Package 697/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ncdfFlow 2.17.0
Mike Jiang
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ncdfFlow
Last Changed Rev: 109592 / Revision: 109948
Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015)
linux2.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows2.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ncdfFlow
Version: 2.17.0
Command: C:\cygwin64\bin\curl.exe -O http://linux2.bioconductor.org/BBS/3.3/bioc/src/contrib/ncdfFlow_2.17.0.tar.gz && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch ncdfFlow_2.17.0.tar.gz && rm ncdfFlow_2.17.0.tar.gz
StartedAt: 2015-10-26 21:06:17 -0400 (Mon, 26 Oct 2015)
EndedAt: 2015-10-26 21:06:56 -0400 (Mon, 26 Oct 2015)
EllapsedTime: 39.6 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin64\bin\curl.exe -O http://linux2.bioconductor.org/BBS/3.3/bioc/src/contrib/ncdfFlow_2.17.0.tar.gz && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch ncdfFlow_2.17.0.tar.gz && rm ncdfFlow_2.17.0.tar.gz
###
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##############################################################################


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100 3000k  100 3000k    0     0   119M      0 --:--:-- --:--:-- --:--:--  139M

install for i386

* installing to library 'c:/biocbld/bbs-3.3-bioc/R/library'
* 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 .
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local320/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local320/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]
gcc -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local320/include"  -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c hdfFlow.c -o hdfFlow.o
gcc -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local320/include"  -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local320/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:140:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readFrame.cpp:237:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readFrame.cpp: In function 'Rcpp::S4 readFrame(Rcpp::S4, Rcpp::RObject, Rcpp::RObject, bool)':
readFrame.cpp:379:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -L. -llibhdf5ForBioC-7 -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to c:/biocbld/bbs-3.3-bioc/R/library/ncdfFlow/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'lapply' from package 'base' in package 'ncdfFlow'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing to library 'c:/biocbld/bbs-3.3-bioc/R/library'
* 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 .
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local320/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local320/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]
gcc -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local320/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c hdfFlow.c -o hdfFlow.o
gcc -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local320/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local320/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:140:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readFrame.cpp:237:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -L. -llibhdf5ForBioC-7 -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to c:/biocbld/bbs-3.3-bioc/R/library/ncdfFlow/libs/x64
** testing if installed package can be loaded
* DONE (ncdfFlow)