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BioC 2.14: INSTALL report for flowWorkspace on moscato2

This page was generated on 2014-10-08 08:53:58 -0700 (Wed, 08 Oct 2014).

Package 298/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 3.10.09
Greg Finak ,Mike Jiang
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/flowWorkspace
Last Changed Rev: 91108 / Revision: 95116
Last Changed Date: 2014-06-09 15:12:19 -0700 (Mon, 09 Jun 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: flowWorkspace
Version: 3.10.09
Command: C:\cygwin\bin\curl.exe -O http://zin2/BBS/2.14/bioc/src/contrib/flowWorkspace_3.10.09.tar.gz && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch flowWorkspace_3.10.09.tar.gz && rm flowWorkspace_3.10.09.tar.gz
StartedAt: 2014-10-07 18:49:43 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 18:57:37 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 474.0 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://zin2/BBS/2.14/bioc/src/contrib/flowWorkspace_3.10.09.tar.gz && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch flowWorkspace_3.10.09.tar.gz && rm flowWorkspace_3.10.09.tar.gz
###
##############################################################################
##############################################################################




install for i386

* installing to library 'E:/biocbld/bbs-2.14-bioc/R/library'
* installing *source* package 'flowWorkspace' ...

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


** libs
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GatingHierarchy.cpp -o GatingHierarchy.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GatingSet.cpp -o GatingSet.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c POPINDICES.cpp -o POPINDICES.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
R_GatingHierarchy.cpp: In function 'SEXPREC* R_getSingleCellExpression(SEXP, SEXP, SEXP, SEXP, SEXP)':
R_GatingHierarchy.cpp:762:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
R_GatingHierarchy.cpp:764:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_GatingSet.cpp -o R_GatingSet.o
R_GatingSet.cpp: In function 'SEXPREC* R_combineGatingSet(SEXP, SEXP)':
R_GatingSet.cpp:186:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c calibrationTable.cpp -o calibrationTable.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c flowData.cpp -o flowData.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c gate.cpp -o gate.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c global.cpp -o global.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c nodeProperties.cpp -o nodeProperties.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c spline.cpp -o spline.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c transformation.cpp -o transformation.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:479:27: warning: "/*" within comment [-Wcomment]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c workspace.cpp -o workspace.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c wsNode.cpp -o wsNode.o
g++ -m32 -shared -s -static-libgcc -o flowWorkspace.dll tmp.def GatingHierarchy.o GatingSet.o POPINDICES.o R_GatingHierarchy.o R_GatingSet.o calibrationTable.o flowData.o flowJoWorkspace.o gate.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o -L/usr/lib/x86_64-linux-gnu -Lc:/libxml2//i386/lib c:/libxml2//i386/lib/libxml2.a c:/boost//i386/lib/libboost_serialization-mgw46-mt-1_52.a c:/boost//i386/lib/libboost_regex-mgw46-mt-1_52.a -lws2_32 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.14-bioc/R/library/flowWorkspace/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 to library 'E:/biocbld/bbs-2.14-bioc/R/library'
* installing *source* package 'flowWorkspace' ...

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


** libs
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GatingHierarchy.cpp -o GatingHierarchy.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GatingSet.cpp -o GatingSet.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c POPINDICES.cpp -o POPINDICES.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
R_GatingHierarchy.cpp: In function 'SEXPREC* R_getSingleCellExpression(SEXP, SEXP, SEXP, SEXP, SEXP)':
R_GatingHierarchy.cpp:762:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
R_GatingHierarchy.cpp:764:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_GatingSet.cpp -o R_GatingSet.o
R_GatingSet.cpp: In function 'SEXPREC* R_combineGatingSet(SEXP, SEXP)':
R_GatingSet.cpp:186:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c calibrationTable.cpp -o calibrationTable.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c flowData.cpp -o flowData.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c gate.cpp -o gate.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c global.cpp -o global.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c nodeProperties.cpp -o nodeProperties.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c spline.cpp -o spline.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c transformation.cpp -o transformation.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:479:27: warning: "/*" within comment [-Wcomment]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c workspace.cpp -o workspace.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c wsNode.cpp -o wsNode.o
g++ -m64 -shared -s -static-libgcc -o flowWorkspace.dll tmp.def GatingHierarchy.o GatingSet.o POPINDICES.o R_GatingHierarchy.o R_GatingSet.o calibrationTable.o flowData.o flowJoWorkspace.o gate.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o -L/usr/lib/x86_64-linux-gnu -Lc:/libxml2//x64/lib c:/libxml2//x64/lib/libxml2.a c:/boost//x64/lib/libboost_serialization-mgw46-mt-1_52.a c:/boost//x64/lib/libboost_regex-mgw46-mt-1_52.a -lws2_32 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.14-bioc/R/library/flowWorkspace/libs/x64
** testing if installed package can be loaded
* DONE (flowWorkspace)