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BioC 3.6: INSTALL report for flowWorkspace on malbec1

This page was generated on 2017-08-16 13:19:27 -0400 (Wed, 16 Aug 2017).

Package 483/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 3.25.7
Greg Finak ,Mike Jiang
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowWorkspace
Last Changed Rev: 131603 / Revision: 131943
Last Changed Date: 2017-07-26 19:47:35 -0400 (Wed, 26 Jul 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowWorkspace
Version: 3.25.7
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD INSTALL flowWorkspace
StartedAt: 2017-08-15 18:10:57 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 18:14:45 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 228.8 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD INSTALL flowWorkspace
###
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* installing to library ‘/home/biocbuild/bbs-3.6-bioc/R/library’
* installing *source* package ‘flowWorkspace’ ...
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: Using the following compilation and linking flags for flowWorkspace
configure:    PKG_CPPFLAGS=-I/usr/include/libxml2
configure:    PKG_LIBS=-lxml2
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/home/biocbuild/bbs-3.6-bioc/R/library/flowWorkspace/include/flowWorkspace"
cp include/* /home/biocbuild/bbs-3.6-bioc/R/library/flowWorkspace/include/flowWorkspace
cp GatingSet.pb.h /home/biocbuild/bbs-3.6-bioc/R/library/flowWorkspace/include #GatingSet.pb.h is autogenerated by protoc and thus kept at the same folder as GatingSet.proto
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c GatingSet.cpp -o GatingSet.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c GatingSet.pb.cc -o GatingSet.pb.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c POPINDICES.cpp -o POPINDICES.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c R_API.cpp -o R_API.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c R_GatingSet.cpp -o R_GatingSet.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c calibrationTable.cpp -o calibrationTable.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c compensation.cpp -o compensation.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c delimitedMessage.cpp -o delimitedMessage.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c ellipse2points.cpp -o ellipse2points.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c flowData.cpp -o flowData.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c gate.cpp -o gate.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c getSingleCellExpression.cpp -o getSingleCellExpression.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c global.cpp -o global.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c nodeProperties.cpp -o nodeProperties.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c spline.cpp -o spline.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c transformation.cpp -o transformation.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c workspace.cpp -o workspace.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c wsNode.cpp -o wsNode.o
mkdir -p "/home/biocbuild/bbs-3.6-bioc/R/library/flowWorkspace/lib"
ar rs "/home/biocbuild/bbs-3.6-bioc/R/library/flowWorkspace/lib/libflowWorkspace.a" GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o calibrationTable.o compensation.o delimitedMessage.o ellipse2points.o flowData.o flowJoWorkspace.o gate.o getSingleCellExpression.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o
ar: creating /home/biocbuild/bbs-3.6-bioc/R/library/flowWorkspace/lib/libflowWorkspace.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o flowWorkspace.so GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o calibrationTable.o compensation.o delimitedMessage.o ellipse2points.o flowData.o flowJoWorkspace.o gate.o getSingleCellExpression.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o /home/biocbuild/bbs-3.6-bioc/R/library/flowCore/lib/libboost_regex.a /home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/lib/libprotobuf.a -lxml2 -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/R/library/flowWorkspace/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowWorkspace)