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BioC 3.5: BUILD BIN report for CytoML on oaxaca

This page was generated on 2017-03-04 16:52:46 -0500 (Sat, 04 Mar 2017).

Package 297/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoML 1.1.13
Mike Jiang
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CytoML
Last Changed Rev: 127128 / Revision: 127142
Last Changed Date: 2017-03-02 19:19:41 -0500 (Thu, 02 Mar 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS YES, new version is higher than in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  ERROR  OK 
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK YES, new version is higher than in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS [ OK ]

Summary

Package: CytoML
Version: 1.1.13
Command: rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_1.1.13.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CytoML.buildbin-libdir
StartedAt: 2017-03-04 11:10:43 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 11:11:41 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 57.5 seconds
RetCode: 0
Status:  OK 
PackageFile: CytoML_1.1.13.tgz
PackageFileSize: 3.123 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_1.1.13.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CytoML.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CytoML.buildbin-libdir CytoML_1.1.13.tar.gz'
>>>>>>> 

* installing *source* package ‘CytoML’ ...
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 clang++ -std=gnu++11 accepts -g... yes
checking for gcc... clang
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang 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 CytoML
configure:    PKG_CPPFLAGS=-I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -ftemplate-depth=900
configure:    PKG_LIBS=-lxml2
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./CytoML_types.h:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/gate.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from RcppExports.cpp:4:
In file included from ./CytoML_types.h:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/gate.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from RcppExports.cpp:4:
In file included from ./CytoML_types.h:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c setCounts.cpp -o setCounts.o
In file included from setCounts.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/gate.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from setCounts.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/gate.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from setCounts.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CytoML.so RcppExports.o setCounts.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib/libflowWorkspace.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib/libprotobuf.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowCore/lib/libboost_regex.a -lxml2 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/CytoML.buildbin-libdir/CytoML/libs
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (CytoML)


>>>>>>> 
>>>>>>> FIXING LINKS FOR CytoML.buildbin-libdir/CytoML/libs//CytoML.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "CytoML.buildbin-libdir/CytoML/libs//CytoML.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "CytoML.buildbin-libdir/CytoML/libs//CytoML.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "CytoML.buildbin-libdir/CytoML/libs//CytoML.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "CytoML.buildbin-libdir/CytoML/libs//CytoML.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "CytoML.buildbin-libdir/CytoML/libs//CytoML.so"