Greg Finak
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/flowWorkspace |
| Branch: RELEASE_3_6 |
| Last Commit: 8cbfbca |
| Last Changed Date: 2018-04-04 13:28:25 -0400 (Wed, 04 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:34:19 -0400 (Thu, 12 Apr 2018).
| Package 500/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowWorkspace 3.26.9 Greg Finak
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | [ OK ] | OK | OK | OK | |
| Package: flowWorkspace |
| Version: 3.26.9 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowWorkspace |
| StartedAt: 2018-04-11 18:17:08 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 18:19:35 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 146.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowWorkspace
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/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 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 flowWorkspace
configure: PKG_CPPFLAGS=-I/usr/include/libxml2 -ftemplate-depth=900
configure: PKG_LIBS=-lxml2 -lz -lpthread -licucore -lm
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/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/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_API.cpp -o R_API.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/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/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
R_GatingHierarchy.cpp:357:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)
˜^˜
R_GatingHierarchy.cpp:476:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)throw(domain_error("not valid vertexID!"));
˜^˜
R_GatingHierarchy.cpp:506:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)throw(domain_error("not valid vertexID!"));
˜^˜
R_GatingHierarchy.cpp:517:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)throw(domain_error("not valid vertexID!"));
˜^˜
R_GatingHierarchy.cpp:526:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)throw(domain_error("not valid vertexID!"));
˜^˜
5 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/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/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_GatingSet.cpp -o R_GatingSet.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/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/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/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/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/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/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c getSingleCellExpression.cpp -o getSingleCellExpression.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/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/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/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/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c setCounts.cpp -o setCounts.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/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/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:113:11: warning: unused variable 'minRange' [-Wunused-variable]
double minRange=atof(transNode.getProperty("minRange").c_str());
^
winFlowJoWorkspace.cpp:562:27: warning: '/*' within block comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
^
winFlowJoWorkspace.cpp:546:10: warning: variable 'quad' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if(quadPattern == "--")
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
winFlowJoWorkspace.cpp:554:42: note: uninitialized use occurs here
CurlyGuadGate * g=new CurlyGuadGate(pp, quad);
^˜˜˜
winFlowJoWorkspace.cpp:546:7: note: remove the 'if' if its condition is always true
else if(quadPattern == "--")
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
winFlowJoWorkspace.cpp:539:2: note: variable 'quad' is declared here
QUAD quad;
^
3 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/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/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c workspace.cpp -o workspace.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/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/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ws2gh.cpp -o ws2gh.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/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/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ws2gs.cpp -o ws2gs.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I/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/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c wsNode.cpp -o wsNode.o
mkdir -p "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib"
ar rs "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o flowJoWorkspace.o getSingleCellExpression.o macFlowJoWorkspace.o setCounts.o winFlowJoWorkspace.o workspace.o ws2gh.o ws2gs.o wsNode.o
ar: creating archive /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib/libflowWorkspace.a
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 flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o flowJoWorkspace.o getSingleCellExpression.o macFlowJoWorkspace.o setCounts.o winFlowJoWorkspace.o workspace.o ws2gh.o ws2gs.o wsNode.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/lib/libprotobuf.a -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowWorkspace.so; fi
installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/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)