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 | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowWorkspace_3.25.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘3.25.7’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowWorkspace’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 37.4Mb
sub-directories of 1Mb or more:
doc 2.4Mb
lib 30.7Mb
libs 3.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘BH’ is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘RSVGTipsDevice’ ‘parallel’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
‘RBGL’ ‘graphics’
All declared Imports should be used.
Unexported objects imported by ':::' calls:
‘Rgraphviz:::getRenderPar’ ‘flowCore:::.estimateLogicle’
‘flowCore:::checkClass’ ‘flowCore:::copyFlowSet’ ‘flowCore:::guid’
‘flowCore:::logicle_transform’ ‘graph:::.makeEdgeKeys’
‘lattice:::updateList’ ‘ncdfFlow:::.isValidSamples’
‘stats:::.splinefun’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.load_gs’ ‘.preprocessMap’ ‘.uuid_gen’ ‘isNegated’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GatingSet,GatingHierarchy-character: warning in list.files(pattern =
paste("^", file, "$", sep = ""), path = path, recursive = TRUE, full
= TRUE): partial argument match of 'full' to 'full.names'
getGate,GatingSetList-character: warning in unlist(res, recur = FALSE):
partial argument match of 'recur' to 'recursive'
.addGatingHierarchies: no visible global function definition for ‘is’
.computeCV : <anonymous>: no visible binding for global variable
‘xml.count’
.computeCV : <anonymous>: no visible binding for global variable
‘openCyto.count’
.computeCV : <anonymous> : <anonymous>: no visible global function
definition for ‘IQR’
.computeCV : <anonymous> : <anonymous>: no visible global function
definition for ‘median’
.computeCV_gh : <anonymous>: no visible global function definition for
‘IQR’
.computeCV_gh : <anonymous>: no visible global function definition for
‘median’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable ‘max_val’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable ‘decade’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable ‘offset’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable ‘min_val’
.convertTrans : <anonymous>: multiple local function definitions for
‘f’ with different formal arguments
.dropRedundantNodes : <anonymous>: no visible global function
definition for ‘is’
.graph_handler : asGraphNEL: no visible global function definition for
‘new’
.graph_handler : asGraphNEL: no visible global function definition for
‘validObject’
.load_gs: no visible global function definition for ‘new’
.load_gs: no visible global function definition for ‘.hasSlot’
.load_gs: no visible global function definition for ‘slot’
.mergeGates : <anonymous>: no visible global function definition for
‘extends’
.parse.pData: no visible binding for global variable ‘.’
.plotGate: no visible global function definition for ‘new’
.plotGate: no visible global function definition for ‘as.formula’
.plotGatingTree: no visible global function definition for ‘dev.prev’
.plotGatingTree: no visible global function definition for ‘dev.off’
.plotGatingTree: no visible global function definition for ‘dev.set’
.preplot: no visible global function definition for ‘as’
.preprocessMap: no visible binding for global variable ‘old’
.preprocessMap: no visible binding for global variable ‘.’
.preprocessor: no visible binding for global variable ‘groupName’
.renderNodes.svgAnno : <anonymous>: no visible global function
definition for ‘symbols’
.renderNodes.svgAnno: no visible global function definition for ‘rect’
.renderNodes.svgAnno : <anonymous>: no visible global function
definition for ‘polygon’
.renderNodes.svgAnno: no visible global function definition for
‘polygon’
.renderNodes.svgAnno: no visible global function definition for
‘strwidth’
.renderNodes.svgAnno: no visible global function definition for
‘strheight’
.renderNodes.svgAnno: no visible global function definition for
‘dev.prev’
.renderNodes.svgAnno: no visible global function definition for
‘dev.off’
.renderNodes.svgAnno: no visible global function definition for
‘dev.set’
.renderNodes.svgAnno: no visible global function definition for ‘text’
GatingSetList: no visible global function definition for ‘as’
GatingSetList: no visible global function definition for ‘validObject’
booleanFilter: no visible global function definition for ‘new’
char2booleanFilter: no visible global function definition for ‘new’
dropRedundantNodes : <anonymous>: no visible global function definition
for ‘is’
flowWorkspace.par.init: no visible global function definition for
‘gray’
getMergedStats: no visible binding for global variable ‘sampleName’
mkformula: no visible global function definition for ‘as.formula’
save_gslist: no visible binding for global variable ‘slot’
transformerList: no visible global function definition for ‘is’
transformerList: no visible binding for global variable ‘is’
GatingSet,GatingHierarchy-character: no visible global function
definition for ‘new’
GatingSet,character-character: no visible global function definition
for ‘new’
GatingSet,flowSet-ANY: no visible global function definition for ‘new’
Rm,character-GatingSetList-character: no visible global function
definition for ‘selectMethod’
[,GatingSet-ANY: no visible global function definition for ‘extends’
[,GatingSetList-ANY: no visible global function definition for
‘callNextMethod’
[,GatingSetList-ANY: no visible global function definition for ‘as’
[[,GatingSet-character: no visible global function definition for ‘new’
add,GatingSet-filtersList: no visible global function definition for
‘selectMethod’
add,GatingSet-list : <anonymous>: no visible global function definition
for ‘extends’
add,GatingSet-list: no visible global function definition for
‘selectMethod’
add,GatingSetList-filter: no visible global function definition for
‘selectMethod’
add,GatingSetList-filterList: no visible global function definition for
‘selectMethod’
add,GatingSetList-filters: no visible global function definition for
‘selectMethod’
add,GatingSetList-filtersList: no visible global function definition
for ‘selectMethod’
add,GatingSetList-list: no visible global function definition for
‘selectMethod’
getPopStats,GatingHierarchy: no visible binding for global variable
‘node’
keyword,GatingSetList-character: no visible global function definition
for ‘selectMethod’
keyword,GatingSetList-missing: no visible global function definition
for ‘selectMethod’
openWorkspace,character: no visible global function definition for
‘new’
pData<-,GatingSetList-data.frame: no visible global function definition
for ‘callNextMethod’
pData<-,GatingSetList-data.frame: no visible global function definition
for ‘as’
plotGate,GatingSetList-character: no visible global function definition
for ‘selectMethod’
rbind2,GatingSetList-missing: no visible global function definition for
‘new’
rbind2,GatingSetList-missing: no visible binding for global variable
‘slot’
recompute,GatingSetList: no visible global function definition for
‘selectMethod’
transform,GatingSet: no visible global function definition for ‘is’
Undefined global functions or variables:
. .hasSlot IQR as as.formula callNextMethod decade dev.off dev.prev
dev.set extends gray groupName is max_val median min_val new node
offset old openCyto.count polygon rect sampleName selectMethod slot
strheight strwidth symbols text validObject xml.count
Consider adding
importFrom("grDevices", "dev.off", "dev.prev", "dev.set", "gray")
importFrom("graphics", "polygon", "rect", "strheight", "strwidth",
"symbols", "text")
importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
"is", "new", "selectMethod", "slot", "validObject")
importFrom("stats", "IQR", "as.formula", "median", "offset")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.
* 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
mkdir -p "/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/include/flowWorkspace"
cp include/* /Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/include/flowWorkspace
cp GatingSet.pb.h /Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/include #GatingSet.pb.h is autogenerated by protoc and thus kept at the same folder as GatingSet.proto
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from GatingHierarchy.cpp:8:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c GatingSet.cpp -o GatingSet.o
In file included from GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c GatingSet.pb.cc -o GatingSet.pb.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c POPINDICES.cpp -o POPINDICES.o
In file included from POPINDICES.cpp:8:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c R_API.cpp -o R_API.o
In file included from R_API.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from R_GatingHierarchy.cpp:17:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
R_GatingHierarchy.cpp:326:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)
˜^˜
R_GatingHierarchy.cpp:445:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)throw(domain_error("not valid vertexID!"));
˜^˜
R_GatingHierarchy.cpp:475:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)throw(domain_error("not valid vertexID!"));
˜^˜
R_GatingHierarchy.cpp:486:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)throw(domain_error("not valid vertexID!"));
˜^˜
R_GatingHierarchy.cpp:495:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if(u<0)throw(domain_error("not valid vertexID!"));
˜^˜
6 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c R_GatingSet.cpp -o R_GatingSet.o
In file included from R_GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/flowWorkspace.h:5:
In file included from ./../inst/include/../../src/include/GatingSet.hpp:12:
In file included from ./../inst/include/../../src/include/GatingHierarchy.hpp:13:
In file included from ./../inst/include/../../src/include/populationTree.hpp:11:
In file included from ./../inst/include/../../src/include/nodeProperties.hpp:11:
In file included from ./../inst/include/../../src/include/POPINDICES.hpp:15:
./../inst/include/../../src/include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c calibrationTable.cpp -o calibrationTable.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c compensation.cpp -o compensation.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c delimitedMessage.cpp -o delimitedMessage.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c ellipse2points.cpp -o ellipse2points.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c flowData.cpp -o flowData.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
In file included from flowJoWorkspace.cpp:7:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c gate.cpp -o gate.o
In file included from gate.cpp:10:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from getSingleCellExpression.cpp:2:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c global.cpp -o global.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
In file included from macFlowJoWorkspace.cpp:9:
In file included from ./include/macFlowJoWorkspace.hpp:10:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c nodeProperties.cpp -o nodeProperties.o
In file included from nodeProperties.cpp:7:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c spline.cpp -o spline.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c transformation.cpp -o transformation.o
transformation.cpp:273:68: warning: field 'T' will be initialized after field 'scale' [-Wreorder]
logTrans::logTrans():transformation(false,LOG),offset(0),decade(1),T(262144), scale(1){
^
transformation.cpp:278:139: warning: field 'T' will be initialized after field 'scale' [-Wreorder]
logTrans::logTrans(double _offset,double _decade, unsigned _T, unsigned _scale):transformation(false,LOG),offset(_offset),decade(_decade),T(_T), scale(_scale){
^
transformation.cpp:281:57: warning: field 'length' will be initialized after field 'maxRange' [-Wreorder]
fasinhTrans::fasinhTrans():transformation(false,FASINH),length(256),maxRange(262144), T(262144),A(0),M(4.5){
^
transformation.cpp:285:123: warning: field 'length' will be initialized after field 'maxRange' [-Wreorder]
fasinhTrans::fasinhTrans(double _length, double _maxRange, double _T, double _A, double _M):transformation(false, FASINH),length(_length),maxRange(_maxRange), T(_T),A(_A),M(_M){
^
transformation.cpp:431:10: warning: unused variable 'thisMin' [-Wunused-variable]
double thisMin=0;//input.min();
^
5 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
In file included from winFlowJoWorkspace.cpp:8:
In file included from ./include/winFlowJoWorkspace.hpp:10:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
winFlowJoWorkspace.cpp:561:27: warning: '/*' within block comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
^
winFlowJoWorkspace.cpp:545:10: warning: variable 'quad' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if(quadPattern == "--")
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
winFlowJoWorkspace.cpp:553:42: note: uninitialized use occurs here
CurlyGuadGate * g=new CurlyGuadGate(pp, quad);
^˜˜˜
winFlowJoWorkspace.cpp:545:7: note: remove the 'if' if its condition is always true
else if(quadPattern == "--")
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
winFlowJoWorkspace.cpp:538:2: 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/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/usr/local/include -fPIC -Wall -g -O2 -c workspace.cpp -o workspace.o
In file included from workspace.cpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -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/usr/local/include -fPIC -Wall -g -O2 -c wsNode.cpp -o wsNode.o
In file included from wsNode.cpp:10:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
mkdir -p "/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib"
ar rs "/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/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 archive /Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/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 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 /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowCore/lib/libboost_regex.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
installing to /Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/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)