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CHECK report for CytoML on malbec2

This page was generated on 2019-04-09 11:46:21 -0400 (Tue, 09 Apr 2019).

Package 377/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoML 1.9.6
Mike Jiang
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CytoML
Branch: master
Last Commit: 32ed47d
Last Changed Date: 2019-04-02 22:35:43 -0400 (Tue, 02 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: CytoML
Version: 1.9.6
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CytoML.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CytoML_1.9.6.tar.gz
StartedAt: 2019-04-08 23:50:11 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:57:42 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 451.1 seconds
RetCode: 0
Status:  OK 
CheckDir: CytoML.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CytoML.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CytoML_1.9.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CytoML.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CytoML/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CytoML’ version ‘1.9.6’
* package encoding: UTF-8
* 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 ‘CytoML’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 38.7Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    lib      15.1Mb
    libs     17.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
Versioned 'LinkingTo' values for
  ‘BH’ ‘RProtoBufLib’ ‘cytolib’
are 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
Unexported objects imported by ':::' calls:
  ‘flowWorkspace:::.addGatingHierarchies’ ‘lattice:::updateList’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.parse.pData: no visible binding for global variable ‘.’
.parse.pData: no visible global function definition for
  ‘read.FCSheader’
.parse.pData : <anonymous>: no visible global function definition for
  ‘read.FCSheader’
.preprocessor: no visible binding for global variable ‘groupName’
.preprocessorDiva: no visible binding for global variable ‘specimen’
.preprocessorDiva: no visible binding for global variable
  ‘sampleSelected’
DerivedParameterNode: no visible global function definition for
  ‘write.csv’
addGate: no visible binding for global variable ‘id’
addGate: no visible binding for global variable ‘gate_id’
addGate: no visible binding for global variable ‘fcs’
addGate: no visible binding for global variable ‘gate_def’
addGate: no visible binding for global variable ‘name’
compare.counts: no visible binding for global variable ‘population’
compare.counts: no visible binding for global variable ‘parent’
compare.counts: no visible binding for global variable ‘count’
compare.counts: no visible binding for global variable ‘parent_count’
compare.counts: no visible global function definition for ‘.’
compare.counts: no visible binding for global variable ‘fcs_filename’
constructTree: no visible binding for global variable ‘id’
constructTree: no visible binding for global variable ‘name’
cytobank2GatingSet.cytobankExperiment: no visible binding for global
  variable ‘desc’
cytobankExperiment: no visible global function definition for ‘unzip’
extend.polygonGate: no visible binding for global variable ‘..dim’
extend.polygonGate : <anonymous>: no visible binding for global
  variable ‘y’
extend.polygonGate : <anonymous>: no visible binding for global
  variable ‘x’
extend.polygonGate: no visible binding for global variable ‘id’
extend.polygonGate: no visible binding for global variable ‘x’
extend.polygonGate: no visible binding for global variable ‘y’
extend.polygonGate: no visible binding for global variable ‘is.smaller’
read.gatingML.cytobank: no visible binding for global variable ‘id’
read.gatingML.cytobank: no visible binding for global variable
  ‘comp_ref’
show,flowJoWorkspace: no visible global function definition for ‘.’
show,flowJoWorkspace: no visible binding for global variable
  ‘groupName’
Undefined global functions or variables:
  . ..dim comp_ref count desc fcs fcs_filename gate_def gate_id
  groupName id is.smaller name parent parent_count population
  read.FCSheader sampleSelected specimen unzip write.csv x y
Consider adding
  importFrom("utils", "unzip", "write.csv")
to your NAMESPACE file.
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* 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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/CytoML/libs/CytoML.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘__assert_fail’, possibly from ‘assert’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
compare.counts 138.562  0.637  25.560
extend           6.149  0.019   0.903
* 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: 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/CytoML.Rcheck/00check.log’
for details.

Installation output

CytoML.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CytoML
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘CytoML’ ...
** using staged installation
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
configure:    PKG_CPPFLAGS=-I/usr/include/libxml2
configure:    PKG_LIBS=-lxml2
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ˜˜^˜˜˜˜˜˜˜˜˜
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ˜˜^˜˜˜˜˜˜˜˜
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:0,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/flowWorkspace/workspace.hpp: In member function ‘void workspace::toArray(std::__cxx11::string, std::vector<double>&, std::vector<double>&)’:
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i<nLen;i++)
                      ˜^˜˜˜˜
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp: In member function ‘virtual trans_local xFlowJoWorkspace::getTransformation(wsRootNode, const compensation&, PARAM_VEC&, trans_global_vec*, biexpTrans*, linTrans*, bool)’:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:802:12: warning: unused variable ‘minRange’ [-Wunused-variable]
     double minRange=atof(transNode.getProperty("minRange").c_str());
            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from parseFlowJoWorkspace.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ˜˜^˜˜˜˜˜˜˜˜˜
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ˜˜^˜˜˜˜˜˜˜˜
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:0,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
../inst/include/flowWorkspace/workspace.hpp: In member function ‘void workspace::toArray(std::__cxx11::string, std::vector<double>&, std::vector<double>&)’:
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i<nLen;i++)
                      ˜^˜˜˜˜
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from parseFlowJoWorkspace.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp: In member function ‘virtual trans_local xFlowJoWorkspace::getTransformation(wsRootNode, const compensation&, PARAM_VEC&, trans_global_vec*, biexpTrans*, linTrans*, bool)’:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:802:12: warning: unused variable ‘minRange’ [-Wunused-variable]
     double minRange=atof(transNode.getProperty("minRange").c_str());
            ^˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function ‘CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:1314:94: warning: ‘quad’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),interpolated(false),quadrant(_quad){
                                                                                              ^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from parseFlowJoWorkspace.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:10: note: ‘quad’ was declared here
     QUAD quad;
          ^˜˜˜
mkdir -p "/home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-CytoML/00new/CytoML/lib"
ar rs "/home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-CytoML/00new/CytoML/lib/libflowWorkspace.a" RcppExports.o parseFlowJoWorkspace.o
ar: creating /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-CytoML/00new/CytoML/lib/libflowWorkspace.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o CytoML.so RcppExports.o parseFlowJoWorkspace.o /home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/lib/GatingSet.pb.o /home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/lib/libprotobuf.a -lxml2 -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib CytoML.so; fi
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-CytoML/00new/CytoML/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CytoML)

Tests output

CytoML.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CytoML)
> 
> 
> test_check("CytoML")
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: ggplot2
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-H. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter SSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

mac version of flowJo workspace recognized.
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 98 SKIPPED: 0 FAILED: 0
> 
> #devtools::test()
> 
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/flowjo2gs_internalTestSuite.R")
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R")
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R")
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/diva2gs-InternalTestSuite.R")
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-cytobank.R")
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-diva2gs.R")
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-extend.R")
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-GatingSet2flowJo.R")
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-flowjo2gs.R")
> 
> proc.time()
    user   system  elapsed 
1449.422    7.163  295.307

Example timings

CytoML.Rcheck/CytoML-Ex.timings

nameusersystemelapsed
CytoML.par.get0.0010.0000.001
GatingSet2cytobank2.0180.1482.166
GatingSet2flowJo1.3420.0281.391
compare.counts138.562 0.637 25.560
cytobank2GatingSet0.0010.0000.001
extend6.1490.0190.903
flowJoWorkspace-class0.1700.0080.123
getChildren-graphGML-character-method000
getKeywords0.2310.0120.279
getNodes-graphGML-method000
getSampleGroups000
getSamples000
openDiva000
openWorkspace000
parseWorkspace0.0010.0000.001
plot-graphGML-missing-method0.0010.0000.001
range.GatingHierarchy000
read.gatingML.cytobank000