BioC 3.5: CHECK report for CytoML on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CytoML_1.1.13.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/CytoML.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.13’
* 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 ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/CytoML.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   3.0Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘flowUtils:::.fuEnv’ ‘flowUtils:::smartTreeParse’
  ‘flowWorkspace:::.cpp_getCompensation’
  ‘flowWorkspace:::.fix_channel_slash’ ‘flowWorkspace:::.groupByTree’
  ‘flowWorkspace:::compute.timestep’ ‘flowWorkspace:::isHidden’
  ‘flowWorkspace:::isNegated’
  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
.preprocessorDiva: no visible global function definition for ‘menu’
.preprocessorDiva: no visible binding for global variable ‘specimen’
.preprocessorDiva: no visible binding for global variable
  ‘sampleSelected’
GatingSet2flowJo: no visible global function definition for ‘pData<-’
addCustomInfo : <anonymous>: no visible global function definition for
  ‘is’
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 : <anonymous>: no visible binding for global variable
  ‘slot’
constructTree: no visible binding for global variable ‘id’
constructTree: no visible binding for global variable ‘name’
extend.ellipsoidGate: no visible global function definition for ‘as’
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’
extend.polygonGate: no visible global function definition for ‘rgb’
extend.rectangleGate: no visible global function definition for ‘as’
gateNode.ellipsoidGate: no visible global function definition for ‘as’
inverse.ellipsoidGate: no visible global function definition for ‘as’
inverse.rectangleGate: no visible global function definition for ‘as’
openDiva: no visible global function definition for ‘new’
read.gatingML.cytobank: no visible global function definition for ‘is’
read.gatingML.cytobank: no visible binding for global variable ‘id’
read.gatingML.cytobank: no visible binding for global variable
  ‘comp_ref’
read.gatingML.cytobank : <anonymous>: no visible global function
  definition for ‘is’
read.gatingML.cytobank: no visible global function definition for ‘as’
subPopulationNode : <anonymous>: no visible global function definition
  for ‘is’
subPopulationNode : <anonymous> : <anonymous>: no visible global
  function definition for ‘is’
xmlTag: no visible global function definition for ‘is’
compensate,GatingSet-graphGML: no visible global function definition
  for ‘is’
getSamples,divaWorkspace: no visible global function definition for
  ‘selectMethod’
getTransformations,graphGML : <anonymous>: no visible global function
  definition for ‘extends’
transform,ellipsoidGate: no visible global function definition for ‘as’
Undefined global functions or variables:
  . as comp_ref count extends fcs fcs_filename gate_def gate_id id is
  is.smaller menu name new pData<- parent parent_count population rgb
  sampleSelected selectMethod slot specimen x y
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("methods", "as", "extends", "is", "new", "selectMethod",
             "slot")
  importFrom("utils", "menu")
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 ... WARNING
Undocumented arguments in documentation object 'divaWorkspace-class'
  ‘x’ ‘object’ ‘obj’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
compare.counts     8.448  0.356   8.910
cytobank2GatingSet 4.944  0.287   5.233
* 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: 2 WARNINGs, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/CytoML.Rcheck/00check.log’
for details.

* installing *source* package ‘CytoML’ ...
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=gnu++11 accepts -g... yes
checking for gcc... clang
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: Using the following compilation and linking flags for CytoML
configure:    PKG_CPPFLAGS=-I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -ftemplate-depth=900
configure:    PKG_LIBS=-lxml2
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./CytoML_types.h:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/gate.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from RcppExports.cpp:4:
In file included from ./CytoML_types.h:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/gate.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from RcppExports.cpp:4:
In file included from ./CytoML_types.h:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c setCounts.cpp -o setCounts.o
In file included from setCounts.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/gate.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from setCounts.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/gate.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from setCounts.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CytoML.so RcppExports.o setCounts.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib/libflowWorkspace.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib/libprotobuf.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowCore/lib/libboost_regex.a -lxml2 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/CytoML.Rcheck/CytoML/libs
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (CytoML)

name	user	system	elapsed
GatingSet2cytobank	3.967	0.087	4.364
GatingSet2flowJo	2.279	0.085	2.460
compare.counts	8.448	0.356	8.910
cytobank2GatingSet	4.944	0.287	5.233
extend	0.088	0.001	0.089
getChildren-graphGML-character-method	1.261	0.022	1.284
getNodes-graphGML-method	1.199	0.020	1.219
openDiva	0.001	0.000	0.001
plot-graphGML-missing-method	1.591	0.022	1.616
read.gatingML.cytobank	1.120	0.016	1.136
set.count.xml	0.000	0.000	0.001

BioC 3.5: CHECK report for CytoML on oaxaca

Summary

Command output