Multiple platform build/check report for BioC 3.9 - CHECK report for CytoML on merida2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CytoML.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CytoML_1.9.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CytoML.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.9.6’
* 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 14.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    lib       6.6Mb
    libs      2.3Mb
* 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 ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/CytoML/libs/CytoML.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_printf’, possibly from ‘printf’ (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 16.962 13.442   6.061
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/CytoML.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CytoML
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* 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
configure:    PKG_CPPFLAGS=-I/usr/include/libxml2 -ftemplate-depth=900
configure:    PKG_LIBS=-lxml2 -lz -lpthread -licucore -lm
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/CytoML.h:5:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: '/*' within block comment [-Wcomment]
           * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                                    ^
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:417:13: warning: variable 'quad' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                else if(quadPattern == "--")
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:425:45: note: uninitialized use occurs here
                CurlyGuadGate * g=new CurlyGuadGate(pp, quad);
                                                        ^˜˜˜
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:417:10: note: remove the 'if' if its condition is always true
                else if(quadPattern == "--")
                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:5: note: variable 'quad' is declared here
                QUAD quad;
                ^
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:802:12: warning: unused variable 'minRange' [-Wunused-variable]
                                double minRange=atof(transNode.getProperty("minRange").c_str());
                                       ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: '/*' within block comment [-Wcomment]
           * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                                    ^
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:417:13: warning: variable 'quad' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                else if(quadPattern == "--")
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:425:45: note: uninitialized use occurs here
                CurlyGuadGate * g=new CurlyGuadGate(pp, quad);
                                                        ^˜˜˜
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:417:10: note: remove the 'if' if its condition is always true
                else if(quadPattern == "--")
                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:5: note: variable 'quad' is declared here
                QUAD quad;
                ^
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:802:12: warning: unused variable 'minRange' [-Wunused-variable]
                                double minRange=atof(transNode.getProperty("minRange").c_str());
                                       ^
3 warnings generated.
mkdir -p "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/CytoML/lib"
ar rs "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/CytoML/lib/libflowWorkspace.a" RcppExports.o parseFlowJoWorkspace.o
ar: creating archive /Library/Frameworks/R.framework/Versions/3.6/Resources/library/CytoML/lib/libflowWorkspace.a
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CytoML.so RcppExports.o parseFlowJoWorkspace.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/lib/GatingSet.pb.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/lib/libprotobuf.a -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib CytoML.so; fi
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/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
* DONE (CytoML)

Tests output


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
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 
265.018 154.156 140.035

name	user	system	elapsed
CytoML.par.get	0.001	0.000	0.001
GatingSet2cytobank	2.781	0.218	3.032
GatingSet2flowJo	1.909	0.102	2.021
compare.counts	16.962	13.442	6.061
cytobank2GatingSet	0.002	0.002	0.001
extend	0.652	0.551	0.141
flowJoWorkspace-class	0.338	0.303	0.075
getChildren-graphGML-character-method	0.001	0.001	0.000
getKeywords	0.854	0.842	0.382
getNodes-graphGML-method	0	0	0
getSampleGroups	0	0	0
getSamples	0	0	0
openDiva	0	0	0
openWorkspace	0	0	0
parseWorkspace	0	0	0
plot-graphGML-missing-method	0.000	0.001	0.001
range.GatingHierarchy	0	0	0
read.gatingML.cytobank	0	0	0

CHECK report for CytoML on merida2

Summary

Command output

Installation output

Tests output

Example timings