Package: flowWorkspace

Version: 3.31.15

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowWorkspace_3.31.15.tar.gz

StartedAt: 2019-04-09 00:56:29 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:58:46 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 137.6 seconds

RetCode: 0

Status:  OK

CheckDir: flowWorkspace.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowWorkspace_3.31.15.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/flowWorkspace.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 ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘3.31.15’
* 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 ‘flowWorkspace’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 29.2Mb
  sub-directories of 1Mb or more:
    lib   25.4Mb
    libs   2.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
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
Namespaces in Imports field not imported from:
  ‘RBGL’ ‘grDevices’ ‘graphics’ ‘utils’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘flowCore:::.estimateLogicle’ ‘flowCore:::checkClass’
  ‘flowCore:::copyFlowSet’ ‘flowCore:::guid’
  ‘flowCore:::logicle_transform’ ‘flowCore:::updateTransformKeywords’
  ‘graph:::.makeEdgeKeys’ ‘lattice:::updateList’
  ‘ncdfFlow:::.isValidSamples’ ‘stats:::.splinefun’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.cpp_setIndices’ ‘.getNodeInd’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getGate,GatingSetList-character: warning in unlist(res, recur = FALSE):
  partial argument match of 'recur' to 'recursive'
.addGatingHierarchies: no visible global function definition for ‘is’
.addGatingHierarchies : <anonymous>: no visible global function
  definition for ‘getKeywords’
.computeCV : <anonymous>: no visible binding for global variable
  ‘xml.count’
.computeCV : <anonymous>: no visible binding for global variable
  ‘openCyto.count’
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for ‘IQR’
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
.computeCV_gh : <anonymous>: no visible global function definition for
  ‘IQR’
.computeCV_gh : <anonymous>: no visible global function definition for
  ‘median’
.dropRedundantNodes : <anonymous>: no visible global function
  definition for ‘is’
.getPopChnlMapping: no visible global function definition for ‘%>%’
.getSingleCellExpression: no visible binding for global variable
  ‘parallel’
.graph_handler : asGraphNEL: no visible global function definition for
  ‘new’
.graph_handler : asGraphNEL: no visible global function definition for
  ‘validObject’
.load_gs: no visible global function definition for ‘new’
.load_gs: no visible global function definition for ‘.hasSlot’
.load_gs: no visible global function definition for ‘slot’
.load_gs: no visible global function definition for ‘is’
.mergeGates : <anonymous>: no visible global function definition for
  ‘extends’
.plotGate: no visible global function definition for ‘new’
.plotGate: no visible global function definition for ‘as.formula’
.preplot: no visible global function definition for ‘as’
.preprocessMap: no visible global function definition for ‘%>%’
.preprocessMap: no visible global function definition for ‘group_by’
.preprocessMap: no visible binding for global variable ‘old’
.preprocessMap: no visible global function definition for ‘do’
.preprocessMap: no visible binding for global variable ‘.’
GatingSetList: no visible global function definition for ‘as’
GatingSetList: no visible global function definition for ‘validObject’
booleanFilter: no visible global function definition for ‘new’
booleanFilter: no visible global function definition for ‘is’
char2booleanFilter: no visible global function definition for ‘new’
dropRedundantNodes : <anonymous>: no visible global function definition
  for ‘is’
flowWorkspace.par.init: no visible global function definition for
  ‘gray’
getMergedStats: no visible binding for global variable ‘sampleName’
mkformula: no visible global function definition for ‘as.formula’
pop.MFI: no visible binding for global variable ‘desc’
save_gslist: no visible binding for global variable ‘slot’
transformerList: no visible global function definition for ‘is’
transformerList: no visible binding for global variable ‘is’
GatingSet,GatingHierarchy-character: no visible global function
  definition for ‘new’
GatingSet,flowSet-ANY: no visible global function definition for ‘new’
Rm,character-GatingSetList-character: no visible global function
  definition for ‘selectMethod’
[,GatingSet-ANY: no visible global function definition for ‘extends’
[,GatingSetList-ANY: no visible global function definition for
  ‘callNextMethod’
[,GatingSetList-ANY: no visible global function definition for ‘as’
[[,GatingSet-character: no visible global function definition for ‘new’
add,GatingHierarchy-logicalFilterResult: no visible global function
  definition for ‘selectMethod’
add,GatingSet-filtersList: no visible global function definition for
  ‘selectMethod’
add,GatingSet-list: no visible global function definition for
  ‘selectMethod’
add,GatingSetList-filter: no visible global function definition for
  ‘selectMethod’
add,GatingSetList-filterList: no visible global function definition for
  ‘selectMethod’
add,GatingSetList-filters: no visible global function definition for
  ‘selectMethod’
add,GatingSetList-filtersList: no visible global function definition
  for ‘selectMethod’
add,GatingSetList-list: no visible global function definition for
  ‘selectMethod’
getPopStats,GatingHierarchy: no visible binding for global variable
  ‘node’
keyword,GatingSetList-character: no visible global function definition
  for ‘selectMethod’
keyword,GatingSetList-missing: no visible global function definition
  for ‘selectMethod’
pData<-,GatingSetList-data.frame: no visible global function definition
  for ‘callNextMethod’
pData<-,GatingSetList-data.frame: no visible global function definition
  for ‘as’
plotGate,GatingSetList-character: no visible global function definition
  for ‘selectMethod’
rbind2,GatingSetList-missing: no visible global function definition for
  ‘new’
rbind2,GatingSetList-missing: no visible binding for global variable
  ‘slot’
recompute,GatingSetList: no visible global function definition for
  ‘selectMethod’
transform,GatingSet: no visible global function definition for ‘is’
transform,GatingSet : <anonymous>: no visible global function
  definition for ‘is’
Undefined global functions or variables:
  %>% . .hasSlot IQR as as.formula callNextMethod desc do extends
  getKeywords gray group_by is median new node old openCyto.count
  parallel sampleName selectMethod slot validObject xml.count
Consider adding
  importFrom("grDevices", "gray")
  importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
             "is", "new", "selectMethod", "slot", "validObject")
  importFrom("stats", "IQR", "as.formula", "median")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/flowWorkspace/libs/flowWorkspace.so’:
  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
* 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: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowWorkspace
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘flowWorkspace’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 R_API.cpp -o R_API.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 R_GatingHierarchy.cpp -o R_GatingHierarchy.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 R_GatingSet.cpp -o R_GatingSet.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 getDescendants.cpp -o getDescendants.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 getPopStats.cpp -o getPopStats.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 getSingleCellExpression.cpp -o getSingleCellExpression.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 setCounts.cpp -o setCounts.o
mkdir -p "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/flowWorkspace/lib"
ar rs "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/flowWorkspace/lib/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o
ar: creating archive /Library/Frameworks/R.framework/Versions/3.6/Resources/library/flowWorkspace/lib/libflowWorkspace.a
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowWorkspace.so; fi
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/flowWorkspace/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 (flowWorkspace)

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(flowWorkspace)
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
> 
> test_check("flowWorkspace")

Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

The following object is masked from 'package:ncdfFlow':

    filter

The following object is masked from 'package:flowCore':

    filter

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:dplyr':

    combine, intersect, setdiff, union

The following object is masked from 'package:flowCore':

    normalize

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 772 SKIPPED: 3 FAILED: 0
> 
> #devtools::test("˜/rglab/workspace/flowWorkspace")
> #devtools::check_man()
> #test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-archive.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-parseWorkspace.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingHierarchy-testSuite.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingSet-testSuite.R")
> 
> proc.time()
   user  system elapsed 
 35.639  10.730  34.807 

name	user	system	elapsed
GatingHierarchy-class	0.000	0.000	0.001
GatingSet-class	0	0	0
GatingSet-methods	0	0	0
GatingSetList-class	0.001	0.001	0.002
add	0.001	0.001	0.001
asinh_Gml2	0.001	0.000	0.001
asinhtGml2_trans	0.002	0.000	0.003
booleanFilter-class	0.005	0.000	0.004
checkRedundantNodes	0.000	0.000	0.001
clone	0	0	0
compensate	0.001	0.000	0.000
copyNode	0.125	0.009	0.139
dropRedundantChannels	0	0	0
dropRedundantNodes	0	0	0
estimateLogicle.GatingHierarchy	0.000	0.000	0.001
extract_cluster_pop_name_from_node	0.001	0.000	0.000
flowJo.fasinh	0.001	0.000	0.000
flowJo.flog	0.002	0.001	0.002
flowJoTrans	0.008	0.001	0.009
flowJo_biexp_trans	0.714	0.062	0.780
flowJo_fasinh_trans	0.000	0.000	0.001
flowWorkspace.par.get	0.001	0.001	0.001
flow_breaks	0.716	0.037	0.757
getCompensationMatrices	0	0	0
getData-methods	0	0	0
getDescendants	0.014	0.001	0.016
getGate	0	0	0
getIndices-GatingSet-name-method	0	0	0
getIndices	0.000	0.000	0.001
getMergedStats	0.000	0.001	0.000
getNodes	0.001	0.000	0.001
getParent	0	0	0
getPopStats	0	0	0
getSingleCellExpression	0.000	0.000	0.001
getStats	0.000	0.001	0.000
getTransformations	0	0	0
groupByChannels	0	0	0
groupByTree	0	0	0
insertGate	0	0	0
keyword	0	0	0
logicleGml2_trans	0.001	0.000	0.001
logicle_trans	0.002	0.001	0.003
loglevel	0	0	0
logtGml2_trans	0.000	0.000	0.001
markernames	0	0	0
mkformula	0.002	0.000	0.002
moveNode	0.052	0.016	0.067
plot-methods	0	0	0
plotGate-methods	0	0	0
plotPopCV	0.000	0.000	0.001
plot_diff_tree	0	0	0
prettyAxis	0	0	0
rotate_gate	0.000	0.000	0.001
sampleNames	0	0	0
save_gs	0.000	0.000	0.001
scale_gate	0	0	0
set.count.xml	0	0	0
setGate	0.000	0.001	0.000
setNode-methods	0	0	0
shift_gate	0	0	0
swap_data_cols	0.809	0.053	0.865
transform	0	0	0
transform_gate	0.001	0.000	0.000
transformerList	0.008	0.001	0.009
updateChannels	0.000	0.000	0.001
updateIndices-GatingHierarchy-character-logical-method	1.311	1.004	0.780