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CHECK report for flowWorkspace on malbec1

This page was generated on 2021-05-06 12:27:36 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the flowWorkspace package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 641/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 4.2.0  (landing page)
Greg Finak ,Mike Jiang ,Jake Wagner
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/flowWorkspace
Branch: RELEASE_3_12
Last Commit: 6af477a
Last Changed Date: 2020-10-27 10:41:36 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: flowWorkspace
Version: 4.2.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings flowWorkspace_4.2.0.tar.gz
StartedAt: 2021-05-06 01:38:51 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:42:35 -0400 (Thu, 06 May 2021)
EllapsedTime: 224.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowWorkspace.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings flowWorkspace_4.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/flowWorkspace.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘4.2.0’
* 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 89.9Mb
  sub-directories of 1Mb or more:
    lib   56.4Mb
    libs  32.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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’ ‘RProtoBufLib’ ‘ggplot2’ ‘grDevices’ ‘graphics’ ‘utils’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘flowCore:::.estimateLogicle’ ‘flowCore:::.spillover_pattern’
  ‘flowCore:::checkClass’ ‘flowCore:::guid’
  ‘flowCore:::logicle_transform’ ‘flowCore:::parse_pd_for_read_fs’
  ‘flowCore:::txt2spillmatrix’ ‘flowCore:::updateTransformKeywords’
  ‘flowCore:::validFilterResultList’ ‘graph:::.makeEdgeKeys’
  ‘ncdfFlow:::.isValidSamples’ ‘stats:::.splinefun’
  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
.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’
.graph_handler : asGraphNEL: no visible global function definition for
  ‘new’
.graph_handler : asGraphNEL: no visible global function definition for
  ‘validObject’
.load_legacy: no visible global function definition for ‘is’
.load_legacy: no visible global function definition for ‘new’
.load_legacy: no visible global function definition for ‘.hasSlot’
.load_legacy : <anonymous>: no visible global function definition for
  ‘is’
.mergeGates : <anonymous>: no visible global function definition for
  ‘extends’
.preprocessMap: no visible binding for global variable ‘old’
.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’
cf_append_cols: no visible global function definition for ‘new’
cf_flush_meta: no visible global function definition for ‘is’
cf_get_uri: no visible global function definition for ‘is’
cf_keyword_delete: no visible global function definition for ‘is’
cf_keyword_insert: no visible global function definition for ‘is’
cf_keyword_rename: no visible global function definition for ‘is’
cf_keyword_rename: no visible binding for global variable ‘na_idx’
cf_keyword_set: no visible global function definition for ‘is’
cf_load_meta: no visible global function definition for ‘is’
cf_lock: no visible global function definition for ‘is’
cf_rename_channel: no visible global function definition for ‘is’
cf_rename_marker: no visible global function definition for ‘is’
cf_rename_marker: no visible binding for global variable ‘desc’
cf_scale_time_channel: no visible global function definition for ‘is’
cf_unlock: no visible global function definition for ‘is’
cf_write_disk: no visible global function definition for ‘is’
char2booleanFilter: no visible global function definition for ‘new’
check_comp: no visible global function definition for ‘is’
check_credential: no visible global function definition for ‘is’
convert_backend: no visible binding for global variable ‘output’
copy_view.cytoframe: no visible global function definition for ‘new’
copy_view.cytoset: no visible global function definition for ‘new’
cs_add_cytoframe: no visible global function definition for ‘is’
cs_get_cytoframe: no visible global function definition for ‘is’
cs_get_cytoframe: no visible global function definition for ‘new’
cs_get_uri: no visible global function definition for ‘is’
cs_keyword_delete: no visible global function definition for ‘is’
cs_keyword_insert: no visible global function definition for ‘is’
cs_keyword_rename: no visible global function definition for ‘is’
cs_keyword_rename : <anonymous>: no visible binding for global variable
  ‘keys’
cs_keyword_set: no visible global function definition for ‘is’
cs_set_cytoframe: no visible global function definition for ‘is’
cytoframe_to_flowFrame: no visible global function definition for ‘as’
cytoset: no visible global function definition for ‘new’
cytoset_to_flowSet: no visible global function definition for ‘as’
get_cytoframe_from_cs: no visible global function definition for ‘is’
get_cytoframe_from_cs: no visible global function definition for ‘new’
gh_apply_to_cs: no visible global function definition for ‘new’
gh_pop_compare_stats: no visible binding for global variable ‘node’
gh_pop_get_count: no visible binding for global variable ‘count’
gh_pop_get_proportion: no visible binding for global variable ‘percent’
gh_pop_get_stats_tfilter: no visible global function definition for
  ‘is’
gh_pop_get_stats_tfilter : <anonymous>: no visible binding for global
  variable ‘Population’
gh_pop_set_gate: no visible global function definition for ‘is’
gs_clone: no visible global function definition for ‘new’
gs_copy_tree_only: no visible global function definition for ‘new’
gs_get_singlecell_expression: no visible global function definition for
  ‘is’
gs_get_singlecell_expression: no visible binding for global variable
  ‘parallel’
gs_pop_add: no visible global function definition for ‘is’
gs_pop_get_count_fast: no visible global function definition for ‘is’
gs_pop_get_count_with_meta: no visible binding for global variable
  ‘sampleName’
gs_pop_get_data: no visible global function definition for ‘new’
gs_pop_set_gate: no visible global function definition for ‘is’
gs_remove_redundant_nodes : <anonymous>: no visible global function
  definition for ‘is’
gslist_to_gs: no visible global function definition for ‘new’
load_cytoframe: no visible global function definition for ‘new’
load_cytoframe_from_fcs: no visible global function definition for
  ‘new’
load_cytoset_from_fcs: no visible global function definition for ‘new’
load_gs: no visible global function definition for ‘new’
load_gslist : <anonymous>: no visible global function definition for
  ‘is’
merge_list_to_gs: no visible global function definition for ‘is’
merge_list_to_gs: no visible global function definition for ‘new’
parse_transformer: no visible global function definition for ‘is’
pop.MFI: no visible binding for global variable ‘desc’
realize_view.cytoframe: no visible global function definition for ‘new’
realize_view.cytoset: no visible global function definition for ‘new’
transformerList: no visible global function definition for ‘is’
transformerList: no visible binding for global variable ‘is’
validitycheck: no visible global function definition for ‘is’
GatingSet,cytoset-ANY: no visible global function definition for ‘new’
Subset,cytoset-filterResultList : <anonymous>: no visible global
  function definition for ‘as’
Subset,cytoset-list: no visible global function definition for ‘is’
[,GatingSet-ANY: no visible global function definition for ‘extends’
[,GatingSet-ANY: no visible global function definition for ‘new’
[,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 ‘as’
compensate,GatingSet-ANY: no visible global function definition for
  ‘selectMethod’
compensate,cytoset-ANY: no visible global function definition for
  ‘selectMethod’
flowData,GatingSet: no visible binding for global variable ‘obj’
fsApply,cytoset: no visible global function definition for
  ‘callNextMethod’
gs_cyto_data,GatingSet: no visible global function definition for ‘new’
keyword,GatingSetList-character: no visible global function definition
  for ‘selectMethod’
keyword,GatingSetList-missing: no visible global function definition
  for ‘selectMethod’
keyword<-,cytoframe-list: no visible binding for global variable
  ‘kwdError’
pData<-,GatingSetList-data.frame: no visible global function definition
  for ‘callNextMethod’
pData<-,GatingSetList-data.frame: no visible global function definition
  for ‘as’
parameters,cytoframe: no visible global function definition for ‘new’
phenoData,cytoset: no visible global function definition for ‘new’
sampleNames<-,cytoset-ANY: no visible global function definition for
  ‘selectMethod’
setNode,GatingSet-character-ANY: no visible global function definition
  for ‘is’
show,cytoframe: 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’
transform,cytoframe: no visible global function definition for ‘is’
transform,cytoset: no visible global function definition for ‘is’
transform,cytoset : <anonymous>: no visible global function definition
  for ‘is’
Undefined global functions or variables:
  . .hasSlot IQR Population as callNextMethod count desc extends is
  keys kwdError median na_idx new node obj old openCyto.count output
  parallel percent sampleName selectMethod validObject xml.count
Consider adding
  importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
             "is", "new", "selectMethod", "validObject")
  importFrom("stats", "IQR", "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 ... WARNING
Undocumented code objects:
  ‘gs_clone’ ‘gs_copy_tree_only’
Undocumented S4 methods:
  generic 'show' and siglist 'cytoframe'
  generic 'transform' and siglist 'cytoframe'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'GatingSet-methods':
  ‘...’

Undocumented arguments in documentation object 'cf_append_cols'
  ‘cred’

Undocumented arguments in documentation object 'convert'
  ‘backend’

Undocumented arguments in documentation object 'cs_get_uri'
  ‘x’

Undocumented arguments in documentation object 'delete_gs'
  ‘cred’

Undocumented arguments in documentation object 'gh_apply_to_new_fcs'
  ‘files’

Undocumented arguments in documentation object 'keyword-mutators'
  ‘cs’

Undocumented arguments in documentation object 'load_cytoframe'
  ‘num_threads’

Undocumented arguments in documentation object 'load_cytoframe_from_fcs'
  ‘backend’ ‘uri’

Undocumented arguments in documentation object 'load_cytoset_from_fcs'
  ‘backend’ ‘backend_dir’

Undocumented arguments in documentation object 'save_gs'
  ‘cdf’ ‘backend_readonly’

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 ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.12-bioc/R/library/flowWorkspace/libs/flowWorkspace.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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: 2 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.

Installation output

flowWorkspace.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL flowWorkspace
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
make: R: Command not found
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_API.cpp -o R_API.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_GatingSet.cpp -o R_GatingSet.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:46:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:34,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from ../inst/include/flowWorkspace.h:6,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of ‘void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]’:
RcppExports.cpp:607:45:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type ‘cytolib::CytoFrameView’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete obj;
     ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytoframeAPI.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytoframeAPI.cpp:3:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:46:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:34,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from cytoframeAPI.cpp:3:
/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of ‘void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]’:
cytoframeAPI.cpp:9:45:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type ‘cytolib::CytoFrameView’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete obj;
     ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cytosetAPI.cpp -o cytosetAPI.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytosetAPI.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytosetAPI.cpp:2:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:46:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:34,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from cytosetAPI.cpp:2:
/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of ‘void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]’:
cytosetAPI.cpp:38:81:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type ‘cytolib::CytoFrameView’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete obj;
     ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getDescendants.cpp -o getDescendants.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getPopStats.cpp -o getPopStats.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5_error_r_handler.cpp -o h5_error_r_handler.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from h5_error_r_handler.cpp:8:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from h5_error_r_handler.cpp:8:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c setCounts.cpp -o setCounts.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
mkdir -p "/home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib"
ar rs "/home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o
ar: creating /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath /home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -L/home/biocbuild/bbs-3.12-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 flowWorkspace.so; fi
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-flowWorkspace/00new/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 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 (flowWorkspace)

Tests output

flowWorkspace.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:

  vignette("flowWorkspace-Introduction", "flowWorkspace")
> 
> 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: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 object is masked from 'package:flowCore':

    normalize

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

    combine, intersect, setdiff, union

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, 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, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, 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")'.

/home/biocbuild/bbs-3.12-bioc/R/library/flowWorkspaceData/extdata/legacy_gs/v2/gs_bcell_auto seems to be the legacy archive and it is recommended to convert to the new format by saving it to the new folder!
══ Skipped tests ═══════════════════════════════════════════════════════════════
• dir.exists(legacy) is not TRUE (2)
• empty test (2)
• get_default_backend() != "h5" is TRUE (1)
• get_default_backend() != "mem" is TRUE (1)
• get_default_backend() == "mem" is TRUE (13)
• get_default_backend() == "tile" is not TRUE (2)

[ FAIL 0 | WARN 3 | SKIP 21 | PASS 1643 ]
> 
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-main.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingSet-testSuite.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingHierarchy-testSuite.R")
> 
> 
> 
> proc.time()
   user  system elapsed 
 96.176   4.876 102.063

Example timings

flowWorkspace.Rcheck/flowWorkspace-Ex.timings

nameusersystemelapsed
GatingHierarchy-class0.0000.0000.001
GatingSet-class0.0000.0000.001
GatingSet-methods0.0040.0000.000
GatingSetList-class000
asinh_Gml20.0000.0000.001
asinhtGml2_trans0.0000.0000.004
booleanFilter-class0.0040.0000.003
cf_append_cols1.0280.0401.071
compensate000
convert0.8080.0240.832
convert_legacy000
estimateLogicle000
extract_cluster_pop_name_from_node000
flow_breaks0.5720.0200.590
flowjo_biexp0.0000.0000.015
flowjo_biexp_trans0.5120.0160.531
flowjo_fasinh0.0000.0000.001
flowjo_fasinh_trans000
flowjo_log_trans000
gh_copy_gate0.0880.0160.162
gh_get_compensations0.0000.0000.001
gh_get_transformations0.0000.0000.001
gh_pop_get_data0.0000.0000.001
gh_pop_get_descendants0.0120.0040.015
gh_pop_get_indices000
gh_pop_move0.0600.0080.068
gh_pop_set_indices0.2720.0600.332
gh_pop_set_xml_count000
gs_check_redundant_nodes000
gs_get_pop_paths0.0000.0000.001
gs_get_singlecell_expression0.0000.0000.001
gs_plot_diff_tree000
gs_plot_pop_count_cv000
gs_pop_add0.0000.0000.001
gs_pop_get_children0.0000.0000.001
gs_pop_get_count_fast0.0000.0000.001
gs_pop_get_gate000
gs_pop_get_stats000
gs_pop_set_gate000
gs_pop_set_name000
gs_pop_set_visibility000
gs_remove_redundant_channels000
gs_remove_redundant_nodes0.0000.0000.001
gs_split_by_channels0.0000.0000.001
gs_split_by_tree000
gs_update_channels000
keyword-mutators1.2000.0241.231
keyword000
logicleGml2_trans0.0040.0000.001
logicle_trans0.0000.0000.002
loglevel0.0000.0000.001
logtGml2_trans0.0000.0000.001
markernames000
plot-methods000
plotGate-methods-defunct000
prettyAxis000
rotate_gate000
sampleNames000
save_cytoset000
save_gs000
scale_gate0.0040.0000.000
shift_gate0.0000.0000.001
swap_data_cols0.6080.0240.633
transform0.0040.0000.000
transform_gate000
transformerList0.0160.0000.016