Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:04 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for flowWorkspace on nebbiolo2


To the developers/maintainers of the flowWorkspace package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowWorkspace.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 712/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 4.10.1  (landing page)
Greg Finak , Mike Jiang
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/flowWorkspace
git_branch: RELEASE_3_16
git_last_commit: af121c6
git_last_commit_date: 2022-12-28 21:02:10 -0400 (Wed, 28 Dec 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: flowWorkspace
Version: 4.10.1
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings flowWorkspace_4.10.1.tar.gz
StartedAt: 2023-04-10 20:46:54 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:50:11 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 197.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowWorkspace.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings flowWorkspace_4.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/flowWorkspace.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘4.10.1’
* 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 84.4Mb
  sub-directories of 1Mb or more:
    libs  83.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Non-standard license specification:
  AGPL-3.0-only
Standardizable: FALSE
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘RBGL’ ‘RProtoBufLib’ ‘ggplot2’ ‘grDevices’ ‘graphics’ ‘utils’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘DelayedArray:::simplify_NULL_dimnames’ ‘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
generate_gatingset_example_archive: warning in list.files(dataDir,
  pattern = "gs_manual", full = TRUE): partial argument match of 'full'
  to 'full.names'
.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’
convert_backend: no visible binding for global variable ‘output’
convert_backend: no visible global function definition for
  ‘cf_write_tile’
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_plot_pop_count_cv: no visible global function definition for
  ‘barchart’
gh_plot_pop_count_cv: no visible binding for global variable
  ‘ggplot2like’
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 barchart callNextMethod cf_write_tile
  count desc extends ggplot2like 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 'dimnames' and siglist 'cytoframe'
  generic 'rownames' and siglist 'cytoframe'
  generic 'rownames<-' and siglist 'cytoframe'
  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 'convert'
  ‘backend’

Undocumented arguments in documentation object 'cs_get_uri'
  ‘x’

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_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 ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
  -Wno-pedantic
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING
  apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.16-bioc/R/site-library/flowWorkspace/libs/flowWorkspace.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘srand’, possibly from ‘srand’ (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 ...
  ‘HowToMergeGatingSet.Rmd’ using ‘UTF-8’... OK
  ‘flowWorkspace-Introduction.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.



Installation output

flowWorkspace.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL flowWorkspace
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_API.cpp -o R_API.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:15,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:15,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_GatingHierarchy.cpp:18:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_GatingHierarchy.cpp:18:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_GatingSet.cpp -o R_GatingSet.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:15,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrameView.hpp:12,
                 from flowWorkspace_types.h:7,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrameView.hpp:12,
                 from flowWorkspace_types.h:7,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cpp11.cpp -o cpp11.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:15,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrameView.hpp:12,
                 from flowWorkspace_types.h:7,
                 from cpp11.cpp:4:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrameView.hpp:12,
                 from flowWorkspace_types.h:7,
                 from cpp11.cpp:4:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include/cpp11.hpp:10,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include/cpp11/declarations.hpp:8,
                 from flowWorkspace_types.h:5,
                 from cpp11.cpp:4:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include/cpp11/external_pointer.hpp: In instantiation of ‘void cpp11::default_deleter(T*) [with T = cytolib::CytoFrameView]’:
cpp11.cpp:9:56:   required from here
/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: deleting object of polymorphic class type ‘cytolib::CytoFrameView’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
   17 |   delete obj;
      |   ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:15,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytoframeAPI.cpp:3:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytoframeAPI.cpp:3:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from cytoframeAPI.cpp:8:
../inst/include/flowWorkspace/pairVectorCpp11Convert.h: In function ‘cpp11::writable::doubles_matrix<> arma_to_rmatrix(const mat&)’:
../inst/include/flowWorkspace/pairVectorCpp11Convert.h:33:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
   33 |  for (auto j = 0; j < m; j++) {
      |                   ~~^~~
../inst/include/flowWorkspace/pairVectorCpp11Convert.h:34:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
   34 |   for (auto i = 0; i < n; i++) {
      |                    ~~^~~
cytoframeAPI.cpp: In function ‘cpp11::writable::doubles_matrix<> cf_getData(cpp11::external_pointer<cytolib::CytoFrameView>)’:
cytoframeAPI.cpp:223:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  223 |   for(int i = 0; i < ncol; i++)
      |                  ~~^~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include/cpp11.hpp:10,
                 from cytoframeAPI.cpp:1:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include/cpp11/external_pointer.hpp: In instantiation of ‘void cpp11::default_deleter(T*) [with T = cytolib::CytoFrameView]’:
cytoframeAPI.cpp:12:76:   required from here
/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: deleting object of polymorphic class type ‘cytolib::CytoFrameView’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
   17 |   delete obj;
      |   ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cytosetAPI.cpp -o cytosetAPI.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:15,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytosetAPI.cpp:1:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytosetAPI.cpp:1:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from cytosetAPI.cpp:2:
../inst/include/flowWorkspace/pairVectorCpp11Convert.h: In function ‘cpp11::writable::doubles_matrix<> arma_to_rmatrix(const mat&)’:
../inst/include/flowWorkspace/pairVectorCpp11Convert.h:33:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
   33 |  for (auto j = 0; j < m; j++) {
      |                   ~~^~~
../inst/include/flowWorkspace/pairVectorCpp11Convert.h:34:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
   34 |   for (auto i = 0; i < n; i++) {
      |                    ~~^~~
cytosetAPI.cpp: In function ‘cpp11::external_pointer<cytolib::GatingSet> fcs_to_cytoset(cpp11::strings, cpp11::list, std::string, std::string)’:
cytosetAPI.cpp:71:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
   71 |     for (size_t i = 0; i < n; i++)
      |                        ~~^~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include/cpp11.hpp:10,
                 from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:10,
                 from cytosetAPI.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include/cpp11/external_pointer.hpp: In instantiation of ‘void cpp11::default_deleter(T*) [with T = cytolib::CytoFrameView]’:
cytosetAPI.cpp:32:107:   required from here
/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: deleting object of polymorphic class type ‘cytolib::CytoFrameView’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
   17 |   delete obj;
      |   ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getDescendants.cpp -o getDescendants.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:15,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getPopStats.cpp -o getPopStats.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:15,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
getPopStats.cpp: In function ‘cpp11::list getPopCounts_cpp(cpp11::external_pointer<cytolib::GatingSet>, bool, cytolib::StringVec, bool, bool)’:
getPopStats.cpp:37:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   37 |     for(int i = 0; i < nSample; i++)
      |                    ~~^~~~~~~~~
getPopStats.cpp:48:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   48 |         for(int j = 0; j < nPop; j++){
      |                        ~~^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:15,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/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-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:15,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:12,
                 from h5_error_r_handler.cpp:8:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:12,
                 from h5_error_r_handler.cpp:8:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from h5_error_r_handler.cpp:8:
../inst/include/flowWorkspace/pairVectorCpp11Convert.h: In function ‘cpp11::writable::doubles_matrix<> arma_to_rmatrix(const mat&)’:
../inst/include/flowWorkspace/pairVectorCpp11Convert.h:33:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
   33 |  for (auto j = 0; j < m; j++) {
      |                   ~~^~~
../inst/include/flowWorkspace/pairVectorCpp11Convert.h:34:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
   34 |   for (auto i = 0; i < n; i++) {
      |                    ~~^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c setCounts.cpp -o setCounts.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:18,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:15,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o cpp11.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/lib/libcytolib.a /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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

Attaching package: 'BiocGenerics'

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, aperm, 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-3.16-bioc/R/site-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!
[ FAIL 0 | WARN 3 | SKIP 23 | PASS 1645 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• dir.exists(legacy) is not TRUE (2)
• edge case no longer works under cpp11 .needs to be investigated (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)
• rownames feature is to be deprecated (2)

[ FAIL 0 | WARN 3 | SKIP 23 | PASS 1645 ]
> 
> # 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 
 67.159   5.199  72.333 

Example timings

flowWorkspace.Rcheck/flowWorkspace-Ex.timings

nameusersystemelapsed
GatingHierarchy-class000
GatingSet-class000
GatingSet-methods000
GatingSetList-class0.0010.0000.000
asinh_Gml20.0010.0000.001
asinhtGml2_trans0.0000.0020.002
booleanFilter-class0.0010.0010.002
cf_append_cols1.7080.2611.968
compensate000
convert1.8030.0161.820
convert_legacy0.0010.0000.000
estimateLogicle000
extract_cluster_pop_name_from_node0.0010.0000.000
flow_breaks1.5120.0231.536
flowjo_biexp0.0020.0000.002
flowjo_biexp_trans1.4680.0241.492
flowjo_fasinh0.0000.0000.001
flowjo_fasinh_trans0.0010.0000.001
flowjo_log_trans0.0000.0000.001
gh_copy_gate0.0860.0200.106
gh_get_compensations000
gh_get_transformations000
gh_pop_get_data000
gh_pop_get_descendants0.0140.0000.015
gh_pop_get_indices000
gh_pop_move0.0380.0190.058
gh_pop_set_indices0.2190.0920.311
gh_pop_set_xml_count000
gs_check_redundant_nodes000
gs_get_pop_paths000
gs_get_singlecell_expression000
gs_plot_diff_tree000
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