##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings flowWorkspace_4.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/flowWorkspace.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘4.18.0’
* 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
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is 60.9Mb
  sub-directories of 1Mb or more:
    libs  59.5Mb
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) subset.Rd:18: Lost braces
    18 | a code{GatingSet} or \code{GatingSetList} object
       |       ^
* 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 Rd file 'GatingSet-methods.Rd':
  ‘...’

Undocumented arguments in Rd file 'convert.Rd'
  ‘backend’

Undocumented arguments in Rd file 'cs_get_uri.Rd'
  ‘x’

Undocumented arguments in Rd file 'gh_apply_to_new_fcs.Rd'
  ‘files’

Undocumented arguments in Rd file 'load_cytoframe_from_fcs.Rd'
  ‘backend’ ‘uri’

Undocumented arguments in Rd file 'load_cytoset_from_fcs.Rd'
  ‘backend’ ‘backend_dir’

Undocumented arguments in Rd file 'save_gs.Rd'
  ‘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 -w -Wfatal-errors
* 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.4.1/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 ‘sprintf’, possibly from ‘sprintf’ (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 nor [v]sprintf. 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL flowWorkspace
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21,
                 from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_API.cpp:9:
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair<double, double> cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const':
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  260 |         {
      |         ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21,
                 from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_GatingHierarchy.cpp:18:
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair<double, double> cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const':
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  260 |         {
      |         ^
In file included from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_algobase.h:64,
                 from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/specfun.h:43,
                 from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/cmath:3898,
                 from /home/biocbuild/R/R-4.4.1/site-library/cpp11/include/cpp11/as.hpp:3,
                 from /home/biocbuild/R/R-4.4.1/site-library/cpp11/include/cpp11.hpp:5,
                 from R_GatingHierarchy.cpp:16:
/home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_pair.h: In instantiation of 'constexpr std::pair<typename std::__strip_reference_wrapper<typename std::decay<_Tp>::type>::__type, typename std::__strip_reference_wrapper<typename std::decay<_Tp2>::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float; _T2 = float; typename __strip_reference_wrapper<typename decay<_Tp>::type>::__type = float; typename decay<_Tp>::type = float; typename __strip_reference_wrapper<typename decay<_Tp2>::type>::__type = float; typename decay<_Tp2>::type = float]':
R_GatingHierarchy.cpp:824:22:   required from here
  824 |               std::make_pair(static_cast<float>(ranges_input.at(i)),
      |               ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  825 |                       static_cast<float>(ranges_input.at(i + 1))));
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
 1132 |     make_pair(_T1&& __x, _T2&& __y)
      |     ^~~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:13:
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/H5CytoFrame.hpp: In member function 'virtual void cytolib::H5CytoFrame::set_range(const std::string&, cytolib::ColType, std::pair<double, double>, bool)':
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/H5CytoFrame.hpp:204:14: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  204 |         void set_range(const string & colname, ColType ctype, pair<EVENT_DATA_TYPE, EVENT_DATA_TYPE> new_range, bool is_update_keywords = true){
      |              ^~~~~~~~~
R_GatingHierarchy.cpp: In function 'cytolib::gatePtr newGate(cpp11::list)':
R_GatingHierarchy.cpp:824:29: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
  824 |               std::make_pair(static_cast<float>(ranges_input.at(i)),
      |               ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  825 |                       static_cast<float>(ranges_input.at(i + 1))));
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c R_GatingSet.cpp -o R_GatingSet.o
In file included from flowWorkspace_types.h:7,
                 from R_GatingSet.cpp:10:
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair<double, double> cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const':
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  260 |         {
      |         ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c cpp11.cpp -o cpp11.o
In file included from flowWorkspace_types.h:7,
                 from cpp11.cpp:4:
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair<double, double> cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const':
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  260 |         {
      |         ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from cytoframeAPI.cpp:5:
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair<double, double> cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const':
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  260 |         {
      |         ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c cytosetAPI.cpp -o cytosetAPI.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21,
                 from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:12,
                 from cytosetAPI.cpp:2:
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair<double, double> cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const':
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  260 |         {
      |         ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c getDescendants.cpp -o getDescendants.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21,
                 from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getDescendants.cpp:1:
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair<double, double> cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const':
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  260 |         {
      |         ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c getPopStats.cpp -o getPopStats.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21,
                 from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getPopStats.cpp:1:
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair<double, double> cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const':
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  260 |         {
      |         ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21,
                 from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair<double, double> cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const':
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  260 |         {
      |         ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21,
                 from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:12,
                 from h5_error_r_handler.cpp:8:
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair<double, double> cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const':
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  260 |         {
      |         ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic  -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c setCounts.cpp -o setCounts.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21,
                 from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from setCounts.cpp:1:
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair<double, double> cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const':
/home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  260 |         {
      |         ^
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/site-library/cytolib/lib/libcytolib.a /home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lopenblas -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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, saveRDS, setdiff, 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/R/R-4.4.1/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 1672 ]

══ Skipped tests (23) ══════════════════════════════════════════════════════════
• dir.exists(legacy) is not TRUE (2): 'test-main.R:15:1', 'test-main.R:15:1'
• edge case no longer works under cpp11 .needs to be investigated (2):
  'test-main.R:8:1', 'test-main.R:27:1'
• get_default_backend() != "h5" is TRUE (1): 'test-main.R:28:1'
• get_default_backend() != "mem" is TRUE (1): 'test-main.R:9:1'
• get_default_backend() == "mem" is TRUE (13): 'test-main.R:27:1',
  'test-main.R:27:1', 'test-main.R:27:1', 'test-main.R:27:1',
  'test-main.R:27:1', 'test-main.R:27:1', 'test-main.R:27:1',
  'test-main.R:28:1', 'test-main.R:28:1', 'test-main.R:28:1',
  'test-main.R:28:1', 'test-main.R:28:1', 'test-main.R:28:1'
• get_default_backend() == "tile" is not TRUE (2): 'test-main.R:9:1',
  'test-main.R:28:1'
• rownames feature is to be deprecated (2): 'test-main.R:8:1',
  'test-main.R:27:1'

[ FAIL 0 | WARN 3 | SKIP 23 | PASS 1672 ]
> 
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-main.R")
> #Sys.setenv(test_gs_compatibility="yes")
> #Sys.getenv("test_gs_compatibility")
> #test_file("/home/rstudio/opensource/workspace/flowWorkspace/tests/testthat/gs-archive.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingHierarchy-testSuite.R")
> 
> 
> 
> proc.time()
   user  system elapsed 
111.362   6.047 114.944