Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 734/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 4.12.2  (landing page)
Greg Finak , Mike Jiang
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/flowWorkspace
git_branch: RELEASE_3_17
git_last_commit: b51e3f26
git_last_commit_date: 2023-08-20 18:27:39 -0400 (Sun, 20 Aug 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for flowWorkspace on kjohnson2


To the developers/maintainers of the flowWorkspace package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: flowWorkspace
Version: 4.12.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowWorkspace_4.12.2.tar.gz
StartedAt: 2023-10-17 20:15:18 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 20:20:54 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 335.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowWorkspace.Rcheck
Warnings: 6

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowWorkspace_4.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/flowWorkspace.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘4.12.2’
* 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 ... WARNING
Found the following significant warnings:
  /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/flowWorkspace.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
* 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 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 ... 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/flowWorkspace/libs/flowWorkspace.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (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)

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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 WARNINGs, 7 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/flowWorkspace.Rcheck/00check.log’
for details.



Installation output

flowWorkspace.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowWorkspace
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_API.cpp -o R_API.o
In file included from R_API.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
    for (const pb::Range range : gate_pb.mrg().ranges()) {
                         ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
    for (const pb::Range range : gate_pb.mrg().ranges()) {
         ^~~~~~~~~~~~~~~~~~~~~~~
                         &
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from R_GatingHierarchy.cpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
    for (const pb::Range range : gate_pb.mrg().ranges()) {
                         ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
    for (const pb::Range range : gate_pb.mrg().ranges()) {
         ^~~~~~~~~~~~~~~~~~~~~~~
                         &
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_GatingSet.cpp -o R_GatingSet.o
In file included from R_GatingSet.cpp:10:
In file included from ./flowWorkspace_types.h:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
    for (const pb::Range range : gate_pb.mrg().ranges()) {
                         ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
    for (const pb::Range range : gate_pb.mrg().ranges()) {
         ^~~~~~~~~~~~~~~~~~~~~~~
                         &
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cpp11.cpp -o cpp11.o
In file included from cpp11.cpp:4:
In file included from ./flowWorkspace_types.h:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
    for (const pb::Range range : gate_pb.mrg().ranges()) {
                         ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
    for (const pb::Range range : gate_pb.mrg().ranges()) {
         ^~~~~~~~~~~~~~~~~~~~~~~
                         &
In file included from cpp11.cpp:4:
In file included from ./flowWorkspace_types.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include/cpp11/declarations.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include/cpp11.hpp:10:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
  delete obj;
  ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include/cpp11/external_pointer.hpp:20:42: note: in instantiation of function template specialization 'cpp11::default_deleter<cytolib::CytoFrameView>' requested here
template <typename T, void Deleter(T*) = default_deleter<T>>
                                         ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from cytoframeAPI.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
    for (const pb::Range range : gate_pb.mrg().ranges()) {
                         ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
    for (const pb::Range range : gate_pb.mrg().ranges()) {
         ^~~~~~~~~~~~~~~~~~~~~~~
                         &
In file included from cytoframeAPI.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include/cpp11.hpp:10:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
  delete obj;
  ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include/cpp11/external_pointer.hpp:20:42: note: in instantiation of function template specialization 'cpp11::default_deleter<cytolib::CytoFrameView>' requested here
template <typename T, void Deleter(T*) = default_deleter<T>>
                                         ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cytosetAPI.cpp -o cytosetAPI.o
In file included from cytosetAPI.cpp:2:
In file included from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
    for (const pb::Range range : gate_pb.mrg().ranges()) {
                         ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
    for (const pb::Range range : gate_pb.mrg().ranges()) {
         ^~~~~~~~~~~~~~~~~~~~~~~
                         &
In file included from cytosetAPI.cpp:2:
In file included from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include/cpp11.hpp:10:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
  delete obj;
  ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include/cpp11/external_pointer.hpp:20:42: note: in instantiation of function template specialization 'cpp11::default_deleter<cytolib::CytoFrameView>' requested here
template <typename T, void Deleter(T*) = default_deleter<T>>
                                         ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c getDescendants.cpp -o getDescendants.o
In file included from getDescendants.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
    for (const pb::Range range : gate_pb.mrg().ranges()) {
                         ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
    for (const pb::Range range : gate_pb.mrg().ranges()) {
         ^~~~~~~~~~~~~~~~~~~~~~~
                         &
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c getPopStats.cpp -o getPopStats.o
In file included from getPopStats.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
    for (const pb::Range range : gate_pb.mrg().ranges()) {
                         ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
    for (const pb::Range range : gate_pb.mrg().ranges()) {
         ^~~~~~~~~~~~~~~~~~~~~~~
                         &
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from getSingleCellExpression.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
    for (const pb::Range range : gate_pb.mrg().ranges()) {
                         ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
    for (const pb::Range range : gate_pb.mrg().ranges()) {
         ^~~~~~~~~~~~~~~~~~~~~~~
                         &
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5_error_r_handler.cpp -o h5_error_r_handler.o
In file included from h5_error_r_handler.cpp:8:
In file included from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
    for (const pb::Range range : gate_pb.mrg().ranges()) {
                         ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
    for (const pb::Range range : gate_pb.mrg().ranges()) {
         ^~~~~~~~~~~~~~~~~~~~~~~
                         &
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c setCounts.cpp -o setCounts.o
In file included from setCounts.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
    for (const pb::Range range : gate_pb.mrg().ranges()) {
                         ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
    for (const pb::Range range : gate_pb.mrg().ranges()) {
         ^~~~~~~~~~~~~~~~~~~~~~~
                         &
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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")'.

/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 25 | PASS 1663 ]

══ Skipped tests (25) ══════════════════════════════════════════════════════════
• On Mac (2): ???, ???
• 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 25 | PASS 1663 ]
> 
> # 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 
 82.342   9.994 137.770 

Example timings

flowWorkspace.Rcheck/flowWorkspace-Ex.timings

nameusersystemelapsed
GatingHierarchy-class0.0000.0000.001
GatingSet-class0.0010.0000.000
GatingSet-methods0.0000.0000.001
GatingSetList-class0.0010.0010.001
asinh_Gml20.0010.0010.001
asinhtGml2_trans0.0020.0010.003
booleanFilter-class0.0020.0010.002
cf_append_cols2.7180.0524.147
compensate000
convert2.7200.0494.217
convert_legacy000
estimateLogicle0.0000.0000.001
extract_cluster_pop_name_from_node000
flow_breaks2.5320.0373.863
flowjo_biexp0.0010.0000.002
flowjo_biexp_trans2.4660.0333.786
flowjo_fasinh000
flowjo_fasinh_trans0.0010.0010.001
flowjo_log_trans0.0000.0010.002
gh_copy_gate0.0850.0140.156
gh_get_compensations000
gh_get_transformations000
gh_pop_get_data0.0000.0000.001
gh_pop_get_descendants0.0160.0020.028
gh_pop_get_indices0.0010.0000.000
gh_pop_move0.0410.0070.073
gh_pop_set_indices0.1640.0770.356
gh_pop_set_xml_count0.0000.0000.001
gs_check_redundant_nodes0.0000.0000.001
gs_get_pop_paths0.0000.0010.003
gs_get_singlecell_expression000
gs_plot_diff_tree000
gs_plot_pop_count_cv0.0000.0010.003
gs_pop_add0.0000.0010.005
gs_pop_get_children0.0000.0010.000
gs_pop_get_count_fast0.0000.0010.000
gs_pop_get_gate000
gs_pop_get_stats0.0000.0000.001
gs_pop_set_gate000
gs_pop_set_name000
gs_pop_set_visibility0.0010.0000.003
gs_remove_redundant_channels000
gs_remove_redundant_nodes0.0000.0010.000
gs_split_by_channels000
gs_split_by_tree000
gs_update_channels0.0000.0000.001
keyword-mutators2.8190.0604.387
keyword0.0000.0010.000
logicleGml2_trans0.0010.0010.004
logicle_trans0.0010.0000.001
loglevel000
logtGml2_trans0.0000.0000.001
markernames0.0000.0010.000
plot-methods0.0000.0000.001
prettyAxis000
rotate_gate0.0000.0010.000
sampleNames0.0000.0000.003
save_cytoset0.0000.0000.001
save_gs0.0000.0010.000
scale_gate0.0000.0000.002
shift_gate000
swap_data_cols2.4770.0343.838
transform0.0000.0000.001
transform_gate0.0000.0000.001
transformerList0.0320.0030.054