Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-28 11:11:47 -0500 (Fri, 28 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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 merida1


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? here 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 676/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 4.7.0  (landing page)
Greg Finak , Mike Jiang
Snapshot Date: 2022-01-27 13:55:17 -0500 (Thu, 27 Jan 2022)
git_url: https://git.bioconductor.org/packages/flowWorkspace
git_branch: master
git_last_commit: d3559f6
git_last_commit_date: 2021-10-26 11:59:12 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: flowWorkspace
Version: 4.7.0
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_4.7.0.tar.gz
StartedAt: 2022-01-28 01:07:20 -0500 (Fri, 28 Jan 2022)
EndedAt: 2022-01-28 01:14:13 -0500 (Fri, 28 Jan 2022)
EllapsedTime: 412.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowWorkspace.Rcheck
Warnings: 3

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_4.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/flowWorkspace.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘4.7.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘RBGL’ ‘RProtoBufLib’ ‘ggplot2’ ‘grDevices’ ‘graphics’ ‘utils’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  print.cytoctx
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.computeCV : <anonymous>: no visible binding for global variable
  ‘xml.count’
.computeCV : <anonymous>: no visible binding for global variable
  ‘openCyto.count’
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for ‘IQR’
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
.computeCV_gh : <anonymous>: no visible global function definition for
  ‘IQR’
.computeCV_gh : <anonymous>: no visible global function definition for
  ‘median’
.graph_handler : asGraphNEL: no visible global function definition for
  ‘new’
.graph_handler : asGraphNEL: no visible global function definition for
  ‘validObject’
.load_legacy: no visible global function definition for ‘is’
.load_legacy: no visible global function definition for ‘new’
.load_legacy: no visible global function definition for ‘.hasSlot’
.load_legacy : <anonymous>: no visible global function definition for
  ‘is’
.mergeGates : <anonymous>: no visible global function definition for
  ‘extends’
.preprocessMap: no visible binding for global variable ‘old’
.preprocessMap: no visible binding for global variable ‘.’
GatingSetList: no visible global function definition for ‘as’
GatingSetList: no visible global function definition for ‘validObject’
booleanFilter: no visible global function definition for ‘new’
booleanFilter: no visible global function definition for ‘is’
cf_append_cols: no visible global function definition for ‘new’
cf_flush_meta: no visible global function definition for ‘is’
cf_get_uri: no visible global function definition for ‘is’
cf_keyword_delete: no visible global function definition for ‘is’
cf_keyword_insert: no visible global function definition for ‘is’
cf_keyword_rename: no visible global function definition for ‘is’
cf_keyword_rename: no visible binding for global variable ‘na_idx’
cf_keyword_set: no visible global function definition for ‘is’
cf_load_meta: no visible global function definition for ‘is’
cf_lock: no visible global function definition for ‘is’
cf_rename_channel: no visible global function definition for ‘is’
cf_rename_marker: no visible global function definition for ‘is’
cf_rename_marker: no visible binding for global variable ‘desc’
cf_scale_time_channel: no visible global function definition for ‘is’
cf_unlock: no visible global function definition for ‘is’
cf_write_disk: no visible global function definition for ‘is’
char2booleanFilter: no visible global function definition for ‘new’
check_comp: no visible global function definition for ‘is’
convert_backend: no visible binding for global variable ‘output’
copy_view.cytoframe: no visible global function definition for ‘new’
copy_view.cytoset: no visible global function definition for ‘new’
cs_add_cytoframe: no visible global function definition for ‘is’
cs_get_cytoframe: no visible global function definition for ‘is’
cs_get_cytoframe: no visible global function definition for ‘new’
cs_get_uri: no visible global function definition for ‘is’
cs_keyword_delete: no visible global function definition for ‘is’
cs_keyword_insert: no visible global function definition for ‘is’
cs_keyword_rename: no visible global function definition for ‘is’
cs_keyword_rename : <anonymous>: no visible binding for global variable
  ‘keys’
cs_keyword_set: no visible global function definition for ‘is’
cs_set_cytoframe: no visible global function definition for ‘is’
cytoframe_to_flowFrame: no visible global function definition for ‘as’
cytoset: no visible global function definition for ‘new’
cytoset_to_flowSet: no visible global function definition for ‘as’
get_cytoframe_from_cs: no visible global function definition for ‘is’
get_cytoframe_from_cs: no visible global function definition for ‘new’
gh_apply_to_cs: no visible global function definition for ‘new’
gh_pop_compare_stats: no visible binding for global variable ‘node’
gh_pop_get_count: no visible binding for global variable ‘count’
gh_pop_get_proportion: no visible binding for global variable ‘percent’
gh_pop_get_stats_tfilter: no visible global function definition for
  ‘is’
gh_pop_get_stats_tfilter : <anonymous>: no visible binding for global
  variable ‘Population’
gh_pop_set_gate: no visible global function definition for ‘is’
gs_clone: no visible global function definition for ‘new’
gs_copy_tree_only: no visible global function definition for ‘new’
gs_get_singlecell_expression: no visible global function definition for
  ‘is’
gs_get_singlecell_expression: no visible binding for global variable
  ‘parallel’
gs_pop_add: no visible global function definition for ‘is’
gs_pop_get_count_fast: no visible global function definition for ‘is’
gs_pop_get_count_with_meta: no visible binding for global variable
  ‘sampleName’
gs_pop_get_data: no visible global function definition for ‘new’
gs_pop_set_gate: no visible global function definition for ‘is’
gs_remove_redundant_nodes : <anonymous>: no visible global function
  definition for ‘is’
gslist_to_gs: no visible global function definition for ‘new’
load_cytoframe: no visible global function definition for ‘new’
load_cytoframe_from_fcs: no visible global function definition for
  ‘new’
load_cytoset_from_fcs: no visible global function definition for ‘new’
load_gs: no visible global function definition for ‘new’
load_gslist : <anonymous>: no visible global function definition for
  ‘is’
merge_list_to_gs: no visible global function definition for ‘is’
merge_list_to_gs: no visible global function definition for ‘new’
parse_transformer: no visible global function definition for ‘is’
pop.MFI: no visible binding for global variable ‘desc’
realize_view.cytoframe: no visible global function definition for ‘new’
realize_view.cytoset: no visible global function definition for ‘new’
transformerList: no visible global function definition for ‘is’
transformerList: no visible binding for global variable ‘is’
validitycheck: no visible global function definition for ‘is’
GatingSet,cytoset-ANY: no visible global function definition for ‘new’
Subset,cytoset-filterResultList : <anonymous>: no visible global
  function definition for ‘as’
Subset,cytoset-list: no visible global function definition for ‘is’
[,GatingSet-ANY: no visible global function definition for ‘extends’
[,GatingSet-ANY: no visible global function definition for ‘new’
[,GatingSetList-ANY: no visible global function definition for
  ‘callNextMethod’
[,GatingSetList-ANY: no visible global function definition for ‘as’
[[,GatingSet-character: no visible global function definition for ‘as’
compensate,GatingSet-ANY: no visible global function definition for
  ‘selectMethod’
compensate,cytoset-ANY: no visible global function definition for
  ‘selectMethod’
flowData,GatingSet: no visible binding for global variable ‘obj’
fsApply,cytoset: no visible global function definition for
  ‘callNextMethod’
gs_cyto_data,GatingSet: no visible global function definition for ‘new’
keyword,GatingSetList-character: no visible global function definition
  for ‘selectMethod’
keyword,GatingSetList-missing: no visible global function definition
  for ‘selectMethod’
keyword<-,cytoframe-list: no visible binding for global variable
  ‘kwdError’
pData<-,GatingSetList-data.frame: no visible global function definition
  for ‘callNextMethod’
pData<-,GatingSetList-data.frame: no visible global function definition
  for ‘as’
parameters,cytoframe: no visible global function definition for ‘new’
phenoData,cytoset: no visible global function definition for ‘new’
sampleNames<-,cytoset-ANY: no visible global function definition for
  ‘selectMethod’
setNode,GatingSet-character-ANY: no visible global function definition
  for ‘is’
show,cytoframe: no visible global function definition for
  ‘selectMethod’
transform,GatingSet: no visible global function definition for ‘is’
transform,GatingSet : <anonymous>: no visible global function
  definition for ‘is’
transform,cytoframe: no visible global function definition for ‘is’
transform,cytoset: no visible global function definition for ‘is’
transform,cytoset : <anonymous>: no visible global function definition
  for ‘is’
Undefined global functions or variables:
  . .hasSlot IQR Population as callNextMethod count desc extends is
  keys kwdError median na_idx new node obj old openCyto.count output
  parallel percent sampleName selectMethod validObject xml.count
Consider adding
  importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
             "is", "new", "selectMethod", "validObject")
  importFrom("stats", "IQR", "median")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘gs_clone’ ‘gs_copy_tree_only’
Undocumented S4 methods:
  generic '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 'cf_append_cols'
  ‘ctx’

Undocumented arguments in documentation object 'convert'
  ‘backend’

Undocumented arguments in documentation object 'cs_get_uri'
  ‘x’

Undocumented arguments in documentation object 'cytoctx'
  ‘...’

Undocumented arguments in documentation object 'delete_gs'
  ‘ctx’

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.
S3 methods shown with full name in documentation object 'cytoctx':
  ‘print.cytoctx’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/flowWorkspace/libs/flowWorkspace.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (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 ‘_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. 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: 3 WARNINGs, 8 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/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/4.2/Resources/library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_API.cpp -o R_API.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_GatingSet.cpp -o R_GatingSet.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/flowWorkspace.h:6:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:46:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/XPtr.h:31:5: 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/4.2/Resources/library/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<cytolib::CytoFrameView>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cytoctxAPI.cpp -o cytoctxAPI.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from cytoframeAPI.cpp:3:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:46:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/XPtr.h:31:5: 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/4.2/Resources/library/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<cytolib::CytoFrameView>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cytosetAPI.cpp -o cytosetAPI.o
In file included from cytosetAPI.cpp:2:
In file included from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:46:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/XPtr.h:31:5: 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/4.2/Resources/library/Rcpp/include/Rcpp/XPtr.h:54:26: note: in instantiation of function template specialization 'Rcpp::standard_delete_finalizer<cytolib::CytoFrameView>' requested here
    void Finalizer(T*) = standard_delete_finalizer<T>,
                         ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getDescendants.cpp -o getDescendants.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getPopStats.cpp -o getPopStats.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getSingleCellExpression.cpp -o getSingleCellExpression.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c h5_error_r_handler.cpp -o h5_error_r_handler.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c setCounts.cpp -o setCounts.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoctxAPI.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o /Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib/libsz.a /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib/libaec.a -lz -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/4.2/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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> 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, 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/4.2/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 204 | SKIP 23 | PASS 1659 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Mac (2)
• dir.exists(legacy) is not TRUE (2)
• empty test (2)
• get_default_backend() != "h5" is TRUE (1)
• get_default_backend() != "mem" is TRUE (1)
• get_default_backend() == "mem" is TRUE (13)
• get_default_backend() == "tile" is not TRUE (2)

[ FAIL 0 | WARN 204 | SKIP 23 | PASS 1659 ]
> 
> # 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 
224.998  10.897 237.346 

Example timings

flowWorkspace.Rcheck/flowWorkspace-Ex.timings

nameusersystemelapsed
GatingHierarchy-class0.0000.0000.001
GatingSet-class000
GatingSet-methods0.0000.0010.000
GatingSetList-class0.0010.0000.001
asinh_Gml20.0020.0000.002
asinhtGml2_trans0.0040.0000.004
booleanFilter-class0.0030.0000.003
cf_append_cols1.3630.0701.435
compensate0.0000.0010.001
convert1.3020.0411.357
convert_legacy0.0010.0000.000
estimateLogicle0.0010.0000.000
extract_cluster_pop_name_from_node0.0010.0000.001
flow_breaks0.9020.0220.925
flowjo_biexp0.0020.0000.002
flowjo_biexp_trans0.9220.0280.952
flowjo_fasinh0.0010.0010.000
flowjo_fasinh_trans0.0010.0000.001
flowjo_log_trans0.0010.0010.002
gh_copy_gate0.1400.0210.161
gh_get_compensations0.0010.0000.001
gh_get_transformations0.0010.0000.000
gh_pop_get_data000
gh_pop_get_descendants0.0240.0040.027
gh_pop_get_indices000
gh_pop_move0.0640.0080.073
gh_pop_set_indices0.3300.0930.425
gh_pop_set_xml_count000
gs_check_redundant_nodes000
gs_get_pop_paths000
gs_get_singlecell_expression0.0000.0000.001
gs_plot_diff_tree000
gs_plot_pop_count_cv0.0000.0000.001
gs_pop_add0.0000.0010.001
gs_pop_get_children0.0000.0010.000
gs_pop_get_count_fast000
gs_pop_get_gate0.0000.0010.001
gs_pop_get_stats000
gs_pop_set_gate0.0000.0000.001
gs_pop_set_name000
gs_pop_set_visibility0.0000.0010.000
gs_remove_redundant_channels0.0000.0000.001
gs_remove_redundant_nodes000
gs_split_by_channels000
gs_split_by_tree0.0000.0000.001
gs_update_channels000
keyword-mutators1.2300.0401.272
keyword000
logicleGml2_trans0.0010.0010.001
logicle_trans0.0020.0000.002
loglevel0.0010.0000.000
logtGml2_trans0.0000.0000.001
markernames000
plot-methods000
plotGate-methods-defunct000
prettyAxis000
rotate_gate000
sampleNames000
save_cytoset000
save_gs000
scale_gate000
shift_gate000
swap_data_cols1.1990.0321.233
transform000
transform_gate0.0000.0000.001
transformerList0.0380.0010.039