Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:39:16 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 750/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowWorkspace 4.15.5 (landing page) Greg Finak
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the flowWorkspace package: - 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 Troubleshooting Build Report for more information. - 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. |
Package: flowWorkspace |
Version: 4.15.5 |
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_4.15.5.tar.gz |
StartedAt: 2024-03-27 21:12:54 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 21:17:00 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 246.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: flowWorkspace.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### 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_4.15.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/flowWorkspace.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-apple-darwin20 * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flowWorkspace/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowWorkspace’ version ‘4.15.5’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... OK Not all R platforms support C++17 * 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. 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 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 ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 ... 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 ‘/Users/biocbuild/bbs-3.19-bioc/meat/flowWorkspace.Rcheck/00check.log’ for details.
flowWorkspace.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowWorkspace ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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++17 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_API.cpp -o R_API.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_GatingSet.cpp -o R_GatingSet.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cpp11.cpp -o cpp11.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cytoframeAPI.cpp -o cytoframeAPI.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cytosetAPI.cpp -o cytosetAPI.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c getDescendants.cpp -o getDescendants.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c getPopStats.cpp -o getPopStats.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c getSingleCellExpression.cpp -o getSingleCellExpression.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5_error_r_handler.cpp -o h5_error_r_handler.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c setCounts.cpp -o setCounts.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.4-x86_64/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.4-x86_64/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/4.4-x86_64/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)
flowWorkspace.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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, 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/4.4-x86_64/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): 'test-main.R:10:1', 'test-main.R:10:1' • 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 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 90.930 16.027 108.689
flowWorkspace.Rcheck/flowWorkspace-Ex.timings
name | user | system | elapsed | |
GatingHierarchy-class | 0.000 | 0.001 | 0.001 | |
GatingSet-class | 0.000 | 0.001 | 0.000 | |
GatingSet-methods | 0.000 | 0.001 | 0.000 | |
GatingSetList-class | 0.000 | 0.001 | 0.001 | |
asinh_Gml2 | 0.001 | 0.000 | 0.001 | |
asinhtGml2_trans | 0.003 | 0.000 | 0.004 | |
booleanFilter-class | 0.003 | 0.000 | 0.003 | |
cf_append_cols | 2.445 | 0.065 | 2.535 | |
compensate | 0.000 | 0.000 | 0.001 | |
convert | 2.323 | 0.064 | 2.413 | |
convert_legacy | 0 | 0 | 0 | |
estimateLogicle | 0.000 | 0.000 | 0.001 | |
extract_cluster_pop_name_from_node | 0.000 | 0.000 | 0.001 | |
flow_breaks | 2.028 | 0.046 | 2.101 | |
flowjo_biexp | 0.001 | 0.000 | 0.002 | |
flowjo_biexp_trans | 2.041 | 0.049 | 2.110 | |
flowjo_fasinh | 0 | 0 | 0 | |
flowjo_fasinh_trans | 0.000 | 0.000 | 0.001 | |
flowjo_log_trans | 0.001 | 0.000 | 0.002 | |
gh_copy_gate | 0.095 | 0.017 | 0.114 | |
gh_get_compensations | 0 | 0 | 0 | |
gh_get_transformations | 0 | 0 | 0 | |
gh_pop_get_data | 0 | 0 | 0 | |
gh_pop_get_descendants | 0.018 | 0.004 | 0.023 | |
gh_pop_get_indices | 0.000 | 0.000 | 0.001 | |
gh_pop_move | 0.040 | 0.007 | 0.048 | |
gh_pop_set_indices | 0.196 | 0.054 | 0.254 | |
gh_pop_set_xml_count | 0.000 | 0.001 | 0.000 | |
gs_check_redundant_nodes | 0 | 0 | 0 | |
gs_get_pop_paths | 0.000 | 0.000 | 0.001 | |
gs_get_singlecell_expression | 0.000 | 0.001 | 0.000 | |
gs_plot_diff_tree | 0 | 0 | 0 | |
gs_plot_pop_count_cv | 0.000 | 0.001 | 0.000 | |
gs_pop_add | 0.001 | 0.000 | 0.000 | |
gs_pop_get_children | 0 | 0 | 0 | |
gs_pop_get_count_fast | 0.001 | 0.001 | 0.000 | |
gs_pop_get_gate | 0.000 | 0.000 | 0.001 | |
gs_pop_get_stats | 0.001 | 0.001 | 0.001 | |
gs_pop_set_gate | 0.000 | 0.001 | 0.000 | |
gs_pop_set_name | 0 | 0 | 0 | |
gs_pop_set_visibility | 0.000 | 0.001 | 0.000 | |
gs_remove_redundant_channels | 0 | 0 | 0 | |
gs_remove_redundant_nodes | 0.000 | 0.001 | 0.000 | |
gs_split_by_channels | 0 | 0 | 0 | |
gs_split_by_tree | 0 | 0 | 0 | |
gs_update_channels | 0.000 | 0.001 | 0.000 | |
keyword-mutators | 2.350 | 0.076 | 2.447 | |
keyword | 0 | 0 | 0 | |
logicleGml2_trans | 0.000 | 0.000 | 0.001 | |
logicle_trans | 0.001 | 0.001 | 0.001 | |
loglevel | 0.001 | 0.000 | 0.000 | |
logtGml2_trans | 0.000 | 0.000 | 0.001 | |
markernames | 0.000 | 0.000 | 0.001 | |
plot-methods | 0 | 0 | 0 | |
prettyAxis | 0.000 | 0.001 | 0.000 | |
rotate_gate | 0 | 0 | 0 | |
sampleNames | 0 | 0 | 0 | |
save_cytoset | 0.001 | 0.000 | 0.000 | |
save_gs | 0.000 | 0.000 | 0.001 | |
scale_gate | 0 | 0 | 0 | |
shift_gate | 0.000 | 0.001 | 0.000 | |
swap_data_cols | 1.931 | 0.036 | 1.987 | |
transform | 0.000 | 0.000 | 0.001 | |
transform_gate | 0 | 0 | 0 | |
transformerList | 0.033 | 0.002 | 0.036 | |