Greg Finak
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/flowWorkspace |
| git_branch: devel |
| git_last_commit: 586e9e6 |
| git_last_commit_date: 2024-10-29 09:37:06 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:17 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| 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 742/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowWorkspace 4.19.0 (landing page) Greg Finak
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
|
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: 4.19.0 |
| 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_4.19.0.tar.gz |
| StartedAt: 2024-11-27 22:02:39 -0500 (Wed, 27 Nov 2024) |
| EndedAt: 2024-11-27 22:08:55 -0500 (Wed, 27 Nov 2024) |
| EllapsedTime: 375.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flowWorkspace.Rcheck |
| Warnings: 5 |
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### 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_4.19.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/flowWorkspace.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘4.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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
* checking installed package size ... INFO
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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
booleanFilter-class.Rd: expressionFilter
convert.Rd: flowFrame, flowSet
cytoframe.Rd: exprs, parameters, description, filterResult,
filter-class, %on%, flowSet-class, compensation-class, read.FCS
cytoset.Rd: flowFrame-class
flowjo_log_trans.Rd: logtGml2
gs_plot_pop_count_cv.Rd: barchart
logicleGml2_trans.Rd: logicletGml2
rotate_gate.Rd: ellipsoidGate-class, polygonGate-class
scale_gate.Rd: quadGate-class, rectangleGate-class,
ellipsoidGate-class, polygonGate-class
shift_gate.Rd: ellipsoidGate-class, polygonGate-class
transform_gate.Rd: quadGate-class, rectangleGate-class,
ellipsoidGate-class, polygonGate-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... INFO
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/4.5-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, 6 NOTEs
See
‘/Users/biocbuild/bbs-3.21-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/4.5-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++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/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c R_API.cpp -o R_API.o clang++ -arch x86_64 -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/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o clang++ -arch x86_64 -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/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c R_GatingSet.cpp -o R_GatingSet.o clang++ -arch x86_64 -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/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c cpp11.cpp -o cpp11.o clang++ -arch x86_64 -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/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c cytoframeAPI.cpp -o cytoframeAPI.o clang++ -arch x86_64 -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/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c cytosetAPI.cpp -o cytosetAPI.o clang++ -arch x86_64 -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/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c getDescendants.cpp -o getDescendants.o clang++ -arch x86_64 -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/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c getPopStats.cpp -o getPopStats.o clang++ -arch x86_64 -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/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c getSingleCellExpression.cpp -o getSingleCellExpression.o clang++ -arch x86_64 -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/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c h5_error_r_handler.cpp -o h5_error_r_handler.o clang++ -arch x86_64 -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/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c setCounts.cpp -o setCounts.o clang++ -arch x86_64 -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/4.5-x86_64/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.5-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/4.5-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) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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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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> 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
Loading required package: generics
Attaching package: 'generics'
The following object is masked from 'package:dplyr':
explain
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following object is masked from 'package:flowCore':
normalize
The following object is masked from 'package:dplyr':
combine
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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/4.5-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
52.768 10.546 63.876
flowWorkspace.Rcheck/flowWorkspace-Ex.timings
| name | user | system | elapsed | |
| GatingHierarchy-class | 0 | 0 | 0 | |
| GatingSet-class | 0 | 0 | 0 | |
| GatingSet-methods | 0 | 0 | 0 | |
| GatingSetList-class | 0.000 | 0.001 | 0.001 | |
| asinh_Gml2 | 0.001 | 0.000 | 0.001 | |
| asinhtGml2_trans | 0.002 | 0.001 | 0.002 | |
| booleanFilter-class | 0.002 | 0.000 | 0.001 | |
| cf_append_cols | 1.357 | 0.025 | 1.387 | |
| compensate | 0 | 0 | 0 | |
| convert | 1.321 | 0.028 | 1.352 | |
| 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 | 1.070 | 0.019 | 1.093 | |
| flowjo_biexp | 0.001 | 0.000 | 0.002 | |
| flowjo_biexp_trans | 1.095 | 0.020 | 1.116 | |
| flowjo_fasinh | 0.000 | 0.000 | 0.001 | |
| flowjo_fasinh_trans | 0.001 | 0.000 | 0.001 | |
| flowjo_log_trans | 0.001 | 0.001 | 0.002 | |
| gh_copy_gate | 0.066 | 0.013 | 0.079 | |
| gh_get_compensations | 0.000 | 0.000 | 0.001 | |
| gh_get_transformations | 0.001 | 0.000 | 0.000 | |
| gh_pop_get_data | 0 | 0 | 0 | |
| gh_pop_get_descendants | 0.012 | 0.001 | 0.014 | |
| gh_pop_get_indices | 0 | 0 | 0 | |
| gh_pop_move | 0.032 | 0.006 | 0.038 | |
| gh_pop_set_indices | 0.121 | 0.033 | 0.155 | |
| gh_pop_set_xml_count | 0 | 0 | 0 | |
| gs_check_redundant_nodes | 0 | 0 | 0 | |
| gs_get_pop_paths | 0.000 | 0.000 | 0.001 | |
| gs_get_singlecell_expression | 0 | 0 | 0 | |
| gs_plot_diff_tree | 0 | 0 | 0 | |
| gs_plot_pop_count_cv | 0 | 0 | 0 | |
| gs_pop_add | 0.000 | 0.001 | 0.001 | |
| gs_pop_get_children | 0.001 | 0.000 | 0.000 | |
| gs_pop_get_count_fast | 0.000 | 0.000 | 0.001 | |
| gs_pop_get_gate | 0.000 | 0.000 | 0.001 | |
| gs_pop_get_stats | 0.000 | 0.001 | 0.000 | |
| gs_pop_set_gate | 0 | 0 | 0 | |
| gs_pop_set_name | 0 | 0 | 0 | |
| gs_pop_set_visibility | 0.000 | 0.000 | 0.001 | |
| 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 | 0 | 0 | |
| keyword-mutators | 1.421 | 0.047 | 1.473 | |
| keyword | 0 | 0 | 0 | |
| logicleGml2_trans | 0.001 | 0.000 | 0.001 | |
| logicle_trans | 0.001 | 0.001 | 0.002 | |
| loglevel | 0.000 | 0.000 | 0.001 | |
| logtGml2_trans | 0.001 | 0.001 | 0.001 | |
| markernames | 0 | 0 | 0 | |
| plot-methods | 0 | 0 | 0 | |
| prettyAxis | 0 | 0 | 0 | |
| rotate_gate | 0.000 | 0.001 | 0.001 | |
| sampleNames | 0 | 0 | 0 | |
| save_cytoset | 0 | 0 | 0 | |
| save_gs | 0 | 0 | 0 | |
| scale_gate | 0 | 0 | 0 | |
| shift_gate | 0.000 | 0.000 | 0.001 | |
| swap_data_cols | 1.126 | 0.015 | 1.151 | |
| transform | 0 | 0 | 0 | |
| transform_gate | 0 | 0 | 0 | |
| transformerList | 0.017 | 0.001 | 0.019 | |