CHECK report for flowWorkspace on celaya2
This page was generated on 2020-01-16 13:33:31 -0500 (Thu, 16 Jan 2020).
flowWorkspace 3.35.7
Greg Finak ,Mike Jiang
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/flowWorkspace |
| Branch: master |
| Last Commit: 3e483f84 |
| Last Changed Date: 2019-12-26 16:51:52 -0500 (Thu, 26 Dec 2019) |
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowWorkspace_3.35.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/flowWorkspace.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘3.35.7’
* 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
* checking installed package size ... NOTE
installed size is 31.5Mb
sub-directories of 1Mb or more:
lib 29.5Mb
* 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:
‘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 ... WARNING
realize_view:
function(x, ...)
realize_view.cytoframe:
function(x, filepath)
realize_view:
function(x, ...)
realize_view.cytoset:
function(x, filepath)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.addGatingHierarchies: no visible global function definition for ‘is’
.addGatingHierarchies : <anonymous>: no visible global function
definition for ‘fj_ws_get_keywords’
.addGatingHierarchies : <anonymous>: no visible global function
definition for ‘.cpp_gating’
.addGatingHierarchies : <anonymous>: no visible global function
definition for ‘.cpp_computeGates’
.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_rename_marker: no visible binding for global variable ‘desc’
char2booleanFilter: no visible global function definition for ‘new’
check_comp: no visible global function definition for ‘is’
copy_view.cytoframe: no visible global function definition for ‘new’
copy_view.cytoset: no visible global function definition for ‘new’
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’
flowWorkspace.par.init: no visible global function definition for
‘gray’
flowWorkspace.par.set: no visible global function definition for
‘modifyList’
get_cytoframe_from_cs: no visible global function definition for ‘new’
gh_apply_to_new_fcs: 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’
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_from_fcs: no visible global function definition for
‘new’
load_cytoframe_from_h5: 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’
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’
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-missing: no visible global function definition for
‘kwfilter’
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’
transform,GatingSet: no visible global function definition for ‘is’
transform,GatingSet : <anonymous>: 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:
. .cpp_computeGates .cpp_gating .hasSlot IQR as callNextMethod count
desc extends fj_ws_get_keywords gray is kwdError kwfilter median
modifyList new node obj old openCyto.count parallel percent
sampleName selectMethod validObject xml.count
Consider adding
importFrom("grDevices", "gray")
importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
"is", "new", "selectMethod", "validObject")
importFrom("stats", "IQR", "median")
importFrom("utils", "modifyList")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
checkRd: (7) cytoset.Rd:33: Tag \cr is invalid in a \code block
prepare_Rd: scale_gate.Rd:23-25: Dropping empty section \description
checkRd: (5) scale_gate.Rd:0-59: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'cytoframe.Rd':
‘realize_view’
Missing link or links in documentation object 'cytoset.Rd':
‘realize_view’ ‘cytoframe-class’ ‘cytoframes-class’ ‘filterSet’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘GatingSet’ ‘cf_rename_channel’ ‘cf_rename_marker’ ‘cf_swap_colnames’
‘cs_swap_colnames’ ‘flowData<-’ ‘get_cytoframe_from_cs’
‘gs_cyto_data<-’ ‘gs_get_compensations’ ‘realize_view’
Undocumented S4 classes:
‘cytoframe’ ‘cytoset’
Undocumented S4 methods:
generic 'GatingSet' and siglist 'flowSet,ANY'
generic '[' and siglist 'cytoframe,ANY'
generic '[' and siglist 'cytoset,ANY'
generic '[[' and siglist 'cytoset,ANY'
generic '[[<-' and siglist 'cytoset,ANY,ANY,flowFrame'
generic 'compensate' and siglist 'GatingSet,ANY'
generic 'identifier' and siglist 'cytoset'
generic 'identifier<-' and siglist 'GatingSetList,character'
generic 'identifier<-' and siglist 'cytoset,ANY'
generic 'keyword' and siglist 'cytoframe,character'
generic 'keyword' and siglist 'cytoframe,missing'
generic 'length' and siglist 'GatingSet'
generic 'markernames<-' and siglist 'cytoframe'
generic 'pData<-' and siglist 'cytoset,data.frame'
generic 'phenoData' and siglist 'cytoset'
generic 'phenoData<-' and siglist 'cytoset,ANY'
generic 'sampleNames<-' and siglist 'cytoset,ANY'
generic 'setNode' and siglist 'GatingSet,character,ANY'
generic 'show' and siglist 'cytoset'
generic 'transform' and siglist 'cytoset'
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 ... WARNING
Functions or methods with usage in documentation object '[,GatingSet,ANY-method' but not in code:
‘[’ ‘[[’
Functions or methods with usage in documentation object 'estimateLogicle' but not in code:
‘estimateLogicle’
Functions or methods with usage in documentation object 'length' but not in code:
‘length’
Functions or methods with usage in documentation object 'rotate_gate' but not in code:
‘rotate_gate’
Functions or methods with usage in documentation object 'scale_gate' but not in code:
‘scale_gate’
Functions or methods with usage in documentation object 'shift_gate' but not in code:
‘shift_gate’
Functions or methods with usage in documentation object 'subset' but not in code:
‘subset’
Functions or methods with usage in documentation object 'transform_gate' but not in code:
‘transform_gate’
Codoc mismatches from documentation object 'GatingSet-methods':
GatingSet
Code: function(x, y, ...)
Docs: function(x)
Argument names in code not in docs:
y ...
Codoc mismatches from documentation object 'compensate':
compensate
Code: function(x, spillover, ...)
Docs: function(x, spillover)
Argument names in code not in docs:
...
Codoc mismatches from documentation object 'keyword':
keyword
Code: function(object, keyword, ...)
Docs: function(object, keyword)
Argument names in code not in docs:
...
Codoc mismatches from documentation object 'markernames':
markernames
Code: function(object, ...)
Docs: function(object)
Argument names in code not in docs:
...
colnames
Code: function(x, do.NULL = TRUE, prefix = "col")
Docs: function(object)
Argument names in code not in docs:
x do.NULL prefix
Argument names in docs not in code:
object
Mismatches in argument names:
Position: 1 Code: x Docs: object
colnames<-
Code: function(x, value)
Docs: function(object, value)
Argument names in code not in docs:
x
Argument names in docs not in code:
object
Mismatches in argument names:
Position: 1 Code: x Docs: object
Codoc mismatches from documentation object 'recompute':
recompute
Code: function(x, ...)
Docs: function(x, y = "root", alwaysLoadData = FALSE, ...)
Argument names in docs not in code:
y alwaysLoadData
Mismatches in argument names:
Position: 2 Code: ... Docs: y
Codoc mismatches from documentation object 'transform':
transform
Code: function(_data, ...)
Docs: function(_data, translist, ...)
Argument names in docs not in code:
translist
Mismatches in argument names:
Position: 2 Code: ... Docs: translist
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'GatingSet-methods':
‘GatingSet’
Undocumented arguments in documentation object 'cs_add_sample'
‘cs’ ‘sn’ ‘fr’
Undocumented arguments in documentation object 'cs_get_h5_file_path'
‘x’
Undocumented arguments in documentation object 'cyto_flow_coerce_methods'
‘fr’ ‘...’ ‘cs’ ‘fs’ ‘path’
Undocumented arguments in documentation object 'flowjo_log_trans'
‘n’ ‘equal.space’
Documented arguments not in \usage in documentation object 'flowjo_log_trans':
‘inverse’
Documented arguments not in \usage in documentation object 'gh_apply_to_new_fcs':
‘y’ ‘path’
Undocumented arguments in documentation object 'clone'
‘h5_dir’
Undocumented arguments in documentation object 'gs_cyto_data'
‘...’
Documented arguments not in \usage in documentation object 'gs_cyto_data':
‘inverse.transform’
Objects in \usage without \alias in documentation object 'gs_cyto_data':
‘gs_cyto_data<-’
Undocumented arguments in documentation object 'gs_pop_get_stats_tfilter'
‘x’ ‘...’
Objects in \usage without \alias in documentation object 'identifier-methods':
‘identifier<-’
Objects in \usage without \alias in documentation object 'length':
‘show’
Undocumented arguments in documentation object 'load_cytoframe_from_fcs'
‘text.only’
Documented arguments not in \usage in documentation object 'load_cytoframe_from_fcs':
‘files’
Documented arguments not in \usage in documentation object 'markernames':
‘x’ ‘do.NULL’ ‘prefix’
Objects in \usage without \alias in documentation object 'markernames':
‘colnames’ ‘markernames<-’ ‘colnames<-’
Undocumented arguments in documentation object 'save_gs'
‘gs’
Documented arguments not in \usage in documentation object 'save_gs':
‘G’
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-deprecated-declarations -Wno-unknown-pragmas -Wno-comment
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* 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/4.0/Resources/library/flowWorkspace/libs/flowWorkspace.so’:
Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (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: 7 WARNINGs, 6 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.
Installation output
flowWorkspace.Rcheck/00install.out
Tests output
flowWorkspace.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(flowWorkspace)
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:
vignette("flowWorkspace-Introduction", "flowWorkspace")
>
> test_check("flowWorkspace")
Attaching package: 'dplyr'
The following objects are masked from 'package:data.table':
between, first, last
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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")'.
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1049 | SKIPPED: 7 | WARNINGS: 3 | FAILED: 0 ]
>
> #devtools::test("~/rglab/workspace/flowWorkspace")
> #devtools::check_man()
> # test_file("~/rglab/workspace/flowWorkspace/tests/testthat/test-cytoframe.R")
> # test_file("~/rglab/workspace/flowWorkspace/tests/testthat/test-cytoset.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-archive.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingSetList-testSuite.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")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-parseWorkspace.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-add.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-compensate.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/InternalTestSuite.R")
>
>
> proc.time()
user system elapsed
86.012 18.371 94.628
Example timings
flowWorkspace.Rcheck/flowWorkspace-Ex.timings