openCyto 1.15.0
Mike Jiang
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/openCyto | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings openCyto_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/openCyto.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘openCyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘openCyto’ version ‘1.15.0’
* 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 ‘openCyto’ can be installed ... WARNING
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.6-bioc/meat/openCyto.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘flowWorkspace’
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to ‘parallel’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘flowViz’
All declared Imports should be used.
Unexported objects imported by ':::' calls:
‘flowClust:::.ellipsePoints’ ‘flowStats:::drvkde’
‘flowStats:::warpSetNCDF’ ‘flowWorkspace:::.cpp_addGate’
‘flowWorkspace:::.getAllDescendants’ ‘flowWorkspace:::trimWhiteSpace’
‘lattice:::updateList’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘groupBy’ ‘isCollapse’ ‘ppMethod’ ‘unlockNamespace’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘openCyto/R/pluginFramework.R’:
unlockBinding(methodName, ENV)
unlockBinding(methodName, ENV)
.boundary: no visible global function definition for ‘rectangleGate’
.center_mode: no visible global function definition for ‘density’
.find_peaks: no visible global function definition for ‘density’
.find_peaks: no visible global function definition for ‘points’
.find_valleys: no visible global function definition for ‘density’
.gateToFilterResult: no visible global function definition for ‘exprs’
.gateToFilterResult: no visible global function definition for ‘as’
.gatingTemplate: no visible global function definition for ‘as’
.gatingTemplate: no visible global function definition for ‘new’
.gatingTemplate: no visible binding for global variable ‘pop’
.gatingTemplate: no visible binding for global variable ‘gating_method’
.gatingTemplate: no visible binding for global variable ‘gating_args’
.gatingTemplate: no visible binding for global variable
‘collapseDataForGating’
.gatingTemplate: no visible binding for global variable
‘preprocessing_method’
.gatingTemplate: no visible binding for global variable
‘preprocessing_args’
.gatingTemplate: no visible global function definition for ‘extends’
.gating_adaptor: no visible global function definition for ‘as’
.gating_adaptor: no visible global function definition for ‘na.omit’
.gating_adaptor: no visible global function definition for
‘rectangleGate’
.gating_adaptor: no visible global function definition for ‘filters’
.gating_adaptor: no visible global function definition for ‘extends’
.gating_gtMethod : <anonymous>: no visible global function definition
for ‘extends’
.gating_gtMethod: no visible global function definition for ‘extends’
.gating_refGate : <anonymous>: no visible global function definition
for ‘rectangleGate’
.gating_refGate: no visible global function definition for ‘filterList’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘parent’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘gating_method’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘gating_args’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘collapseDataForGating’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘preprocessing_method’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘preprocessing_args’
.gen_dummy_ref_gate: no visible binding for global variable ‘parent’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘pop’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘gating_method’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘gating_args’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘collapseDataForGating’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘preprocessing_method’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘preprocessing_args’
.gen_refGate: no visible binding for global variable ‘parent’
.gen_refGate: no visible binding for global variable ‘gating_args’
.getEllipse: no visible global function definition for ‘qf’
.getEllipse: no visible global function definition for ‘qchisq’
.getEllipseGate: no visible global function definition for ‘qf’
.getEllipseGate: no visible global function definition for ‘qchisq’
.getEllipseGate: no visible global function definition for
‘polygonGate’
.getEllipseGate: no visible global function definition for
‘ellipsoidGate’
.getFullPath: no visible binding for global variable ‘parent’
.improvedMindensity: no visible global function definition for
‘density’
.improvedMindensity: no visible global function definition for
‘smooth.spline’
.improvedMindensity: no visible global function definition for
‘predict’
.improvedMindensity: no visible global function definition for ‘median’
.improvedMindensity : .plots: no visible global function definition for
‘abline’
.improvedMindensity: no visible global function definition for ‘par’
.improvedMindensity: no visible global function definition for ‘abline’
.plotTree: no visible global function definition for ‘as’
.plotTree: no visible global function definition for ‘par’
.plotTree: no visible global function definition for ‘legend’
.preprocess_csv: no visible binding for global variable ‘pop’
.preprocess_csv: no visible binding for global variable ‘parent’
.preprocess_csv: no visible binding for global variable ‘gating_method’
.preprocess_csv: no visible binding for global variable ‘gating_args’
.preprocess_csv: no visible binding for global variable
‘collapseDataForGating’
.preprocess_csv: no visible binding for global variable
‘preprocessing_method’
.preprocess_csv: no visible binding for global variable
‘preprocessing_args’
.preprocess_row: no visible binding for global variable ‘pop’
.preprocess_row: no visible binding for global variable ‘gating_method’
.preprocess_row: no visible binding for global variable ‘parent’
.preprocess_row: no visible binding for global variable ‘gating_args’
.preprocess_row: no visible binding for global variable
‘preprocessing_method’
.preprocess_row: no visible binding for global variable
‘preprocessing_args’
.prior_flowClust1d: no visible global function definition for ‘fsApply’
.prior_flowClust1d : <anonymous>: no visible global function definition
for ‘exprs’
.prior_flowClust1d: no visible global function definition for ‘hclust’
.prior_flowClust1d: no visible global function definition for ‘dist’
.prior_flowClust1d: no visible global function definition for ‘median’
.prior_flowClust1d: no visible global function definition for ‘cutree’
.prior_flowClust1d: no visible global function definition for ‘kmeans’
.prior_flowClust1d : <anonymous>: no visible global function definition
for ‘sd’
.prior_flowClust1d: no visible binding for global variable ‘var’
.prior_flowClust1d : <anonymous>: no visible global function definition
for ‘embed’
.prior_flowClust1d : <anonymous>: no visible binding for global
variable ‘var’
.prior_kmeans : <anonymous>: no visible global function definition for
‘exprs’
.prior_kmeans : <anonymous>: no visible global function definition for
‘kmeans’
.prior_kmeans : <anonymous> : <anonymous>: no visible global function
definition for ‘cov’
.prior_kmeans : <anonymous>: no visible global function definition for
‘dist’
.prior_kmeans: no visible binding for global variable ‘cov.wt’
.quadGate2rectangleGates: no visible global function definition for
‘rectangleGate’
.quadGate2rectangleGates: no visible global function definition for
‘filters’
.quantile_flowClust : cdf_target : <anonymous>: no visible global
function definition for ‘pt’
.quantile_flowClust : cdf_target: no visible global function definition
for ‘weighted.mean’
.quantile_flowClust: no visible global function definition for
‘uniroot’
.read.FCS.csv: no visible global function definition for ‘new’
.read.FCS.csv: no visible global function definition for ‘parameters<-’
.read.flowSet.csv: no visible global function definition for ‘flowSet’
.standardize_flowFrame: no visible global function definition for
‘exprs’
.standardize_flowFrame: no visible global function definition for
‘exprs<-’
.standardize_flowset: no visible global function definition for
‘fsApply’
.standardize_flowset: no visible global function definition for
‘flowSet’
.standardize_flowset: no visible global function definition for ‘as’
.tailgate: no visible global function definition for ‘exprs’
.tailgate: no visible global function definition for ‘exprs<-’
.tailgate: no visible global function definition for ‘rectangleGate’
.truncate_flowframe: no visible global function definition for
‘rectangleGate’
.truncate_flowframe: no visible global function definition for ‘Subset’
.truncate_flowset: no visible global function definition for
‘rectangleGate’
.truncate_flowset: no visible global function definition for ‘Subset’
.unique_check_alias: no visible binding for global variable ‘parent’
as.data.table.gatingTemplate : <anonymous>: no visible global function
definition for ‘extends’
fcEllipsoidGate: no visible global function definition for ‘as’
fcFilterList : <anonymous>: no visible global function definition for
‘extends’
fcFilterList: no visible global function definition for ‘filterList’
fcFilterList: no visible global function definition for ‘as’
fcPolygonGate: no visible global function definition for ‘as’
fcRectangleGate: no visible global function definition for ‘as’
fcTree: no visible global function definition for ‘as’
fcTree: no visible global function definition for ‘new’
flowClust.1d: no visible global function definition for ‘exprs’
flowClust.1d: no visible global function definition for ‘rectangleGate’
flowClust.1d: no visible global function definition for ‘abline’
flowClust.1d: no visible global function definition for ‘rainbow’
flowClust.1d: no visible global function definition for ‘lines’
flowClust.2d: no visible global function definition for ‘new’
flowClust.2d: no visible global function definition for ‘dist’
flowClust.2d: no visible global function definition for ‘qchisq’
flowClust.2d: no visible global function definition for ‘exprs’
flowClust.2d: no visible global function definition for ‘sd’
flowClust.2d: no visible global function definition for ‘polygonGate’
flowClust.2d: no visible global function definition for ‘lines’
flowClust.2d: no visible global function definition for ‘points’
gate_flowClust_1d: no visible global function definition for ‘exprs’
gate_flowClust_1d: no visible global function definition for
‘rectangleGate’
gate_flowClust_1d: no visible global function definition for ‘abline’
gate_flowClust_1d: no visible global function definition for ‘rainbow’
gate_flowClust_1d: no visible global function definition for ‘lines’
gate_flowClust_2d: no visible global function definition for ‘new’
gate_flowClust_2d: no visible global function definition for ‘dist’
gate_flowClust_2d: no visible global function definition for ‘qchisq’
gate_flowClust_2d: no visible global function definition for ‘exprs’
gate_flowClust_2d: no visible global function definition for ‘sd’
gate_flowClust_2d: no visible global function definition for
‘polygonGate’
gate_flowClust_2d: no visible global function definition for ‘lines’
gate_flowClust_2d: no visible global function definition for ‘points’
gate_mindensity: no visible global function definition for ‘exprs’
gate_mindensity: no visible global function definition for
‘rectangleGate’
gate_mindensity2: no visible global function definition for ‘exprs’
gate_mindensity2: no visible global function definition for
‘rectangleGate’
gate_quad_sequential : <anonymous>: no visible global function
definition for ‘exprs’
gate_quad_sequential: no visible global function definition for
‘filter’
gate_quad_sequential: no visible global function definition for ‘as’
gate_quad_sequential : <anonymous>: no visible global function
definition for ‘rectangleGate’
gate_quad_sequential: no visible global function definition for
‘filters’
gate_quad_tmix: no visible global function definition for ‘filter’
gate_quad_tmix: no visible global function definition for ‘as’
gate_quad_tmix: no visible global function definition for ‘polygonGate’
gate_quad_tmix: no visible global function definition for ‘filters’
gate_quantile: no visible global function definition for ‘exprs’
gate_quantile: no visible global function definition for ‘quantile’
gate_quantile: no visible global function definition for ‘hist’
gate_quantile: no visible global function definition for ‘density’
gate_quantile: no visible global function definition for ‘abline’
gate_quantile: no visible global function definition for ‘text’
gate_quantile: no visible global function definition for
‘rectangleGate’
gate_tail: no visible global function definition for ‘exprs’
gate_tail: no visible global function definition for ‘rectangleGate’
mindensity: no visible global function definition for ‘exprs’
mindensity: no visible global function definition for ‘rectangleGate’
mindensity2: no visible global function definition for ‘exprs’
mindensity2: no visible global function definition for ‘rectangleGate’
ocRectRefGate: no visible global function definition for ‘as’
quadGate.seq : <anonymous>: no visible global function definition for
‘exprs’
quadGate.seq: no visible global function definition for ‘filter’
quadGate.seq: no visible global function definition for ‘as’
quadGate.seq : <anonymous>: no visible global function definition for
‘rectangleGate’
quadGate.seq: no visible global function definition for ‘filters’
quadGate.tmix: no visible global function definition for ‘filter’
quadGate.tmix: no visible global function definition for ‘as’
quadGate.tmix: no visible global function definition for ‘polygonGate’
quadGate.tmix: no visible global function definition for ‘filters’
quantileGate: no visible global function definition for ‘exprs’
quantileGate: no visible global function definition for ‘quantile’
quantileGate: no visible global function definition for ‘hist’
quantileGate: no visible global function definition for ‘density’
quantileGate: no visible global function definition for ‘abline’
quantileGate: no visible global function definition for ‘text’
quantileGate: no visible global function definition for ‘rectangleGate’
tailgate: no visible global function definition for ‘exprs’
tailgate: no visible global function definition for ‘rectangleGate’
add,GatingHierarchy-ocRectRefGate: no visible global function
definition for ‘selectMethod’
coerce,ncdfFlowList-flowFrame: no visible global function definition
for ‘selectMethod’
coerce,ncdfFlowSet-flowFrame: no visible global function definition for
‘fsApply’
coerce,ncdfFlowSet-flowFrame : <anonymous>: no visible global function
definition for ‘exprs’
coerce,ncdfFlowSet-flowFrame: no visible global function definition for
‘new’
gatingTemplate,character: no visible binding for global variable
‘isMultiPops’
gatingTemplate,character: no visible binding for global variable ‘pop’
gatingTemplate,character: no visible binding for global variable
‘gating_args’
plot,fcFilterList-ANY : <anonymous>: no visible global function
definition for ‘dnorm’
plot,fcFilterList-ANY: no visible global function definition for ‘hist’
plot,fcFilterList-ANY: no visible global function definition for
‘exprs’
plot,fcFilterList-ANY: no visible global function definition for
‘lines’
plot,fcFilterList-ANY: no visible global function definition for
‘rainbow’
plot,fcFilterList-ANY: no visible global function definition for
‘abline’
show,fcFilter: no visible global function definition for
‘callNextMethod’
Undefined global functions or variables:
Subset abline as callNextMethod collapseDataForGating cov cov.wt
cutree density dist dnorm ellipsoidGate embed exprs exprs<- extends
filter filterList filters flowSet fsApply gating_args gating_method
hclust hist isMultiPops kmeans legend lines median na.omit new par
parameters<- parent points polygonGate pop predict preprocessing_args
preprocessing_method pt qchisq qf quantile rainbow rectangleGate sd
selectMethod smooth.spline text uniroot var weighted.mean
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "abline", "hist", "legend", "lines", "par",
"points", "text")
importFrom("methods", "as", "callNextMethod", "extends", "new",
"selectMethod")
importFrom("stats", "cov", "cov.wt", "cutree", "density", "dist",
"dnorm", "embed", "filter", "hclust", "kmeans", "median",
"na.omit", "predict", "pt", "qchisq", "qf", "quantile",
"sd", "smooth.spline", "uniroot", "var", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* 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 ... NOTE
'library' or 'require' call not declared from: ‘ggcyto’
* 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: 1 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/openCyto.Rcheck/00check.log’
for details.
* installing *source* package ‘openCyto’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c misc.cpp -o misc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c unlockNamespace.c -o unlockNamespace.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o openCyto.so RcppExports.o misc.o unlockNamespace.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/openCyto.Rcheck/openCyto/libs
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (openCyto)