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BioC 3.4: CHECK report for openCyto on zin1

This page was generated on 2016-09-21 03:38:38 -0700 (Wed, 21 Sep 2016).

Package 847/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openCyto 1.11.8
Mike Jiang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/openCyto
Last Changed Rev: 120277 / Revision: 121152
Last Changed Date: 2016-08-18 16:21:45 -0700 (Thu, 18 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: openCyto
Version: 1.11.8
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings openCyto_1.11.8.tar.gz
StartedAt: 2016-09-20 10:10:23 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:12:33 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 130.4 seconds
RetCode: 0
Status:  OK 
CheckDir: openCyto.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings openCyto_1.11.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/openCyto.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.11.8’
* 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 ‘openCyto’ can be installed ... OK
* 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 ... NOTE
Foreign function calls to a different package:
  .C("flowClust", ..., PACKAGE = "flowClust")
  .C("flowClustGaussian", ..., PACKAGE = "flowClust")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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’
.flowClustFast: no visible global function definition for ‘exprs’
.flowClustFast: no visible global function definition for ‘detectCores’
.flowClustFast: no visible global function definition for ‘mclapply’
.flowClustFast: no visible global function definition for ‘new’
.flowClustKfast: no visible global function definition for ‘var’
.flowClustKfast: no visible global function definition for ‘box’
.flowClustKfast: no visible global function definition for ‘qf’
.flowClustKfast: no visible global function definition for ‘qchisq’
.flowClustKfast: no visible global function definition for ‘quantile’
.flowClustKfast: no visible global function definition for ‘kmeans’
.flowClustKfast: no visible global function definition for ‘new’
.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’
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 ‘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 ‘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’
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 box callNextMethod collapseDataForGating cov cov.wt
  cutree density detectCores dist dnorm ellipsoidGate embed exprs
  exprs<- extends filterList filters flowSet fsApply gating_args
  gating_method hclust hist isMultiPops kmeans legend lines mclapply
  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", "box", "hist", "legend", "lines",
             "par", "points", "text")
  importFrom("methods", "as", "callNextMethod", "extends", "new",
             "selectMethod")
  importFrom("stats", "cov", "cov.wt", "cutree", "density", "dist",
             "dnorm", "embed", "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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/openCyto.Rcheck/00check.log’
for details.

openCyto.Rcheck/00install.out:

* installing *source* package ‘openCyto’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c misc.cpp -o misc.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c unlockNamespace.c -o unlockNamespace.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o openCyto.so RcppExports.o misc.o unlockNamespace.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/openCyto.Rcheck/openCyto/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (openCyto)

openCyto.Rcheck/openCyto-Ex.timings:

nameusersystemelapsed
add_pop000
flowClust1d0.0040.0000.000
flowClust2d0.0000.0000.001
gating-methods0.0000.0000.001
gatingTemplate-class0.0040.0000.000
getChildren-gatingTemplate-character-method0.0000.0000.001
getGate-gatingTemplate-character-method0.0000.0000.001
getNodes0.0040.0000.000
getParent-gatingTemplate-character-method000
gtMethod-class0.0000.0000.001
gtPopulation-class000
mindensity000
mindensity20.0000.0000.001
names-gtMethod-method0.0000.0000.001
openCyto000
plot-fcFilterList-ANY-method000
plot-gatingTemplate-missing-method0.0000.0000.001
ppMethod-class000
ppMethod-gatingTemplate-character-method000
quantileGate000
tailgate0.0000.0000.001
toggle.helperGates000