BioC 3.5: CHECK report for scde on oaxaca

Package: scde

Version: 2.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scde_2.3.0.tar.gz

StartedAt: 2017-03-04 08:47:02 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 08:50:31 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 209.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: scde.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scde_2.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/scde.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scde/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scde’ version ‘2.3.0’
* 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 ‘scde’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
  ‘Rook’ ‘extRemes’ ‘rjson’
'library' or 'require' calls in package code:
  ‘Rook’ ‘extRemes’ ‘rjson’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘tools:::httpdPort’
  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
File ‘scde/R/functions.R’:
  .onAttach calls:
    require(Rook)
    require(rjson)
    message(e)

Package startup functions should not change the search path.
Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

FLXMRglmC: no visible global function definition for ‘new’
FLXMRglmCf: no visible global function definition for ‘new’
FLXMRnb2glm : glmrefit: no visible binding for global variable
  ‘glm.fit’
FLXMRnb2glm: no visible global function definition for ‘new’
FLXMRnb2glm : <anonymous>: no visible global function definition for
  ‘coef’
FLXMRnb2glmC: no visible global function definition for ‘new’
FLXMRnb2gth: no visible global function definition for ‘new’
FLXMRnb2gth : <anonymous>: no visible global function definition for
  ‘coef’
FLXMRnb2gth : <anonymous>: no visible global function definition for
  ‘glm’
FLXMRnb2gth : <anonymous>: no visible global function definition for
  ‘poisson’
FLXMRnb2gth : <anonymous>: no visible global function definition for
  ‘weighted.mean’
FLXMRnb2gth : <anonymous>: no visible global function definition for
  ‘quantile’
FLXMRnb2gth : <anonymous>: no visible global function definition for
  ‘nlminb’
FLXMRnb2gthC: no visible global function definition for ‘new’
FLXPmultinomW: no visible global function definition for ‘new’
ViewDiff: no visible global function definition for ‘new’
ViewPagodaApp: no visible global function definition for ‘new’
c.view.pathways: no visible global function definition for ‘as.dist’
c.view.pathways: no visible global function definition for ‘cor’
c.view.pathways: no visible global function definition for
  ‘installed.packages’
c.view.pathways: no visible global function definition for ‘quantile’
c.view.pathways: no visible global function definition for
  ‘colorRampPalette’
c.view.pathways: no visible global function definition for
  ‘as.dendrogram’
calculate.crossfit.models : <anonymous>: no visible global function
  definition for ‘combn’
calculate.crossfit.models : <anonymous> : t.pairs.panel.hist: no
  visible global function definition for ‘par’
calculate.crossfit.models : <anonymous> : t.pairs.panel.hist: no
  visible global function definition for ‘hist’
calculate.crossfit.models : <anonymous> : t.pairs.panel.hist: no
  visible global function definition for ‘rect’
calculate.crossfit.models : <anonymous> :
  t.pairs.smoothScatter.spearman: no visible global function definition
  for ‘smoothScatter’
calculate.crossfit.models : <anonymous> :
  t.pairs.smoothScatter.spearman: no visible global function definition
  for ‘legend’
calculate.crossfit.models : <anonymous> :
  t.pairs.smoothScatter.spearman: no visible global function definition
  for ‘cor’
calculate.crossfit.models : <anonymous> : t.panel.component.scatter: no
  visible global function definition for ‘points’
calculate.crossfit.models : <anonymous> : t.panel.component.scatter: no
  visible global function definition for ‘densCols’
calculate.crossfit.models : <anonymous> : t.panel.component.scatter: no
  visible global function definition for ‘colorRampPalette’
calculate.crossfit.models : <anonymous> : t.panel.component.scatter: no
  visible global function definition for ‘legend’
calculate.crossfit.models : <anonymous> : t.panel.component.scatter: no
  visible global function definition for ‘cor’
calculate.crossfit.models : <anonymous>: no visible global function
  definition for ‘dev.off’
calculate.go.enrichment: no visible binding for global variable
  ‘go.env’
calculate.go.enrichment: no visible global function definition for
  ‘na.omit’
calculate.go.enrichment: no visible global function definition for
  ‘phyper’
calculate.go.enrichment: no visible global function definition for
  ‘qnorm’
calculate.go.enrichment : <anonymous>: no visible global function
  definition for ‘na.omit’
calculate.individual.models : <anonymous>: no visible global function
  definition for ‘combn’
calculate.individual.models : <anonymous>: no visible global function
  definition for ‘pdf’
calculate.individual.models : <anonymous>: no visible global function
  definition for ‘layout’
calculate.individual.models : <anonymous>: no visible global function
  definition for ‘par’
calculate.individual.models : <anonymous>: no visible global function
  definition for ‘dev.off’
clean.gos: no visible global function definition for
  ‘installed.packages’
clean.gos: no visible binding for global variable ‘GO.db’
col2hex : <anonymous>: no visible global function definition for
  ‘col2rgb’
collapse.aspect.clusters : <anonymous>: no visible binding for global
  variable ‘var’
collapse.aspect.clusters : <anonymous>: no visible global function
  definition for ‘cor’
collapse.aspect.clusters : <anonymous>: no visible global function
  definition for ‘var’
collapse.aspect.clusters : <anonymous>: no visible global function
  definition for ‘rnorm’
collapse.aspect.clusters : <anonymous>: no visible binding for global
  variable ‘sd’
custom.glm.fit: no visible global function definition for ‘gaussian’
custom.glm.fit: no visible global function definition for ‘quantile’
estimate.signal.prior: no visible global function definition for
  ‘quantile’
estimate.signal.prior: no visible global function definition for
  ‘density’
estimate.signal.prior: no visible global function definition for ‘par’
estimate.signal.prior: no visible global function definition for
  ‘abline’
fit.nb2gth.mixture.model: no visible global function definition for
  ‘median’
get.component.model.lik: no visible global function definition for
  ‘terms’
get.component.model.lik: no visible global function definition for
  ‘model.frame’
get.component.model.lik: no visible global function definition for
  ‘delete.response’
get.component.model.lik: no visible global function definition for
  ‘model.matrix’
get.component.model.loglik: no visible global function definition for
  ‘terms’
get.component.model.loglik: no visible global function definition for
  ‘model.frame’
get.component.model.loglik: no visible global function definition for
  ‘delete.response’
get.component.model.loglik: no visible global function definition for
  ‘model.matrix’
get.concomitant.prob: no visible global function definition for ‘terms’
get.concomitant.prob: no visible global function definition for
  ‘model.frame’
get.concomitant.prob: no visible global function definition for
  ‘delete.response’
get.concomitant.prob: no visible global function definition for
  ‘model.matrix’
get.exp.posterior.samples : <anonymous> : <anonymous>: no visible
  global function definition for ‘approxfun’
get.exp.posterior.samples : <anonymous> : <anonymous>: no visible
  global function definition for ‘runif’
get.exp.sample : <anonymous>: no visible global function definition for
  ‘approxfun’
get.exp.sample : <anonymous>: no visible global function definition for
  ‘runif’
get.fpm.estimates: no visible global function definition for ‘approx’
get.ratio.posterior.Z.score: no visible global function definition for
  ‘qnorm’
glm.nb.fit: no visible binding for global variable ‘nobs’
knn.error.models : <anonymous>: no visible global function definition
  for ‘installed.packages’
knn.error.models : <anonymous> : <anonymous>: no visible global
  function definition for ‘median’
knn.error.models : <anonymous>: no visible global function definition
  for ‘pdf’
knn.error.models : <anonymous>: no visible global function definition
  for ‘layout’
knn.error.models : <anonymous>: no visible global function definition
  for ‘par’
knn.error.models : <anonymous>: no visible global function definition
  for ‘dev.off’
knn.error.models : <anonymous> : <anonymous>: no visible global
  function definition for ‘dev.off’
make.pagoda.app: no visible global function definition for ‘quantile’
make.pagoda.app: no visible global function definition for ‘hclust’
make.pagoda.app: no visible global function definition for ‘dist’
make.pagoda.app: no visible binding for global variable ‘sd’
make.pagoda.app: no visible global function definition for
  ‘colorRampPalette’
mc.stepFlexmix : <anonymous>: no visible global function definition for
  ‘is’
my.heatmap2: no visible binding for global variable ‘dist’
my.heatmap2: no visible binding for global variable ‘hclust’
my.heatmap2 : <anonymous>: no visible global function definition for
  ‘reorder’
my.heatmap2: no visible global function definition for ‘as.dendrogram’
my.heatmap2: no visible global function definition for
  ‘order.dendrogram’
my.heatmap2: no visible binding for global variable ‘sd’
my.heatmap2: no visible global function definition for ‘dev.size’
my.heatmap2: no visible global function definition for ‘lcm’
my.heatmap2: no visible global function definition for ‘par’
my.heatmap2: no visible global function definition for ‘layout’
my.heatmap2: no visible global function definition for ‘image’
my.heatmap2: no visible global function definition for ‘axis’
my.heatmap2: no visible global function definition for ‘mtext’
my.heatmap2: no visible global function definition for ‘abline’
negbin.th: no visible global function definition for ‘make.link’
one.sided.test.id: no visible global function definition for ‘layout’
one.sided.test.id: no visible global function definition for ‘par’
one.sided.test.id: no visible global function definition for ‘rainbow’
one.sided.test.id : <anonymous>: no visible global function definition
  for ‘lines’
one.sided.test.id: no visible global function definition for ‘legend’
one.sided.test.id: no visible global function definition for ‘na.omit’
one.sided.test.id: no visible global function definition for ‘axis’
one.sided.test.id: no visible global function definition for ‘mtext’
one.sided.test.id: no visible global function definition for ‘polygon’
one.sided.test.id: no visible global function definition for ‘abline’
one.sided.test.id: no visible global function definition for ‘box’
one.sided.test.id: no visible global function definition for ‘qnorm’
pagoda.cluster.cells: no visible global function definition for
  ‘hclust’
pagoda.cluster.cells: no visible global function definition for
  ‘installed.packages’
pagoda.effective.cells: no visible global function definition for
  ‘nlminb’
pagoda.gene.clusters: no visible global function definition for
  ‘installed.packages’
pagoda.gene.clusters: no visible global function definition for
  ‘as.dist’
pagoda.gene.clusters: no visible global function definition for ‘cor’
pagoda.gene.clusters: no visible global function definition for
  ‘cutree’
pagoda.gene.clusters : <anonymous> : <anonymous>: no visible global
  function definition for ‘cor’
pagoda.gene.clusters : <anonymous>: no visible global function
  definition for ‘rnorm’
pagoda.gene.clusters : <anonymous>: no visible global function
  definition for ‘installed.packages’
pagoda.gene.clusters : <anonymous>: no visible global function
  definition for ‘as.dist’
pagoda.gene.clusters : <anonymous>: no visible global function
  definition for ‘cor’
pagoda.gene.clusters : <anonymous>: no visible global function
  definition for ‘cutree’
pagoda.gene.clusters: no visible global function definition for ‘lm’
pagoda.gene.clusters: no visible global function definition for ‘par’
pagoda.gene.clusters: no visible global function definition for
  ‘smoothScatter’
pagoda.gene.clusters: no visible global function definition for
  ‘points’
pagoda.gene.clusters: no visible global function definition for ‘lines’
pagoda.gene.clusters: no visible global function definition for
  ‘legend’
pagoda.gene.clusters: no visible global function definition for
  ‘abline’
pagoda.pathway.wPCA : <anonymous> : <anonymous>: no visible global
  function definition for ‘cor’
pagoda.pathway.wPCA : <anonymous>: no visible global function
  definition for ‘sd’
pagoda.pathway.wPCA : <anonymous>: no visible binding for global
  variable ‘sd’
pagoda.reduce.loading.redundancy: no visible global function definition
  for ‘cor’
pagoda.reduce.loading.redundancy: no visible global function definition
  for ‘as.dist’
pagoda.reduce.loading.redundancy: no visible global function definition
  for ‘installed.packages’
pagoda.reduce.loading.redundancy: no visible global function definition
  for ‘cutree’
pagoda.reduce.loading.redundancy: no visible global function definition
  for ‘colors’
pagoda.reduce.redundancy: no visible global function definition for
  ‘cor’
pagoda.reduce.redundancy: no visible global function definition for
  ‘installed.packages’
pagoda.reduce.redundancy: no visible global function definition for
  ‘cutree’
pagoda.reduce.redundancy: no visible global function definition for
  ‘colors’
pagoda.reduce.redundancy: no visible binding for global variable ‘var’
pagoda.top.aspects: no visible global function definition for ‘qnorm’
pagoda.top.aspects : <anonymous>: no visible global function definition
  for ‘sd’
pagoda.top.aspects : qWishartSpikeFixed: no visible global function
  definition for ‘qnorm’
pagoda.top.aspects : pWishartMaxFixed: no visible global function
  definition for ‘pgamma’
pagoda.top.aspects: no visible global function definition for ‘pnorm’
pagoda.top.aspects: no visible binding for global variable ‘varst’
pagoda.top.aspects: no visible global function definition for ‘par’
pagoda.top.aspects: no visible global function definition for
  ‘colorRampPalette’
pagoda.top.aspects: no visible global function definition for ‘lines’
pagoda.top.aspects: no visible global function definition for ‘points’
pagoda.top.aspects: no visible binding for global variable ‘var’
pagoda.top.aspects: no visible global function definition for ‘qchisq’
pagoda.varnorm: no visible global function definition for ‘data’
pagoda.varnorm: no visible binding for global variable ‘scde.edff’
pagoda.varnorm : <anonymous>: no visible global function definition for
  ‘ppois’
pagoda.varnorm : <anonymous>: no visible global function definition for
  ‘pnbinom’
pagoda.varnorm : <anonymous> : <anonymous>: no visible global function
  definition for ‘ppois’
pagoda.varnorm : <anonymous> : <anonymous>: no visible global function
  definition for ‘pnbinom’
pagoda.varnorm : <anonymous>: no visible binding for global variable
  ‘scde.edff’
pagoda.varnorm: no visible global function definition for ‘par’
pagoda.varnorm: no visible global function definition for
  ‘smoothScatter’
pagoda.varnorm: no visible global function definition for ‘lines’
pagoda.varnorm: no visible global function definition for ‘points’
pagoda.varnorm: no visible global function definition for ‘pchisq’
pagoda.varnorm: no visible global function definition for ‘p.adjust’
pagoda.varnorm: no visible binding for global variable ‘min.sd’
pagoda.varnorm: no visible global function definition for ‘qchisq’
pagoda.varnorm: no visible global function definition for ‘abline’
pagoda.varnorm : wsu: no visible global function definition for ‘qnorm’
pagoda.varnorm : <anonymous>: no visible global function definition for
  ‘qnorm’
pagoda.view.aspects: no visible global function definition for ‘hclust’
pagoda.view.aspects: no visible global function definition for ‘dist’
pagoda.view.aspects: no visible binding for global variable ‘var’
pairs.extended: no visible binding for global variable ‘points’
pairs.extended : textPanel: no visible global function definition for
  ‘text’
pairs.extended : localAxis: no visible global function definition for
  ‘Axis’
pairs.extended: no visible global function definition for ‘par’
pairs.extended: no visible global function definition for ‘box’
pairs.extended: no visible global function definition for ‘strwidth’
pairs.extended: no visible global function definition for ‘mtext’
pairs.panel.cor: no visible global function definition for ‘par’
pairs.panel.cor: no visible global function definition for ‘cor’
pairs.panel.cor: no visible global function definition for ‘strwidth’
pairs.panel.cor: no visible global function definition for ‘text’
pairs.panel.hist: no visible global function definition for ‘par’
pairs.panel.hist: no visible global function definition for ‘hist’
pairs.panel.hist: no visible global function definition for ‘rect’
pairs.panel.scatter: no visible global function definition for ‘points’
pairs.panel.scatter: no visible global function definition for
  ‘densCols’
pairs.panel.scatter: no visible global function definition for
  ‘colorRampPalette’
pairs.panel.smoothScatter: no visible global function definition for
  ‘smoothScatter’
papply: no visible binding for global variable ‘n’
pathway.pc.correlation.distance: no visible global function definition
  for ‘pt’
pathway.pc.correlation.distance: no visible global function definition
  for ‘qt’
plot.nb2.mixture.fit: no visible global function definition for
  ‘layout’
plot.nb2.mixture.fit: no visible global function definition for ‘par’
plot.nb2.mixture.fit: no visible global function definition for
  ‘smoothScatter’
plot.nb2.mixture.fit: no visible global function definition for
  ‘points’
plot.nb2.mixture.fit: no visible global function definition for
  ‘densCols’
plot.nb2.mixture.fit: no visible global function definition for
  ‘colorRampPalette’
plot.nb2.mixture.fit: no visible global function definition for ‘lines’
plot.nb2.mixture.fit: no visible global function definition for
  ‘qnbinom’
plot.nb2.mixture.fit: no visible global function definition for
  ‘legend’
plot.nb2.mixture.fit: no visible global function definition for
  ‘na.omit’
plot.nb2.mixture.fit: no visible global function definition for ‘terms’
plot.nb2.mixture.fit: no visible global function definition for
  ‘model.frame’
plot.nb2.mixture.fit: no visible global function definition for
  ‘delete.response’
plot.nb2.mixture.fit: no visible global function definition for
  ‘model.matrix’
plot.nb2.mixture.fit: no visible global function definition for
  ‘abline’
plot.nb2.mixture.fit: no visible global function definition for
  ‘barplot’
plot.nb2.mixture.fit: no visible global function definition for ‘box’
plot.nb2.mixture.fit: no visible global function definition for
  ‘dev.off’
quick.distribution.summary: no visible global function definition for
  ‘qnorm’
quick.distribution.summary: no visible global function definition for
  ‘p.adjust’
quick.distribution.summary: no visible global function definition for
  ‘pnorm’
scde.browse.diffexp: no visible global function definition for
  ‘browseURL’
scde.expression.difference: no visible global function definition for
  ‘fisher.test’
scde.expression.prior: no visible global function definition for
  ‘quantile’
scde.expression.prior: no visible global function definition for
  ‘density’
scde.expression.prior: no visible global function definition for ‘par’
scde.expression.prior: no visible global function definition for
  ‘abline’
scde.fit.models.to.reference: no visible global function definition for
  ‘pdf’
scde.fit.models.to.reference: no visible global function definition for
  ‘layout’
scde.fit.models.to.reference: no visible global function definition for
  ‘par’
scde.fit.models.to.reference: no visible global function definition for
  ‘dev.off’
scde.test.gene.expression.difference: no visible global function
  definition for ‘fisher.test’
scde.test.gene.expression.difference: no visible global function
  definition for ‘layout’
scde.test.gene.expression.difference: no visible global function
  definition for ‘par’
scde.test.gene.expression.difference: no visible global function
  definition for ‘rainbow’
scde.test.gene.expression.difference : <anonymous>: no visible global
  function definition for ‘lines’
scde.test.gene.expression.difference : <anonymous>: no visible global
  function definition for ‘rgb’
scde.test.gene.expression.difference: no visible global function
  definition for ‘na.omit’
scde.test.gene.expression.difference: no visible global function
  definition for ‘axis’
scde.test.gene.expression.difference: no visible global function
  definition for ‘mtext’
scde.test.gene.expression.difference: no visible global function
  definition for ‘abline’
scde.test.gene.expression.difference: no visible global function
  definition for ‘polygon’
scde.test.gene.expression.difference: no visible global function
  definition for ‘rgb’
scde.test.gene.expression.difference: no visible global function
  definition for ‘legend’
show.app: no visible global function definition for ‘browseURL’
t.view.pathways: no visible global function definition for ‘na.omit’
t.view.pathways: no visible global function definition for ‘as.dist’
t.view.pathways: no visible global function definition for ‘cor’
t.view.pathways: no visible global function definition for
  ‘installed.packages’
t.view.pathways: no visible global function definition for ‘quantile’
t.view.pathways: no visible global function definition for
  ‘colorRampPalette’
t.view.pathways: no visible global function definition for
  ‘as.dendrogram’
view.aspects: no visible global function definition for ‘quantile’
view.aspects: no visible global function definition for
  ‘colorRampPalette’
view.aspects: no visible binding for global variable ‘var’
view.aspects: no visible global function definition for ‘as.dendrogram’
FLXmstep,FLXMRglmC: no visible binding for global variable ‘glm.fit’
FLXmstep,FLXMRglmC : <anonymous>: no visible global function definition
  for ‘as’
FLXmstep,FLXMRglmCf: no visible binding for global variable ‘glm.fit’
FLXmstep,FLXMRnb2glmC: no visible binding for global variable ‘glm.fit’
FLXmstep,FLXMRnb2glmC : <anonymous>: no visible global function
  definition for ‘as’
FLXmstep,FLXMRnb2gthC: no visible binding for global variable ‘glm.fit’
FLXmstep,FLXMRnb2gthC : <anonymous>: no visible global function
  definition for ‘as’
Undefined global functions or variables:
  Axis GO.db abline approx approxfun as as.dendrogram as.dist axis
  barplot box browseURL coef col2rgb colorRampPalette colors combn cor
  cutree data delete.response densCols density dev.off dev.size dist
  fisher.test gaussian glm glm.fit go.env hclust hist image
  installed.packages is layout lcm legend lines lm make.link median
  min.sd model.frame model.matrix mtext n na.omit new nlminb nobs
  order.dendrogram p.adjust par pchisq pdf pgamma phyper pnbinom pnorm
  points poisson polygon ppois pt qchisq qnbinom qnorm qt quantile
  rainbow rect reorder rgb rnorm runif scde.edff sd smoothScatter
  strwidth terms text var varst weighted.mean
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "colors",
             "densCols", "dev.off", "dev.size", "pdf", "rainbow", "rgb")
  importFrom("graphics", "Axis", "abline", "axis", "barplot", "box",
             "hist", "image", "layout", "lcm", "legend", "lines",
             "mtext", "par", "points", "polygon", "rect",
             "smoothScatter", "strwidth", "text")
  importFrom("methods", "as", "is", "new")
  importFrom("stats", "approx", "approxfun", "as.dendrogram", "as.dist",
             "coef", "cor", "cutree", "delete.response", "density",
             "dist", "fisher.test", "gaussian", "glm", "glm.fit",
             "hclust", "lm", "make.link", "median", "model.frame",
             "model.matrix", "na.omit", "nlminb", "nobs",
             "order.dendrogram", "p.adjust", "pchisq", "pgamma",
             "phyper", "pnbinom", "pnorm", "poisson", "ppois", "pt",
             "qchisq", "qnbinom", "qnorm", "qt", "quantile", "reorder",
             "rnorm", "runif", "sd", "terms", "var", "weighted.mean")
  importFrom("utils", "browseURL", "combn", "data", "installed.packages")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘scde/libs/scde.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘jpmatLogBoot.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘jpmatLogBoot.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘diffexp.Rmd’, ‘pagoda.Rmd’
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
scde.posteriors 39.12  0.345  42.838
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/scde.Rcheck/00check.log’
for details.

* installing *source* package ‘scde’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c bwpca.cpp -o bwpca.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c jpmatLogBoot.cpp -o jpmatLogBoot.o
jpmatLogBoot.cpp:200:24: warning: unused variable 'maxv' [-Wunused-variable]
                double maxv=nbp.max(maxij);
                       ^
jpmatLogBoot.cpp:443:10: warning: unused variable 'maxv' [-Wunused-variable]
                double maxv=nbp.max(maxij);
                       ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c matSlideMult.cpp -o matSlideMult.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c pagoda.cpp -o pagoda.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 scde.so bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/scde.Rcheck/scde/libs
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scde)

name	user	system	elapsed
bwpca	0.035	0.004	0.039
clean.counts	0.321	0.015	0.335
clean.gos	0.001	0.000	0.000
knn.error.models	0.253	0.012	0.266
pagoda.cluster.cells	0.100	0.004	0.105
pagoda.effective.cells	0.282	0.006	0.289
pagoda.gene.clusters	0.101	0.005	0.108
pagoda.pathway.wPCA	0.104	0.005	0.110
pagoda.reduce.loading.redundancy	0.098	0.005	0.102
pagoda.reduce.redundancy	0.278	0.005	0.283
pagoda.subtract.aspect	0.078	0.004	0.082
pagoda.top.aspects	0.300	0.009	0.310
pagoda.varnorm	0.100	0.004	0.104
pagoda.view.aspects	0.315	0.007	0.321
scde.browse.diffexp	0.069	0.014	0.083
scde.error.models	0.065	0.012	0.076
scde.expression.difference	0.062	0.009	0.070
scde.expression.magnitude	0.266	0.016	0.282
scde.expression.prior	0.686	0.049	0.736
scde.failure.probability	0.770	0.048	0.818
scde.fit.models.to.reference	0.050	0.009	0.058
scde.posteriors	39.120	0.345	42.838
scde.test.gene.expression.difference	0.764	0.074	1.047
show.app	0	0	0
winsorize.matrix	0.001	0.000	0.001