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BioC 3.5: CHECK report for scde on tokay2

This page was generated on 2017-08-16 13:25:07 -0400 (Wed, 16 Aug 2017).

Package 1188/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scde 2.4.1
Jean Fan
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/scde
Last Changed Rev: 129423 / Revision: 131943
Last Changed Date: 2017-05-05 15:32:27 -0400 (Fri, 05 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: scde
Version: 2.4.1
Command: rm -rf scde.buildbin-libdir scde.Rcheck && mkdir scde.buildbin-libdir scde.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scde.buildbin-libdir scde_2.4.1.tar.gz >scde.Rcheck\00install.out 2>&1 && cp scde.Rcheck\00install.out scde-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=scde.buildbin-libdir --install="check:scde-install.out" --force-multiarch --no-vignettes --timings scde_2.4.1.tar.gz
StartedAt: 2017-08-16 02:45:50 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:52:54 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 423.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: scde.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf scde.buildbin-libdir scde.Rcheck && mkdir scde.buildbin-libdir scde.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scde.buildbin-libdir scde_2.4.1.tar.gz >scde.Rcheck\00install.out 2>&1 && cp scde.Rcheck\00install.out scde-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=scde.buildbin-libdir --install="check:scde-install.out" --force-multiarch --no-vignettes --timings scde_2.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/scde.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scde/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scde' version '2.4.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/scde.buildbin-libdir/scde/libs/i386/scde.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'diffexp.Rmd', 'pagoda.Rmd'
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
scde.posteriors 78.71   0.38    79.1
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
scde.posteriors 81.63   0.25   81.88
* checking PDF version of manual ... OK
* DONE

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


scde.Rcheck/00install.out:


install for i386

* installing *source* package 'scde' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c bwpca.cpp -o bwpca.o
bwpca.cpp: In function 'void set_random_matrix(arma::mat&, arma::mat&)':
bwpca.cpp:23:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<target.n_rows;j++) {
                  ^
bwpca.cpp:27:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<target.n_cols;i++) {
                  ^
bwpca.cpp:30:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int j=0;j<target.n_rows;j++) {
                      ^
bwpca.cpp: In function 'void set_random_matrices(arma::mat&, arma::mat&, arma::mat&, arma::mat&)':
bwpca.cpp:40:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<target1.n_rows;j++) {
                  ^
bwpca.cpp:44:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<target1.n_cols;i++) {
                  ^
bwpca.cpp:47:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int j=0;j<target1.n_rows;j++) {
                      ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c jpmatLogBoot.cpp -o jpmatLogBoot.o
jpmatLogBoot.cpp: In function 'SEXPREC* logBootPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
jpmatLogBoot.cpp:200:24: warning: unused variable 'maxv' [-Wunused-variable]
                 double maxv=nbp.max(maxij);
                        ^
jpmatLogBoot.cpp: In function 'SEXPREC* logBootBatchPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
jpmatLogBoot.cpp:443:10: warning: unused variable 'maxv' [-Wunused-variable]
   double maxv=nbp.max(maxij);
          ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c matSlideMult.cpp -o matSlideMult.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pagoda.cpp -o pagoda.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scde.dll tmp.def bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/scde.buildbin-libdir/scde/libs/i386
** 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

install for x64

* installing *source* package 'scde' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c bwpca.cpp -o bwpca.o
bwpca.cpp: In function 'void set_random_matrix(arma::mat&, arma::mat&)':
bwpca.cpp:23:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<target.n_rows;j++) {
                  ^
bwpca.cpp:27:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<target.n_cols;i++) {
                  ^
bwpca.cpp:30:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int j=0;j<target.n_rows;j++) {
                      ^
bwpca.cpp: In function 'void set_random_matrices(arma::mat&, arma::mat&, arma::mat&, arma::mat&)':
bwpca.cpp:40:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<target1.n_rows;j++) {
                  ^
bwpca.cpp:44:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<target1.n_cols;i++) {
                  ^
bwpca.cpp:47:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int j=0;j<target1.n_rows;j++) {
                      ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c jpmatLogBoot.cpp -o jpmatLogBoot.o
jpmatLogBoot.cpp: In function 'SEXPREC* logBootPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
jpmatLogBoot.cpp:200:24: warning: unused variable 'maxv' [-Wunused-variable]
                 double maxv=nbp.max(maxij);
                        ^
jpmatLogBoot.cpp: In function 'SEXPREC* logBootBatchPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
jpmatLogBoot.cpp:443:10: warning: unused variable 'maxv' [-Wunused-variable]
   double maxv=nbp.max(maxij);
          ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c matSlideMult.cpp -o matSlideMult.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pagoda.cpp -o pagoda.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scde.dll tmp.def bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/scde.buildbin-libdir/scde/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scde' as scde_2.4.1.zip
* DONE (scde)

scde.Rcheck/examples_i386/scde-Ex.timings:

nameusersystemelapsed
bwpca0.160.000.16
clean.counts0.410.010.42
clean.gos000
knn.error.models0.280.000.29
pagoda.cluster.cells0.240.080.31
pagoda.effective.cells0.250.050.29
pagoda.gene.clusters0.260.010.29
pagoda.pathway.wPCA0.100.020.11
pagoda.reduce.loading.redundancy0.110.010.12
pagoda.reduce.redundancy0.230.050.28
pagoda.subtract.aspect0.080.030.11
pagoda.top.aspects0.280.000.28
pagoda.varnorm0.130.000.13
pagoda.view.aspects0.260.000.26
scde.browse.diffexp0.060.020.08
scde.error.models0.040.040.08
scde.expression.difference0.200.020.22
scde.expression.magnitude0.140.030.17
scde.expression.prior1.120.021.16
scde.failure.probability1.140.071.21
scde.fit.models.to.reference0.040.020.05
scde.posteriors78.71 0.3879.10
scde.test.gene.expression.difference1.360.101.48
show.app000
winsorize.matrix000

scde.Rcheck/examples_x64/scde-Ex.timings:

nameusersystemelapsed
bwpca0.010.000.03
clean.counts0.780.020.79
clean.gos000
knn.error.models0.110.050.16
pagoda.cluster.cells0.490.060.55
pagoda.effective.cells0.120.040.17
pagoda.gene.clusters0.500.020.52
pagoda.pathway.wPCA0.500.020.51
pagoda.reduce.loading.redundancy0.450.010.47
pagoda.reduce.redundancy0.470.010.48
pagoda.subtract.aspect0.460.030.49
pagoda.top.aspects0.460.000.46
pagoda.varnorm0.440.020.46
pagoda.view.aspects0.500.020.51
scde.browse.diffexp0.090.000.09
scde.error.models0.10.00.1
scde.expression.difference0.070.010.09
scde.expression.magnitude0.410.030.44
scde.expression.prior1.030.081.11
scde.failure.probability1.220.051.26
scde.fit.models.to.reference0.030.030.06
scde.posteriors81.63 0.2581.88
scde.test.gene.expression.difference1.120.081.20
show.app000
winsorize.matrix000