Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-02-22 11:38:13 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1869/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scde 2.30.0  (landing page)
Evan Biederstedt
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/scde
git_branch: RELEASE_3_18
git_last_commit: 4a9f092
git_last_commit_date: 2023-10-24 10:46:15 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for scde on lconway


To the developers/maintainers of the scde package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scde.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: scde
Version: 2.30.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scde.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scde_2.30.0.tar.gz
StartedAt: 2024-02-21 22:53:33 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 22:56:05 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 151.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: scde.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scde.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scde_2.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/scde.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scde/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scde’ version ‘2.30.0’
* 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 ... WARNING
Found the following significant warnings:
  bwpca.cpp:112:11: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
  bwpca.cpp:129:15: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
  bwpca.cpp:154:19: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
  bwpca.cpp:278:19: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
  pagoda.cpp:56:15: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
  pagoda.cpp:56:23: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
See ‘/Users/biocbuild/bbs-3.18-bioc/meat/scde.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 startup messages can be suppressed ... 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 LazyData ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/scde/libs/scde.so’:
  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 use Fortran I/O
nor system RNGs nor [v]sprintf. 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’
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/diffexp.Rmd’
   ‘vignettes/pagoda.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
scde.posteriors 34.25  0.364  34.758
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/scde.Rcheck/00check.log’
for details.



Installation output

scde.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scde
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘scde’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2  -c bwpca.cpp -o bwpca.o
bwpca.cpp:112:11: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
    totvm %=totvm;
    ~~~~~ ^ ~~~~~
bwpca.cpp:129:15: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
        delta %=delta;
        ~~~~~ ^ ~~~~~
bwpca.cpp:154:19: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
            delta %=delta;
            ~~~~~ ^ ~~~~~
bwpca.cpp:278:19: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
            delta %=delta;
            ~~~~~ ^ ~~~~~
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2  -c matSlideMult.cpp -o matSlideMult.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2  -c pagoda.cpp -o pagoda.o
pagoda.cpp:56:15: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
            ic%=ic; jc%=jc;
            ~~^ ~~
pagoda.cpp:56:23: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
            ic%=ic; jc%=jc;
                    ~~^ ~~
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o scde.so bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -L/usr/lib/ -L. -lpthread -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-scde/00new/scde/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scde)

Tests output


Example timings

scde.Rcheck/scde-Ex.timings

nameusersystemelapsed
bwpca0.0030.0010.006
clean.counts0.1020.0250.138
clean.gos0.0000.0000.001
knn.error.models0.0930.0240.118
pagoda.cluster.cells0.1050.0280.137
pagoda.effective.cells0.0780.0200.098
pagoda.gene.clusters0.0770.0230.100
pagoda.pathway.wPCA0.3290.0260.356
pagoda.reduce.loading.redundancy0.0820.0210.103
pagoda.reduce.redundancy0.0820.0210.103
pagoda.subtract.aspect0.0860.0230.109
pagoda.top.aspects0.0850.0240.109
pagoda.varnorm0.0780.0160.095
pagoda.view.aspects0.0840.0200.105
scde.browse.diffexp0.0540.0220.076
scde.error.models0.0540.0150.070
scde.expression.difference0.0490.0090.057
scde.expression.magnitude0.0780.0200.098
scde.expression.prior0.2120.0560.269
scde.failure.probability0.7110.0800.793
scde.fit.models.to.reference0.0470.0190.065
scde.posteriors34.250 0.36434.758
scde.test.gene.expression.difference0.2660.0550.322
show.app000
winsorize.matrix0.0000.0000.001