Evan Biederstedt
| Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/scde |
| git_branch: devel |
| git_last_commit: 9d12a81 |
| git_last_commit_date: 2024-10-29 10:05:08 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-25 11:39 -0500 (Mon, 25 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4349 |
| 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 1852/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scde 2.35.0 (landing page) Evan Biederstedt
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
|
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. |
| Package: scde |
| Version: 2.35.0 |
| 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_2.35.0.tar.gz |
| StartedAt: 2024-11-25 01:57:15 -0500 (Mon, 25 Nov 2024) |
| EndedAt: 2024-11-25 02:02:57 -0500 (Mon, 25 Nov 2024) |
| EllapsedTime: 342.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scde.Rcheck |
| Warnings: 3 |
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### Running command:
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### /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_2.35.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scde.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scde/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scde’ version ‘2.35.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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-3.21-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 code 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 whether 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 ... NOTE
checkRd: (-1) pagoda.gene.clusters.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.gene.clusters.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.gene.clusters.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.gene.clusters.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.gene.clusters.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.gene.clusters.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.top.aspects.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.top.aspects.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.top.aspects.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.top.aspects.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.varnorm.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.varnorm.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.varnorm.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.varnorm.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.varnorm.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.varnorm.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.varnorm.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pagoda.varnorm.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) scde.browse.diffexp.Rd:24: Lost braces; missing escapes or markup?
24 | \item{geneLookupURL}{The URL that will be used to construct links to view more information on gene names. By default (if can't guess the organism) the links will forward to ENSEMBL site search, using \code{geneLookupURL = "http://useast.ensembl.org/Multi/Search/Results?q = {0}"}. The "{0}" in the end will be substituted with the gene name. For instance, to link to GeneCards, use \code{"http://www.genecards.org/cgi-bin/carddisp.pl?gene = {0}"}.}
| ^
checkRd: (-1) scde.expression.difference.Rd:36-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) scde.expression.difference.Rd:37: Lost braces
37 | \item{ce} { conservative estimate of expression-fold change (equals to the min(abs(c(lb, ub))), or 0 if the CI crosses the 0}
| ^
checkRd: (-1) scde.expression.difference.Rd:37: Lost braces; missing escapes or markup?
37 | \item{ce} { conservative estimate of expression-fold change (equals to the min(abs(c(lb, ub))), or 0 if the CI crosses the 0}
| ^
checkRd: (-1) scde.expression.difference.Rd:38: Lost braces
38 | \item{Z} { uncorrected Z-score of expression difference}
| ^
checkRd: (-1) scde.expression.difference.Rd:38: Lost braces; missing escapes or markup?
38 | \item{Z} { uncorrected Z-score of expression difference}
| ^
checkRd: (-1) scde.expression.difference.Rd:39: Lost braces
39 | \item{cZ} {expression difference Z-score corrected for multiple hypothesis testing using Holm procedure}
| ^
checkRd: (-1) scde.expression.difference.Rd:39: Lost braces; missing escapes or markup?
39 | \item{cZ} {expression difference Z-score corrected for multiple hypothesis testing using Holm procedure}
| ^
* 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/4.5-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 25.162 0.235 25.48
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/scde.Rcheck/00check.log’
for details.
scde.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scde
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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 -lpthread -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/4.5-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)
scde.Rcheck/scde-Ex.timings
| name | user | system | elapsed | |
| bwpca | 0.001 | 0.001 | 0.002 | |
| clean.counts | 0.070 | 0.012 | 0.082 | |
| clean.gos | 0 | 0 | 0 | |
| knn.error.models | 0.086 | 0.016 | 0.103 | |
| pagoda.cluster.cells | 0.256 | 0.030 | 0.308 | |
| pagoda.effective.cells | 0.055 | 0.015 | 0.071 | |
| pagoda.gene.clusters | 0.060 | 0.015 | 0.075 | |
| pagoda.pathway.wPCA | 0.243 | 0.011 | 0.255 | |
| pagoda.reduce.loading.redundancy | 0.059 | 0.017 | 0.076 | |
| pagoda.reduce.redundancy | 0.057 | 0.016 | 0.073 | |
| pagoda.subtract.aspect | 0.056 | 0.013 | 0.068 | |
| pagoda.top.aspects | 0.057 | 0.017 | 0.074 | |
| pagoda.varnorm | 0.051 | 0.011 | 0.061 | |
| pagoda.view.aspects | 0.056 | 0.015 | 0.073 | |
| scde.browse.diffexp | 0.039 | 0.020 | 0.059 | |
| scde.error.models | 0.035 | 0.010 | 0.045 | |
| scde.expression.difference | 0.036 | 0.010 | 0.046 | |
| scde.expression.magnitude | 0.055 | 0.017 | 0.072 | |
| scde.expression.prior | 0.163 | 0.041 | 0.205 | |
| scde.failure.probability | 0.555 | 0.052 | 0.608 | |
| scde.fit.models.to.reference | 0.034 | 0.013 | 0.047 | |
| scde.posteriors | 25.162 | 0.235 | 25.480 | |
| scde.test.gene.expression.difference | 0.383 | 0.065 | 0.464 | |
| show.app | 0 | 0 | 0 | |
| winsorize.matrix | 0.000 | 0.000 | 0.001 | |