Evan Biederstedt
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/scde |
| git_branch: RELEASE_3_17 |
| git_last_commit: 4c3b2db |
| git_last_commit_date: 2023-05-01 20:11:38 -0400 (Mon, 01 May 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:37 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1834/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scde 2.28.2 (landing page) Evan Biederstedt
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 2.28.2 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scde.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings scde_2.28.2.tar.gz |
| StartedAt: 2023-10-16 06:27:42 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 06:30:21 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 158.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scde.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scde.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings scde_2.28.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/scde.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scde/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scde' version '2.28.2'
* 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
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/scde/libs/x64/scde.dll':
Found '_assert', possibly from 'assert' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 47.73 0.39 37.86
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc/meat/scde.Rcheck/00check.log'
for details.
scde.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL scde
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'scde' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bwpca.cpp -o bwpca.o
bwpca.cpp: In function 'void set_random_matrix(arma::mat&, arma::mat&)':
bwpca.cpp:24:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
24 | for(int j=0;j<target.n_rows;j++) {
| ~^~~~~~~~~~~~~~
bwpca.cpp:31:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
31 | for(int i=0;i<target.n_cols;i++) {
| ~^~~~~~~~~~~~~~
bwpca.cpp:34:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
34 | 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:44:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
44 | for(int j=0;j<target1.n_rows;j++) {
| ~^~~~~~~~~~~~~~~
bwpca.cpp:51:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
51 | for(int i=0;i<target1.n_cols;i++) {
| ~^~~~~~~~~~~~~~~
bwpca.cpp:54:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
54 | for(int j=0;j<target1.n_rows;j++) {
| ~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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]
200 | double maxv=nbp.max(maxij);
| ^~~~
jpmatLogBoot.cpp: In function 'SEXPREC* logBootBatchPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
jpmatLogBoot.cpp:443:24: warning: unused variable 'maxv' [-Wunused-variable]
443 | double maxv=nbp.max(maxij);
| ^~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matSlideMult.cpp -o matSlideMult.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pagoda.cpp -o pagoda.o
g++ -std=gnu++17 -shared -s -static-libgcc -o scde.dll tmp.def bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -L/usr/lib/ -L. -lpthread -lm -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-scde/00new/scde/libs/x64
** 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
** 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 | 0 | 0 | |
| clean.counts | 0.06 | 0.02 | 0.08 | |
| clean.gos | 0 | 0 | 0 | |
| knn.error.models | 0.07 | 0.03 | 0.09 | |
| pagoda.cluster.cells | 0.09 | 0.00 | 0.09 | |
| pagoda.effective.cells | 0.05 | 0.02 | 0.07 | |
| pagoda.gene.clusters | 0.06 | 0.00 | 0.06 | |
| pagoda.pathway.wPCA | 0.26 | 0.00 | 0.27 | |
| pagoda.reduce.loading.redundancy | 0.05 | 0.01 | 0.06 | |
| pagoda.reduce.redundancy | 0.06 | 0.00 | 0.07 | |
| pagoda.subtract.aspect | 0.05 | 0.02 | 0.06 | |
| pagoda.top.aspects | 0.06 | 0.01 | 0.08 | |
| pagoda.varnorm | 0.05 | 0.02 | 0.06 | |
| pagoda.view.aspects | 0.06 | 0.00 | 0.06 | |
| scde.browse.diffexp | 0.05 | 0.00 | 0.05 | |
| scde.error.models | 0.03 | 0.01 | 0.04 | |
| scde.expression.difference | 0.03 | 0.03 | 0.07 | |
| scde.expression.magnitude | 0.05 | 0.02 | 0.06 | |
| scde.expression.prior | 0.40 | 0.05 | 0.45 | |
| scde.failure.probability | 0.49 | 0.04 | 0.53 | |
| scde.fit.models.to.reference | 0.06 | 0.02 | 0.08 | |
| scde.posteriors | 47.73 | 0.39 | 37.86 | |
| scde.test.gene.expression.difference | 0.30 | 0.06 | 0.47 | |
| show.app | 0 | 0 | 0 | |
| winsorize.matrix | 0 | 0 | 0 | |