scde 2.4.1
Jean Fan
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/scde | | Last Changed Rev: 129423 / Revision: 131943 | | Last Changed Date: 2017-05-05 15:32:27 -0400 (Fri, 05 May 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings scde_2.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/scde.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scde/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scde’ version ‘2.4.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scde’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
data 1.5Mb
libs 3.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
‘Rook’ ‘extRemes’ ‘rjson’
'library' or 'require' calls in package code:
‘Rook’ ‘extRemes’ ‘rjson’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘tools:::httpdPort’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘scde/R/functions.R’:
.onAttach calls:
require(Rook)
require(rjson)
message(e)
Package startup functions should not change the search path.
Package startup functions should use ‘packageStartupMessage’ to
generate messages.
See section ‘Good practice’ in '?.onAttach'.
FLXMRglmC: no visible global function definition for ‘new’
FLXMRglmCf: no visible global function definition for ‘new’
FLXMRnb2glm : glmrefit: no visible binding for global variable
‘glm.fit’
FLXMRnb2glm: no visible global function definition for ‘new’
FLXMRnb2glm : <anonymous>: no visible global function definition for
‘coef’
FLXMRnb2glmC: no visible global function definition for ‘new’
FLXMRnb2gth: no visible global function definition for ‘new’
FLXMRnb2gth : <anonymous>: no visible global function definition for
‘coef’
FLXMRnb2gth : <anonymous>: no visible global function definition for
‘glm’
FLXMRnb2gth : <anonymous>: no visible global function definition for
‘poisson’
FLXMRnb2gth : <anonymous>: no visible global function definition for
‘weighted.mean’
FLXMRnb2gth : <anonymous>: no visible global function definition for
‘quantile’
FLXMRnb2gth : <anonymous>: no visible global function definition for
‘nlminb’
FLXMRnb2gthC: no visible global function definition for ‘new’
FLXPmultinomW: no visible global function definition for ‘new’
ViewDiff: no visible global function definition for ‘new’
ViewPagodaApp: no visible global function definition for ‘new’
c.view.pathways: no visible global function definition for ‘as.dist’
c.view.pathways: no visible global function definition for ‘cor’
c.view.pathways: no visible global function definition for
‘installed.packages’
c.view.pathways: no visible global function definition for ‘quantile’
c.view.pathways: no visible global function definition for
‘colorRampPalette’
c.view.pathways: no visible global function definition for
‘as.dendrogram’
calculate.crossfit.models : <anonymous>: no visible global function
definition for ‘combn’
calculate.crossfit.models : <anonymous> : t.pairs.panel.hist: no
visible global function definition for ‘par’
calculate.crossfit.models : <anonymous> : t.pairs.panel.hist: no
visible global function definition for ‘hist’
calculate.crossfit.models : <anonymous> : t.pairs.panel.hist: no
visible global function definition for ‘rect’
calculate.crossfit.models : <anonymous> :
t.pairs.smoothScatter.spearman: no visible global function definition
for ‘smoothScatter’
calculate.crossfit.models : <anonymous> :
t.pairs.smoothScatter.spearman: no visible global function definition
for ‘legend’
calculate.crossfit.models : <anonymous> :
t.pairs.smoothScatter.spearman: no visible global function definition
for ‘cor’
calculate.crossfit.models : <anonymous> : t.panel.component.scatter: no
visible global function definition for ‘points’
calculate.crossfit.models : <anonymous> : t.panel.component.scatter: no
visible global function definition for ‘densCols’
calculate.crossfit.models : <anonymous> : t.panel.component.scatter: no
visible global function definition for ‘colorRampPalette’
calculate.crossfit.models : <anonymous> : t.panel.component.scatter: no
visible global function definition for ‘legend’
calculate.crossfit.models : <anonymous> : t.panel.component.scatter: no
visible global function definition for ‘cor’
calculate.crossfit.models : <anonymous>: no visible global function
definition for ‘dev.off’
calculate.go.enrichment: no visible binding for global variable
‘go.env’
calculate.go.enrichment: no visible global function definition for
‘na.omit’
calculate.go.enrichment: no visible global function definition for
‘phyper’
calculate.go.enrichment: no visible global function definition for
‘qnorm’
calculate.go.enrichment : <anonymous>: no visible global function
definition for ‘na.omit’
calculate.individual.models : <anonymous>: no visible global function
definition for ‘combn’
calculate.individual.models : <anonymous>: no visible global function
definition for ‘pdf’
calculate.individual.models : <anonymous>: no visible global function
definition for ‘layout’
calculate.individual.models : <anonymous>: no visible global function
definition for ‘par’
calculate.individual.models : <anonymous>: no visible global function
definition for ‘dev.off’
clean.gos: no visible global function definition for
‘installed.packages’
clean.gos: no visible binding for global variable ‘GO.db’
col2hex : <anonymous>: no visible global function definition for
‘col2rgb’
collapse.aspect.clusters : <anonymous>: no visible binding for global
variable ‘var’
collapse.aspect.clusters : <anonymous>: no visible global function
definition for ‘cor’
collapse.aspect.clusters : <anonymous>: no visible global function
definition for ‘var’
collapse.aspect.clusters : <anonymous>: no visible global function
definition for ‘rnorm’
collapse.aspect.clusters : <anonymous>: no visible binding for global
variable ‘sd’
custom.glm.fit: no visible global function definition for ‘gaussian’
custom.glm.fit: no visible global function definition for ‘quantile’
estimate.signal.prior: no visible global function definition for
‘quantile’
estimate.signal.prior: no visible global function definition for
‘density’
estimate.signal.prior: no visible global function definition for ‘par’
estimate.signal.prior: no visible global function definition for
‘abline’
fit.nb2gth.mixture.model: no visible global function definition for
‘median’
get.component.model.lik: no visible global function definition for
‘terms’
get.component.model.lik: no visible global function definition for
‘model.frame’
get.component.model.lik: no visible global function definition for
‘delete.response’
get.component.model.lik: no visible global function definition for
‘model.matrix’
get.component.model.loglik: no visible global function definition for
‘terms’
get.component.model.loglik: no visible global function definition for
‘model.frame’
get.component.model.loglik: no visible global function definition for
‘delete.response’
get.component.model.loglik: no visible global function definition for
‘model.matrix’
get.concomitant.prob: no visible global function definition for ‘terms’
get.concomitant.prob: no visible global function definition for
‘model.frame’
get.concomitant.prob: no visible global function definition for
‘delete.response’
get.concomitant.prob: no visible global function definition for
‘model.matrix’
get.exp.posterior.samples : <anonymous> : <anonymous>: no visible
global function definition for ‘approxfun’
get.exp.posterior.samples : <anonymous> : <anonymous>: no visible
global function definition for ‘runif’
get.exp.sample : <anonymous>: no visible global function definition for
‘approxfun’
get.exp.sample : <anonymous>: no visible global function definition for
‘runif’
get.fpm.estimates: no visible global function definition for ‘approx’
get.ratio.posterior.Z.score: no visible global function definition for
‘qnorm’
glm.nb.fit: no visible binding for global variable ‘nobs’
knn.error.models : <anonymous>: no visible global function definition
for ‘installed.packages’
knn.error.models : <anonymous> : <anonymous>: no visible global
function definition for ‘median’
knn.error.models : <anonymous>: no visible global function definition
for ‘pdf’
knn.error.models : <anonymous>: no visible global function definition
for ‘layout’
knn.error.models : <anonymous>: no visible global function definition
for ‘par’
knn.error.models : <anonymous>: no visible global function definition
for ‘dev.off’
knn.error.models : <anonymous> : <anonymous>: no visible global
function definition for ‘dev.off’
make.pagoda.app: no visible global function definition for ‘quantile’
make.pagoda.app: no visible global function definition for ‘hclust’
make.pagoda.app: no visible global function definition for ‘dist’
make.pagoda.app: no visible binding for global variable ‘sd’
make.pagoda.app: no visible global function definition for
‘colorRampPalette’
mc.stepFlexmix : <anonymous>: no visible global function definition for
‘is’
my.heatmap2: no visible binding for global variable ‘dist’
my.heatmap2: no visible binding for global variable ‘hclust’
my.heatmap2 : <anonymous>: no visible global function definition for
‘reorder’
my.heatmap2: no visible global function definition for ‘as.dendrogram’
my.heatmap2: no visible global function definition for
‘order.dendrogram’
my.heatmap2: no visible binding for global variable ‘sd’
my.heatmap2: no visible global function definition for ‘dev.size’
my.heatmap2: no visible global function definition for ‘lcm’
my.heatmap2: no visible global function definition for ‘par’
my.heatmap2: no visible global function definition for ‘layout’
my.heatmap2: no visible global function definition for ‘image’
my.heatmap2: no visible global function definition for ‘axis’
my.heatmap2: no visible global function definition for ‘mtext’
my.heatmap2: no visible global function definition for ‘abline’
negbin.th: no visible global function definition for ‘make.link’
one.sided.test.id: no visible global function definition for ‘layout’
one.sided.test.id: no visible global function definition for ‘par’
one.sided.test.id: no visible global function definition for ‘rainbow’
one.sided.test.id : <anonymous>: no visible global function definition
for ‘lines’
one.sided.test.id: no visible global function definition for ‘legend’
one.sided.test.id: no visible global function definition for ‘na.omit’
one.sided.test.id: no visible global function definition for ‘axis’
one.sided.test.id: no visible global function definition for ‘mtext’
one.sided.test.id: no visible global function definition for ‘polygon’
one.sided.test.id: no visible global function definition for ‘abline’
one.sided.test.id: no visible global function definition for ‘box’
one.sided.test.id: no visible global function definition for ‘qnorm’
pagoda.cluster.cells: no visible global function definition for
‘hclust’
pagoda.cluster.cells: no visible global function definition for
‘installed.packages’
pagoda.effective.cells: no visible global function definition for
‘nlminb’
pagoda.gene.clusters: no visible global function definition for
‘installed.packages’
pagoda.gene.clusters: no visible global function definition for
‘as.dist’
pagoda.gene.clusters: no visible global function definition for ‘cor’
pagoda.gene.clusters: no visible global function definition for
‘cutree’
pagoda.gene.clusters : <anonymous> : <anonymous>: no visible global
function definition for ‘cor’
pagoda.gene.clusters : <anonymous>: no visible global function
definition for ‘rnorm’
pagoda.gene.clusters : <anonymous>: no visible global function
definition for ‘installed.packages’
pagoda.gene.clusters : <anonymous>: no visible global function
definition for ‘as.dist’
pagoda.gene.clusters : <anonymous>: no visible global function
definition for ‘cor’
pagoda.gene.clusters : <anonymous>: no visible global function
definition for ‘cutree’
pagoda.gene.clusters: no visible global function definition for ‘lm’
pagoda.gene.clusters: no visible global function definition for ‘par’
pagoda.gene.clusters: no visible global function definition for
‘smoothScatter’
pagoda.gene.clusters: no visible global function definition for
‘points’
pagoda.gene.clusters: no visible global function definition for ‘lines’
pagoda.gene.clusters: no visible global function definition for
‘legend’
pagoda.gene.clusters: no visible global function definition for
‘abline’
pagoda.pathway.wPCA : <anonymous> : <anonymous>: no visible global
function definition for ‘cor’
pagoda.pathway.wPCA : <anonymous>: no visible global function
definition for ‘sd’
pagoda.pathway.wPCA : <anonymous>: no visible binding for global
variable ‘sd’
pagoda.reduce.loading.redundancy: no visible global function definition
for ‘cor’
pagoda.reduce.loading.redundancy: no visible global function definition
for ‘as.dist’
pagoda.reduce.loading.redundancy: no visible global function definition
for ‘installed.packages’
pagoda.reduce.loading.redundancy: no visible global function definition
for ‘cutree’
pagoda.reduce.loading.redundancy: no visible global function definition
for ‘colors’
pagoda.reduce.redundancy: no visible global function definition for
‘cor’
pagoda.reduce.redundancy: no visible global function definition for
‘installed.packages’
pagoda.reduce.redundancy: no visible global function definition for
‘cutree’
pagoda.reduce.redundancy: no visible global function definition for
‘colors’
pagoda.reduce.redundancy: no visible binding for global variable ‘var’
pagoda.top.aspects: no visible global function definition for ‘qnorm’
pagoda.top.aspects : <anonymous>: no visible global function definition
for ‘sd’
pagoda.top.aspects : qWishartSpikeFixed: no visible global function
definition for ‘qnorm’
pagoda.top.aspects : pWishartMaxFixed: no visible global function
definition for ‘pgamma’
pagoda.top.aspects: no visible global function definition for ‘pnorm’
pagoda.top.aspects: no visible binding for global variable ‘varst’
pagoda.top.aspects: no visible global function definition for ‘par’
pagoda.top.aspects: no visible global function definition for
‘colorRampPalette’
pagoda.top.aspects: no visible global function definition for ‘lines’
pagoda.top.aspects: no visible global function definition for ‘points’
pagoda.top.aspects: no visible binding for global variable ‘var’
pagoda.top.aspects: no visible global function definition for ‘qchisq’
pagoda.varnorm: no visible global function definition for ‘data’
pagoda.varnorm: no visible binding for global variable ‘scde.edff’
pagoda.varnorm : <anonymous>: no visible global function definition for
‘ppois’
pagoda.varnorm : <anonymous>: no visible global function definition for
‘pnbinom’
pagoda.varnorm : <anonymous> : <anonymous>: no visible global function
definition for ‘ppois’
pagoda.varnorm : <anonymous> : <anonymous>: no visible global function
definition for ‘pnbinom’
pagoda.varnorm : <anonymous>: no visible binding for global variable
‘scde.edff’
pagoda.varnorm: no visible global function definition for ‘par’
pagoda.varnorm: no visible global function definition for
‘smoothScatter’
pagoda.varnorm: no visible global function definition for ‘lines’
pagoda.varnorm: no visible global function definition for ‘points’
pagoda.varnorm: no visible global function definition for ‘pchisq’
pagoda.varnorm: no visible global function definition for ‘p.adjust’
pagoda.varnorm: no visible binding for global variable ‘min.sd’
pagoda.varnorm: no visible global function definition for ‘qchisq’
pagoda.varnorm: no visible global function definition for ‘abline’
pagoda.varnorm : wsu: no visible global function definition for ‘qnorm’
pagoda.varnorm : <anonymous>: no visible global function definition for
‘qnorm’
pagoda.view.aspects: no visible global function definition for ‘hclust’
pagoda.view.aspects: no visible global function definition for ‘dist’
pagoda.view.aspects: no visible binding for global variable ‘var’
pairs.extended: no visible binding for global variable ‘points’
pairs.extended : textPanel: no visible global function definition for
‘text’
pairs.extended : localAxis: no visible global function definition for
‘Axis’
pairs.extended: no visible global function definition for ‘par’
pairs.extended: no visible global function definition for ‘box’
pairs.extended: no visible global function definition for ‘strwidth’
pairs.extended: no visible global function definition for ‘mtext’
pairs.panel.cor: no visible global function definition for ‘par’
pairs.panel.cor: no visible global function definition for ‘cor’
pairs.panel.cor: no visible global function definition for ‘strwidth’
pairs.panel.cor: no visible global function definition for ‘text’
pairs.panel.hist: no visible global function definition for ‘par’
pairs.panel.hist: no visible global function definition for ‘hist’
pairs.panel.hist: no visible global function definition for ‘rect’
pairs.panel.scatter: no visible global function definition for ‘points’
pairs.panel.scatter: no visible global function definition for
‘densCols’
pairs.panel.scatter: no visible global function definition for
‘colorRampPalette’
pairs.panel.smoothScatter: no visible global function definition for
‘smoothScatter’
papply: no visible binding for global variable ‘n’
pathway.pc.correlation.distance: no visible global function definition
for ‘pt’
pathway.pc.correlation.distance: no visible global function definition
for ‘qt’
plot.nb2.mixture.fit: no visible global function definition for
‘layout’
plot.nb2.mixture.fit: no visible global function definition for ‘par’
plot.nb2.mixture.fit: no visible global function definition for
‘smoothScatter’
plot.nb2.mixture.fit: no visible global function definition for
‘points’
plot.nb2.mixture.fit: no visible global function definition for
‘densCols’
plot.nb2.mixture.fit: no visible global function definition for
‘colorRampPalette’
plot.nb2.mixture.fit: no visible global function definition for ‘lines’
plot.nb2.mixture.fit: no visible global function definition for
‘qnbinom’
plot.nb2.mixture.fit: no visible global function definition for
‘legend’
plot.nb2.mixture.fit: no visible global function definition for
‘na.omit’
plot.nb2.mixture.fit: no visible global function definition for ‘terms’
plot.nb2.mixture.fit: no visible global function definition for
‘model.frame’
plot.nb2.mixture.fit: no visible global function definition for
‘delete.response’
plot.nb2.mixture.fit: no visible global function definition for
‘model.matrix’
plot.nb2.mixture.fit: no visible global function definition for
‘abline’
plot.nb2.mixture.fit: no visible global function definition for
‘barplot’
plot.nb2.mixture.fit: no visible global function definition for ‘box’
plot.nb2.mixture.fit: no visible global function definition for
‘dev.off’
quick.distribution.summary: no visible global function definition for
‘qnorm’
quick.distribution.summary: no visible global function definition for
‘p.adjust’
quick.distribution.summary: no visible global function definition for
‘pnorm’
scde.browse.diffexp: no visible global function definition for
‘browseURL’
scde.expression.difference: no visible global function definition for
‘fisher.test’
scde.expression.prior: no visible global function definition for
‘quantile’
scde.expression.prior: no visible global function definition for
‘density’
scde.expression.prior: no visible global function definition for ‘par’
scde.expression.prior: no visible global function definition for
‘abline’
scde.fit.models.to.reference: no visible global function definition for
‘pdf’
scde.fit.models.to.reference: no visible global function definition for
‘layout’
scde.fit.models.to.reference: no visible global function definition for
‘par’
scde.fit.models.to.reference: no visible global function definition for
‘dev.off’
scde.test.gene.expression.difference: no visible global function
definition for ‘fisher.test’
scde.test.gene.expression.difference: no visible global function
definition for ‘layout’
scde.test.gene.expression.difference: no visible global function
definition for ‘par’
scde.test.gene.expression.difference: no visible global function
definition for ‘rainbow’
scde.test.gene.expression.difference : <anonymous>: no visible global
function definition for ‘lines’
scde.test.gene.expression.difference : <anonymous>: no visible global
function definition for ‘rgb’
scde.test.gene.expression.difference: no visible global function
definition for ‘na.omit’
scde.test.gene.expression.difference: no visible global function
definition for ‘axis’
scde.test.gene.expression.difference: no visible global function
definition for ‘mtext’
scde.test.gene.expression.difference: no visible global function
definition for ‘abline’
scde.test.gene.expression.difference: no visible global function
definition for ‘polygon’
scde.test.gene.expression.difference: no visible global function
definition for ‘rgb’
scde.test.gene.expression.difference: no visible global function
definition for ‘legend’
show.app: no visible global function definition for ‘browseURL’
t.view.pathways: no visible global function definition for ‘na.omit’
t.view.pathways: no visible global function definition for ‘as.dist’
t.view.pathways: no visible global function definition for ‘cor’
t.view.pathways: no visible global function definition for
‘installed.packages’
t.view.pathways: no visible global function definition for ‘quantile’
t.view.pathways: no visible global function definition for
‘colorRampPalette’
t.view.pathways: no visible global function definition for
‘as.dendrogram’
view.aspects: no visible global function definition for ‘quantile’
view.aspects: no visible global function definition for
‘colorRampPalette’
view.aspects: no visible binding for global variable ‘var’
view.aspects: no visible global function definition for ‘as.dendrogram’
FLXmstep,FLXMRglmC: no visible binding for global variable ‘glm.fit’
FLXmstep,FLXMRglmC : <anonymous>: no visible global function definition
for ‘as’
FLXmstep,FLXMRglmCf: no visible binding for global variable ‘glm.fit’
FLXmstep,FLXMRnb2glmC: no visible binding for global variable ‘glm.fit’
FLXmstep,FLXMRnb2glmC : <anonymous>: no visible global function
definition for ‘as’
FLXmstep,FLXMRnb2gthC: no visible binding for global variable ‘glm.fit’
FLXmstep,FLXMRnb2gthC : <anonymous>: no visible global function
definition for ‘as’
Undefined global functions or variables:
Axis GO.db abline approx approxfun as as.dendrogram as.dist axis
barplot box browseURL coef col2rgb colorRampPalette colors combn cor
cutree data delete.response densCols density dev.off dev.size dist
fisher.test gaussian glm glm.fit go.env hclust hist image
installed.packages is layout lcm legend lines lm make.link median
min.sd model.frame model.matrix mtext n na.omit new nlminb nobs
order.dendrogram p.adjust par pchisq pdf pgamma phyper pnbinom pnorm
points poisson polygon ppois pt qchisq qnbinom qnorm qt quantile
rainbow rect reorder rgb rnorm runif scde.edff sd smoothScatter
strwidth terms text var varst weighted.mean
Consider adding
importFrom("grDevices", "col2rgb", "colorRampPalette", "colors",
"densCols", "dev.off", "dev.size", "pdf", "rainbow", "rgb")
importFrom("graphics", "Axis", "abline", "axis", "barplot", "box",
"hist", "image", "layout", "lcm", "legend", "lines",
"mtext", "par", "points", "polygon", "rect",
"smoothScatter", "strwidth", "text")
importFrom("methods", "as", "is", "new")
importFrom("stats", "approx", "approxfun", "as.dendrogram", "as.dist",
"coef", "cor", "cutree", "delete.response", "density",
"dist", "fisher.test", "gaussian", "glm", "glm.fit",
"hclust", "lm", "make.link", "median", "model.frame",
"model.matrix", "na.omit", "nlminb", "nobs",
"order.dendrogram", "p.adjust", "pchisq", "pgamma",
"phyper", "pnbinom", "pnorm", "poisson", "ppois", "pt",
"qchisq", "qnbinom", "qnorm", "qt", "quantile", "reorder",
"rnorm", "runif", "sd", "terms", "var", "weighted.mean")
importFrom("utils", "browseURL", "combn", "data", "installed.packages")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘scde/libs/scde.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Objects: ‘bwpca.o’, ‘jpmatLogBoot.o’
Found ‘srand’, possibly from ‘srand’ (C)
Object: ‘jpmatLogBoot.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘diffexp.Rmd’, ‘pagoda.Rmd’
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
scde.posteriors 49.664 0.072 49.761
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/scde.Rcheck/00check.log’
for details.
* installing *source* package ‘scde’ ...
** libs
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c bwpca.cpp -o bwpca.o
bwpca.cpp: In function ‘void set_random_matrix(arma::mat&, arma::mat&)’:
bwpca.cpp:23:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<target.n_rows;j++) {
^
bwpca.cpp:27:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<target.n_cols;i++) {
^
bwpca.cpp:30:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<target.n_rows;j++) {
^
bwpca.cpp: In function ‘void set_random_matrices(arma::mat&, arma::mat&, arma::mat&, arma::mat&)’:
bwpca.cpp:40:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<target1.n_rows;j++) {
^
bwpca.cpp:44:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<target1.n_cols;i++) {
^
bwpca.cpp:47:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<target1.n_rows;j++) {
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c jpmatLogBoot.cpp -o jpmatLogBoot.o
jpmatLogBoot.cpp: In function ‘SEXPREC* logBootPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
jpmatLogBoot.cpp:200:24: warning: unused variable ‘maxv’ [-Wunused-variable]
double maxv=nbp.max(maxij);
^
jpmatLogBoot.cpp: In function ‘SEXPREC* logBootBatchPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
jpmatLogBoot.cpp:443:10: warning: unused variable ‘maxv’ [-Wunused-variable]
double maxv=nbp.max(maxij);
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c matSlideMult.cpp -o matSlideMult.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c pagoda.cpp -o pagoda.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o scde.so bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/scde.Rcheck/scde/libs
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scde)