Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:21 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the scde package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1693/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scde 2.20.0 (landing page) Jean Fan
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: scde |
Version: 2.20.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scde.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scde_2.20.0.tar.gz |
StartedAt: 2021-10-15 05:10:20 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 05:15:12 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 291.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: scde.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scde.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scde_2.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/scde.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'scde/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'scde' version '2.20.0' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'scde' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking 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 i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/scde/libs/i386/scde.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Found 'rand', possibly from 'rand' (C) Found 'srand', possibly from 'srand' (C) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/scde/libs/x64/scde.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Found 'rand', possibly from 'rand' (C) Found 'srand', possibly from 'srand' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed scde.posteriors 67.72 0.19 67.92 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed scde.posteriors 64.05 0.16 64.27 * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/scde.Rcheck/00check.log' for details.
scde.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/scde_2.20.0.tar.gz && rm -rf scde.buildbin-libdir && mkdir scde.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scde.buildbin-libdir scde_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL scde_2.20.0.zip && rm scde_2.20.0.tar.gz scde_2.20.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 90 1081k 90 983k 0 0 1381k 0 --:--:-- --:--:-- --:--:-- 1381k 100 1081k 100 1081k 0 0 1442k 0 --:--:-- --:--:-- --:--:-- 1441k install for i386 * installing *source* package 'scde' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -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:23:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j=0;j<target.n_rows;j++) { ~^~~~~~~~~~~~~~ bwpca.cpp:27:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int i=0;i<target.n_cols;i++) { ~^~~~~~~~~~~~~~ bwpca.cpp:30:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j=0;j<target1.n_rows;j++) { ~^~~~~~~~~~~~~~~ bwpca.cpp:44:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int i=0;i<target1.n_cols;i++) { ~^~~~~~~~~~~~~~~ bwpca.cpp:47:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j=0;j<target1.n_rows;j++) { ~^~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -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] double maxv=nbp.max(maxij); ^~~~ jpmatLogBoot.cpp: In function 'SEXPREC* logBootBatchPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': jpmatLogBoot.cpp:443:10: warning: unused variable 'maxv' [-Wunused-variable] double maxv=nbp.max(maxij); ^~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matSlideMult.cpp -o matSlideMult.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pagoda.cpp -o pagoda.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o scde.dll tmp.def bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/scde.buildbin-libdir/00LOCK-scde/00new/scde/libs/i386 ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'scde' finding HTML links ... done ViewPagodaApp-class html bwpca html clean.counts html clean.gos html es.mef.small html knn html knn.error.models html make.pagoda.app html o.ifm html pagoda.cluster.cells html pagoda.effective.cells html pagoda.gene.clusters html pagoda.pathway.wPCA html pagoda.reduce.loading.redundancy html pagoda.reduce.redundancy html pagoda.show.pathways html pagoda.subtract.aspect html pagoda.top.aspects html pagoda.varnorm html pagoda.view.aspects html papply html pollen html scde html scde.browse.diffexp html scde.edff html scde.error.models html scde.expression.difference html scde.expression.magnitude html scde.expression.prior html scde.failure.probability html scde.fit.models.to.reference html scde.posteriors html scde.test.gene.expression.difference html show.app html view.aspects html winsorize.matrix html ** 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 install for x64 * installing *source* package 'scde' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -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:23:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j=0;j<target.n_rows;j++) { ~^~~~~~~~~~~~~~ bwpca.cpp:27:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int i=0;i<target.n_cols;i++) { ~^~~~~~~~~~~~~~ bwpca.cpp:30:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j=0;j<target1.n_rows;j++) { ~^~~~~~~~~~~~~~~ bwpca.cpp:44:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int i=0;i<target1.n_cols;i++) { ~^~~~~~~~~~~~~~~ bwpca.cpp:47:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j=0;j<target1.n_rows;j++) { ~^~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -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] double maxv=nbp.max(maxij); ^~~~ jpmatLogBoot.cpp: In function 'SEXPREC* logBootBatchPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': jpmatLogBoot.cpp:443:10: warning: unused variable 'maxv' [-Wunused-variable] double maxv=nbp.max(maxij); ^~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matSlideMult.cpp -o matSlideMult.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pagoda.cpp -o pagoda.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o scde.dll tmp.def bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/scde.buildbin-libdir/scde/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'scde' as scde_2.20.0.zip * DONE (scde) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'scde' successfully unpacked and MD5 sums checked
scde.Rcheck/examples_i386/scde-Ex.timings
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scde.Rcheck/examples_x64/scde-Ex.timings
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