############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scde.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scde_2.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scde.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scde/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scde’ version ‘2.35.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘scde’ can be installed ... WARNING Found the following significant warnings: bwpca.cpp:112:11: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat') to itself [-Wself-assign-overloaded] bwpca.cpp:129:15: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat') to itself [-Wself-assign-overloaded] bwpca.cpp:154:19: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat') to itself [-Wself-assign-overloaded] bwpca.cpp:278:19: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat') to itself [-Wself-assign-overloaded] pagoda.cpp:56:15: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col') to itself [-Wself-assign-overloaded] pagoda.cpp:56:23: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col') to itself [-Wself-assign-overloaded] See ‘/Users/biocbuild/bbs-3.21-bioc/meat/scde.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... WARNING 'library' or 'require' calls not declared from: ‘Rook’ ‘extRemes’ ‘rjson’ 'library' or 'require' calls in package code: ‘Rook’ ‘extRemes’ ‘rjson’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported object imported by a ':::' call: ‘tools:::httpdPort’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘scde/R/functions.R’: .onAttach calls: require(Rook) require(rjson) message(e) Package startup functions should not change the search path. Package startup functions should use ‘packageStartupMessage’ to generate messages. See section ‘Good practice’ in '?.onAttach'. FLXMRglmC: no visible global function definition for ‘new’ FLXMRglmCf: no visible global function definition for ‘new’ FLXMRnb2glm : glmrefit: no visible binding for global variable ‘glm.fit’ FLXMRnb2glm: no visible global function definition for ‘new’ FLXMRnb2glm : : no visible global function definition for ‘coef’ FLXMRnb2glmC: no visible global function definition for ‘new’ FLXMRnb2gth: no visible global function definition for ‘new’ FLXMRnb2gth : : no visible global function definition for ‘coef’ FLXMRnb2gth : : no visible global function definition for ‘glm’ FLXMRnb2gth : : no visible global function definition for ‘poisson’ FLXMRnb2gth : : no visible global function definition for ‘weighted.mean’ FLXMRnb2gth : : no visible global function definition for ‘quantile’ FLXMRnb2gth : : 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 : : no visible global function definition for ‘combn’ calculate.crossfit.models : : t.pairs.panel.hist: no visible global function definition for ‘par’ calculate.crossfit.models : : t.pairs.panel.hist: no visible global function definition for ‘hist’ calculate.crossfit.models : : t.pairs.panel.hist: no visible global function definition for ‘rect’ calculate.crossfit.models : : t.pairs.smoothScatter.spearman: no visible global function definition for ‘smoothScatter’ calculate.crossfit.models : : t.pairs.smoothScatter.spearman: no visible global function definition for ‘legend’ calculate.crossfit.models : : t.pairs.smoothScatter.spearman: no visible global function definition for ‘cor’ calculate.crossfit.models : : t.panel.component.scatter: no visible global function definition for ‘points’ calculate.crossfit.models : : t.panel.component.scatter: no visible global function definition for ‘densCols’ calculate.crossfit.models : : t.panel.component.scatter: no visible global function definition for ‘colorRampPalette’ calculate.crossfit.models : : t.panel.component.scatter: no visible global function definition for ‘legend’ calculate.crossfit.models : : t.panel.component.scatter: no visible global function definition for ‘cor’ calculate.crossfit.models : : 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 : : no visible global function definition for ‘na.omit’ calculate.individual.models : : no visible global function definition for ‘combn’ calculate.individual.models : : no visible global function definition for ‘pdf’ calculate.individual.models : : no visible global function definition for ‘layout’ calculate.individual.models : : no visible global function definition for ‘par’ calculate.individual.models : : 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 : : no visible global function definition for ‘col2rgb’ collapse.aspect.clusters : : no visible binding for global variable ‘var’ collapse.aspect.clusters : : no visible global function definition for ‘cor’ collapse.aspect.clusters : : no visible global function definition for ‘var’ collapse.aspect.clusters : : no visible global function definition for ‘rnorm’ collapse.aspect.clusters : : 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 : : : no visible global function definition for ‘approxfun’ get.exp.posterior.samples : : : no visible global function definition for ‘runif’ get.exp.sample : : no visible global function definition for ‘approxfun’ get.exp.sample : : 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 : : no visible global function definition for ‘installed.packages’ knn.error.models : : : no visible global function definition for ‘median’ knn.error.models : : no visible global function definition for ‘pdf’ knn.error.models : : no visible global function definition for ‘layout’ knn.error.models : : no visible global function definition for ‘par’ knn.error.models : : no visible global function definition for ‘dev.off’ knn.error.models : : : 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 : : 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 : : 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 : : 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 : : : no visible global function definition for ‘cor’ pagoda.gene.clusters : : no visible global function definition for ‘rnorm’ 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: 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 : : : no visible global function definition for ‘cor’ pagoda.pathway.wPCA : : no visible global function definition for ‘sd’ pagoda.pathway.wPCA : : 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 : : 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 : : no visible global function definition for ‘ppois’ pagoda.varnorm : : no visible global function definition for ‘pnbinom’ pagoda.varnorm : : : no visible global function definition for ‘ppois’ pagoda.varnorm : : : no visible global function definition for ‘pnbinom’ pagoda.varnorm : : 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 : : 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 : : no visible global function definition for ‘lines’ scde.test.gene.expression.difference : : 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 : : 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 : : no visible global function definition for ‘as’ FLXmstep,FLXMRnb2gthC: no visible binding for global variable ‘glm.fit’ FLXmstep,FLXMRnb2gthC : : no visible global function definition for ‘as’ Undefined global functions or variables: Axis GO.db abline approx approxfun as as.dendrogram as.dist axis barplot box browseURL coef col2rgb colorRampPalette colors combn cor cutree data delete.response densCols density dev.off dev.size dist fisher.test gaussian glm glm.fit go.env hclust hist image installed.packages is layout lcm legend lines lm make.link median min.sd model.frame model.matrix mtext n na.omit new nlminb nobs order.dendrogram p.adjust par pchisq pdf pgamma phyper pnbinom pnorm points poisson polygon ppois pt qchisq qnbinom qnorm qt quantile rainbow rect reorder rgb rnorm runif scde.edff sd smoothScatter strwidth terms text var varst weighted.mean Consider adding importFrom("grDevices", "col2rgb", "colorRampPalette", "colors", "densCols", "dev.off", "dev.size", "pdf", "rainbow", "rgb") importFrom("graphics", "Axis", "abline", "axis", "barplot", "box", "hist", "image", "layout", "lcm", "legend", "lines", "mtext", "par", "points", "polygon", "rect", "smoothScatter", "strwidth", "text") importFrom("methods", "as", "is", "new") importFrom("stats", "approx", "approxfun", "as.dendrogram", "as.dist", "coef", "cor", "cutree", "delete.response", "density", "dist", "fisher.test", "gaussian", "glm", "glm.fit", "hclust", "lm", "make.link", "median", "model.frame", "model.matrix", "na.omit", "nlminb", "nobs", "order.dendrogram", "p.adjust", "pchisq", "pgamma", "phyper", "pnbinom", "pnorm", "poisson", "ppois", "pt", "qchisq", "qnbinom", "qnorm", "qt", "quantile", "reorder", "rnorm", "runif", "sd", "terms", "var", "weighted.mean") importFrom("utils", "browseURL", "combn", "data", "installed.packages") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) pagoda.gene.clusters.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.gene.clusters.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.gene.clusters.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.gene.clusters.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.gene.clusters.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.gene.clusters.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.top.aspects.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.top.aspects.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.top.aspects.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.top.aspects.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.varnorm.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.varnorm.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.varnorm.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.varnorm.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.varnorm.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.varnorm.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.varnorm.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) pagoda.varnorm.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) scde.browse.diffexp.Rd:24: Lost braces; missing escapes or markup? 24 | \item{geneLookupURL}{The URL that will be used to construct links to view more information on gene names. By default (if can't guess the organism) the links will forward to ENSEMBL site search, using \code{geneLookupURL = "http://useast.ensembl.org/Multi/Search/Results?q = {0}"}. The "{0}" in the end will be substituted with the gene name. For instance, to link to GeneCards, use \code{"http://www.genecards.org/cgi-bin/carddisp.pl?gene = {0}"}.} | ^ checkRd: (-1) scde.expression.difference.Rd:36-40: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) scde.expression.difference.Rd:37: Lost braces 37 | \item{ce} { conservative estimate of expression-fold change (equals to the min(abs(c(lb, ub))), or 0 if the CI crosses the 0} | ^ checkRd: (-1) scde.expression.difference.Rd:37: Lost braces; missing escapes or markup? 37 | \item{ce} { conservative estimate of expression-fold change (equals to the min(abs(c(lb, ub))), or 0 if the CI crosses the 0} | ^ checkRd: (-1) scde.expression.difference.Rd:38: Lost braces 38 | \item{Z} { uncorrected Z-score of expression difference} | ^ checkRd: (-1) scde.expression.difference.Rd:38: Lost braces; missing escapes or markup? 38 | \item{Z} { uncorrected Z-score of expression difference} | ^ checkRd: (-1) scde.expression.difference.Rd:39: Lost braces 39 | \item{cZ} {expression difference Z-score corrected for multiple hypothesis testing using Holm procedure} | ^ checkRd: (-1) scde.expression.difference.Rd:39: Lost braces; missing escapes or markup? 39 | \item{cZ} {expression difference Z-score corrected for multiple hypothesis testing using Holm procedure} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/scde/libs/scde.so’: Found ‘_rand’, possibly from ‘rand’ (C) Found ‘_srand’, possibly from ‘srand’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘diffexp.Rmd’ ‘pagoda.Rmd’ Files named as vignettes but with no recognized vignette engine: ‘vignettes/diffexp.Rmd’ ‘vignettes/pagoda.Rmd’ (Is a VignetteBuilder field missing?) * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed scde.posteriors 25.162 0.235 25.48 * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/scde.Rcheck/00check.log’ for details.