############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dreamlet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dreamlet_1.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/dreamlet.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘dreamlet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dreamlet’ version ‘1.2.1’ * package encoding: UTF-8 * 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 ‘dreamlet’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) meta_analysis.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) meta_analysis.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) meta_analysis.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) outlierByAssay.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) outlierByAssay.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) outlierByAssay.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) outlierByAssay.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) outlierByAssay.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly * 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 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 * checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package. * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed zenith_gsa-methods 175.167 8.151 224.317 fitVarPart 47.707 0.472 61.072 plotVarPart-methods 47.230 0.321 59.104 sortCols-method 46.348 0.299 58.416 plotPercentBars-methods 45.306 0.313 56.807 meta_analysis 36.271 0.538 47.020 stackAssays 27.358 0.249 34.562 aggregateNonCountSignal 14.406 0.792 19.140 run_mash 14.782 0.211 19.299 compositePosteriorTest 12.592 0.188 16.006 diffVar-methods 10.410 0.118 13.230 plotVolcano-methods 10.180 0.098 12.830 plotPCA 9.887 0.089 12.454 plotBeeswarm 9.396 0.097 11.984 dreamlet 8.653 0.110 11.057 plotGeneHeatmap-methods 8.042 0.070 10.206 plotForest-methods 7.943 0.074 10.019 residuals-methods 7.650 0.102 9.597 getTreat-methods 7.583 0.080 9.810 topTable-methods 7.579 0.066 9.641 seeErrors-methods 7.471 0.071 9.516 processAssays 7.440 0.066 9.399 coefNames-methods 7.250 0.092 9.376 pbWeights 6.590 0.106 8.514 getExprGeneNames 6.549 0.089 8.355 plotVoom-methods 6.448 0.072 8.134 dreamletCompareClusters 6.186 0.089 7.957 cellTypeSpecificity 4.877 0.086 5.837 extractData-methods 4.523 0.057 5.614 outlierByAssay 4.427 0.046 5.667 details-methods 4.313 0.065 5.538 as.dreamletResult 4.041 0.077 5.080 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/dreamlet.Rcheck/00check.log’ for details.