############################################################################## ############################################################################## ### ### 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 12.7.6 * 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 178.449 9.649 228.207 fitVarPart 48.265 0.445 61.203 plotVarPart-methods 46.354 0.390 56.939 sortCols-method 46.111 0.381 56.452 plotPercentBars-methods 45.596 0.331 56.200 meta_analysis 36.960 0.567 47.060 stackAssays 25.958 0.227 31.694 aggregateNonCountSignal 14.838 0.907 20.102 run_mash 14.689 0.214 17.550 compositePosteriorTest 12.869 0.184 16.757 diffVar-methods 10.582 0.119 13.250 plotVolcano-methods 10.365 0.133 12.664 plotBeeswarm 9.553 0.115 11.920 plotGeneHeatmap-methods 9.352 0.102 11.466 plotPCA 8.896 0.086 10.962 dreamlet 8.848 0.106 11.173 plotForest-methods 8.108 0.071 9.932 residuals-methods 7.673 0.084 9.301 getTreat-methods 7.643 0.073 9.498 topTable-methods 7.597 0.063 9.008 seeErrors-methods 7.550 0.096 9.316 coefNames-methods 7.549 0.086 9.355 processAssays 7.553 0.068 9.109 pbWeights 6.653 0.105 8.581 getExprGeneNames 6.640 0.091 8.184 plotVoom-methods 6.503 0.075 7.847 dreamletCompareClusters 6.383 0.092 7.736 extractData-methods 4.600 0.058 5.740 outlierByAssay 4.534 0.050 5.630 details-methods 4.357 0.079 5.539 cellTypeSpecificity 3.991 0.134 5.105 * 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.