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### Running command:
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###   /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_1.0.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/dreamlet.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘1.0.3’
* 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 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 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 ... 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 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      157.975  7.968 174.796
fitVarPart               42.982  0.301  47.226
plotVarPart-methods      41.885  0.215  43.561
plotPercentBars-methods  40.947  0.193  42.926
sortCols-method          40.027  0.134  40.740
meta_analysis            32.922  0.406  35.410
stackAssays              22.534  0.140  23.073
run_mash                 14.022  0.168  14.305
aggregateNonCountSignal  12.365  0.720  14.676
compositePosteriorTest   12.202  0.141  13.483
plotVolcano-methods       8.428  0.076   8.729
diffVar-methods           7.868  0.078   8.495
plotBeeswarm              7.813  0.089   8.329
plotPCA                   7.177  0.063   7.850
dreamlet                  7.104  0.065   7.897
plotGeneHeatmap-methods   6.560  0.059   7.031
plotForest-methods        6.461  0.048   6.809
pbWeights                 6.137  0.089   6.598
getExprGeneNames          6.076  0.073   6.435
topTable-methods          6.050  0.064   6.332
getTreat-methods          6.044  0.045   6.334
seeErrors-methods         5.948  0.077   6.095
coefNames-methods         5.945  0.069   6.738
plotVoom-methods          5.930  0.074   6.276
processAssays             5.924  0.044   6.052
residuals-methods         5.897  0.056   6.132
dreamletCompareClusters   5.210  0.069   5.769
cellTypeSpecificity       4.514  0.115   5.100
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/dreamlet.Rcheck/00check.log’
for details.