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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_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/dreamlet.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘1.3.1’
* 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      177.993  8.527 209.486
fitVarPart               47.192  0.312  52.070
plotVarPart-methods      46.814  0.244  52.975
plotPercentBars-methods  45.844  0.216  49.993
sortCols-method          45.654  0.273  50.387
meta_analysis            35.961  0.427  39.608
stackAssays              26.184  0.237  30.094
aggregateNonCountSignal  14.346  0.801  17.556
run_mash                 14.815  0.207  16.255
compositePosteriorTest   12.588  0.148  14.219
diffVar-methods          10.477  0.108  11.839
plotVolcano-methods      10.061  0.085  10.971
plotPCA                   8.775  0.067   9.532
dreamlet                  8.561  0.089   9.809
plotBeeswarm              8.258  0.081   9.117
plotGeneHeatmap-methods   8.019  0.062   9.024
plotForest-methods        7.977  0.070   8.752
topTable-methods          7.590  0.066   8.593
residuals-methods         7.549  0.062   8.243
getTreat-methods          7.463  0.073   8.260
processAssays             7.423  0.047   8.161
coefNames-methods         7.383  0.084   8.184
seeErrors-methods         7.416  0.047   8.087
plotVoom-methods          6.402  0.065   7.016
dreamletCompareClusters   6.255  0.087   7.076
cellTypeSpecificity       4.947  0.094   6.097
* 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-3.20-bioc/meat/dreamlet.Rcheck/00check.log’
for details.