Package: DESeq2

Version: 1.18.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DESeq2_1.18.1.tar.gz

StartedAt: 2018-04-12 02:47:35 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:53:16 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 340.7 seconds

RetCode: 0

Status:  OK

CheckDir: DESeq2.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DESeq2_1.18.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/DESeq2.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DESeq2’ version ‘1.18.1’
* 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 ‘DESeq2’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/DESeq2.Rcheck/00check.log’
for details.

* installing *source* package ‘DESeq2’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c DESeq2.cpp -o DESeq2.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/DESeq2.Rcheck/DESeq2/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DESeq2)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> library("DESeq2")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply

> test_check("DESeq2")
List of 4
 $ type        : chr "normal"
 $ package     : chr "DESeq2"
 $ version     :Classes 'package_version', 'numeric_version'  hidden list of 1
  ..$ : int [1:3] 1 18 1
 $ betaPriorVar: Named num [1:2] 1.0e+06 1.5
  ..- attr(*, "names")= chr [1:2] "Intercept" "conditionB"
List of 4
 $ type         : chr "apeglm"
 $ package      : chr "apeglm"
 $ version      :Classes 'package_version', 'numeric_version'  hidden list of 1
  ..$ : int [1:3] 1 0 3
 $ prior.control:List of 7
  ..$ no.shrink            : int 1
  ..$ prior.mean           : num 0
  ..$ prior.scale          : num 0.716
  ..$ prior.df             : num 1
  ..$ prior.no.shrink.mean : num 0
  ..$ prior.no.shrink.scale: num 15
  ..$ prior.var            : num 0.512
List of 4
 $ type    : chr "ashr"
 $ package : chr "ashr"
 $ version :Classes 'package_version', 'numeric_version'  hidden list of 1
  ..$ : int [1:3] 2 2 7
 $ fitted_g:List of 3
  ..$ pi  : num [1:19] 0 0 0 0 0 ...
  ..$ mean: num [1:19] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ sd  : num [1:19] 0.0173 0.0245 0.0347 0.049 0.0693 ...
  ..- attr(*, "row.names")= int [1:19] 1 2 3 4 5 6 7 8 9 10 ...
  ..- attr(*, "class")= chr "normalmix"
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 215 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
100.677   1.018 103.416 

name	user	system	elapsed
DESeq	4.243	0.024	4.322
DESeqDataSet	0.458	0.001	0.461
coef	1.725	0.021	1.762
collapseReplicates	0.191	0.001	0.193
counts	0.085	0.000	0.086
design	0.063	0.001	0.064
dispersionFunction	1.577	0.013	1.609
estimateDispersions	0.563	0.002	0.581
estimateDispersionsGeneEst	0.623	0.004	0.643
estimateSizeFactors	0.138	0.001	0.140
estimateSizeFactorsForMatrix	0.071	0.001	0.072
fpkm	0.255	0.004	0.260
fpm	0.123	0.011	0.133
lfcShrink	4.626	0.042	4.744
makeExampleDESeqDataSet	0.071	0.001	0.074
nbinomLRT	1.247	0.004	1.293
nbinomWaldTest	1.138	0.003	1.165
normalizationFactors	1.243	0.016	1.293
plotCounts	0.117	0.001	0.121
plotDispEsts	0.681	0.004	0.693
plotMA	1.285	0.005	1.300
plotPCA	4.334	0.010	4.398
plotSparsity	0.089	0.001	0.092
results	3.615	0.024	3.700
rlog	1.640	0.005	1.662
summary	1.530	0.011	1.561
varianceStabilizingTransformation	0.878	0.003	0.893
vst	1.435	0.047	1.504