Michael Love
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/DESeq2 |
| Branch: RELEASE_3_6 |
| Last Commit: ef65091 |
| Last Changed Date: 2017-11-10 15:01:58 -0400 (Fri, 10 Nov 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:36:33 -0400 (Thu, 12 Apr 2018).
| Package 357/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DESeq2 1.18.1 Michael Love
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| 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:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DESeq2_1.18.1.tar.gz
###
##############################################################################
##############################################################################
* 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.
DESeq2.Rcheck/00install.out
* 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)
DESeq2.Rcheck/tests/testthat.Rout
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
DESeq2.Rcheck/DESeq2-Ex.timings
| 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 | |