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 13:10:58 -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: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.18.1.tar.gz |
| StartedAt: 2018-04-11 22:51:29 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:56:11 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 282.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DESeq2.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.18.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/DESeq2.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 6.1Mb
sub-directories of 1Mb or more:
doc 2.3Mb
libs 2.6Mb
* 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
‘/home/biocbuild/bbs-3.6-bioc/meat/DESeq2.Rcheck/00check.log’
for details.
DESeq2.Rcheck/00install.out
* installing *source* package ‘DESeq2’ ... ** libs g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c DESeq2.cpp -o DESeq2.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR installing to /home/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-pc-linux-gnu (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
83.024 0.400 84.055
DESeq2.Rcheck/DESeq2-Ex.timings
| name | user | system | elapsed | |
| DESeq | 3.336 | 0.008 | 3.349 | |
| DESeqDataSet | 0.292 | 0.008 | 0.299 | |
| coef | 1.812 | 0.004 | 1.817 | |
| collapseReplicates | 0.140 | 0.004 | 0.141 | |
| counts | 0.064 | 0.000 | 0.065 | |
| design | 0.052 | 0.000 | 0.051 | |
| dispersionFunction | 1.060 | 0.004 | 1.064 | |
| estimateDispersions | 0.452 | 0.000 | 0.453 | |
| estimateDispersionsGeneEst | 0.460 | 0.004 | 0.466 | |
| estimateSizeFactors | 0.108 | 0.000 | 0.108 | |
| estimateSizeFactorsForMatrix | 0.060 | 0.000 | 0.059 | |
| fpkm | 0.204 | 0.000 | 0.201 | |
| fpm | 0.096 | 0.000 | 0.095 | |
| lfcShrink | 4.060 | 0.008 | 4.086 | |
| makeExampleDESeqDataSet | 0.056 | 0.000 | 0.055 | |
| nbinomLRT | 0.924 | 0.000 | 0.925 | |
| nbinomWaldTest | 0.832 | 0.000 | 0.833 | |
| normalizationFactors | 1.080 | 0.000 | 1.081 | |
| plotCounts | 0.436 | 0.000 | 0.435 | |
| plotDispEsts | 0.468 | 0.000 | 0.466 | |
| plotMA | 0.892 | 0.000 | 0.894 | |
| plotPCA | 2.996 | 0.000 | 3.000 | |
| plotSparsity | 0.068 | 0.000 | 0.068 | |
| results | 3.272 | 0.008 | 3.284 | |
| rlog | 1.356 | 0.000 | 1.358 | |
| summary | 1.336 | 0.008 | 1.347 | |
| varianceStabilizingTransformation | 0.816 | 0.000 | 0.818 | |
| vst | 1.508 | 0.020 | 1.529 | |