BioC 3.2: CHECK report for DESeq2 on zin1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.9.29.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/DESeq2.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.9.29’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘Rcpp’
  ‘RcppArmadillo’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [28s/28s] OK
* 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/31s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [54s/54s]
 [54s/55s] 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-3.2-bioc/meat/DESeq2.Rcheck/00check.log’
for details.

* installing *source* package ‘DESeq2’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c DESeq2.cpp -o DESeq2.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.2-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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)

name	user	system	elapsed
DESeq	1.263	0.003	1.310
DESeqDataSet	0.05	0.00	0.05
coef	2.343	0.008	2.360
collapseReplicates	0.104	0.000	0.105
counts	0.075	0.000	0.076
design	0.069	0.000	0.069
dispersionFunction	1.525	0.016	1.542
estimateDispersions	0.713	0.000	0.713
estimateDispersionsGeneEst	0.731	0.000	0.739
estimateSizeFactors	0.124	0.000	0.124
estimateSizeFactorsForMatrix	0.069	0.000	0.069
fpkm	0.173	0.000	0.174
fpm	0.108	0.000	0.108
makeExampleDESeqDataSet	0.068	0.000	0.069
nbinomLRT	1.200	0.000	1.199
nbinomWaldTest	1.562	0.000	1.561
normalizationFactors	1.558	0.004	1.560
normalizeGeneLength	0.082	0.000	0.083
plotCounts	0.092	0.000	0.092
plotDispEsts	0.716	0.004	0.720
plotMA	1.567	0.004	1.593
plotPCA	1.539	0.000	1.538
plotSparsity	0.087	0.000	0.086
results	4.411	0.008	4.416
rlog	1.640	0.000	1.639
summary	2.016	0.004	2.019
varianceStabilizingTransformation	0.976	0.000	0.992

BioC 3.2: CHECK report for DESeq2 on zin1

Summary

Command output