BioC 3.3: CHECK report for DESeq on linux2.bioconductor.org

Package: DESeq

Version: 1.23.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DESeq_1.23.0.tar.gz

StartedAt: 2015-10-27 03:19:12 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:21:26 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 134.0 seconds

RetCode: 0

Status:  OK

CheckDir: DESeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DESeq_1.23.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/DESeq.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq/DESCRIPTION’ ... OK
* this is package ‘DESeq’ version ‘1.23.0’
* 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 ‘DESeq’ can be installed ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘locfit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotMA: no visible binding for global variable ‘baseMean’
prepareScvBiasCorrectionFits : <anonymous>: no visible global function
  definition for ‘locfit’
Undefined global functions or variables:
  baseMean locfit
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [70s/70s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
nbinomTestForMatrices 31.643  0.004  31.668
nbinomTest            18.247  0.004  18.267
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/DESeq.Rcheck/00check.log’
for details.

* installing *source* package ‘DESeq’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pval.c -o pval.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o DESeq.so pval.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/DESeq.Rcheck/DESeq/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 (DESeq)

name	user	system	elapsed
CountDataSet-class	0.001	0.000	0.000
adjustScvForBias	0.422	0.003	0.428
conditions	0.973	0.000	0.976
counts	0.937	0.000	0.938
dispTable	1.194	0.000	1.196
estimateDispersions	1.194	0.008	1.204
estimateSizeFactors	0.686	0.000	0.686
estimateSizeFactorsForMatrix	0.807	0.000	0.807
fitInfo	1.094	0.004	1.100
fitNbinomGLMs	0.001	0.000	0.001
fitNbinomGLMsForMatrix	0.001	0.000	0.000
getBaseMeansAndVariances	1.223	0.000	1.225
getVarianceStabilizedData	2.335	0.000	2.336
makeExampleCountDataSet	0.884	0.000	0.883
nbinomGLMTest	1.485	0.000	1.484
nbinomTest	18.247	0.004	18.267
nbinomTestForMatrices	31.643	0.004	31.668
newCountDataSet	0.704	0.000	0.705
plotDispEsts	1.115	0.000	1.119
plotMA	0.000	0.000	0.001
plotPCA	1.178	0.004	1.183
sizeFactors	0.978	0.000	0.978