BioC 3.2: CHECK report for EBSeq on linux1.bioconductor.org

Package: EBSeq

Version: 1.10.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings EBSeq_1.10.0.tar.gz

StartedAt: 2015-10-27 03:08:19 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:09:06 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 47.1 seconds

RetCode: 0

Status:  OK

CheckDir: EBSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings EBSeq_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/EBSeq.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 ‘EBSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBSeq’ version ‘1.10.0’
* 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 ‘EBSeq’ can be installed ... [1s/1s] 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
GetMultiFC 6.396  0.003   6.404
GetMultiPP 5.754  0.000   5.755
* 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/EBSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘EBSeq’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EBSeq)

name	user	system	elapsed
DenNHist	3.039	0.016	3.055
EBMultiTest	4.378	0.001	4.378
EBSeq_NingLeng-package	0.521	0.000	0.521
EBTest	0.381	0.000	0.381
GeneMat	0.002	0.000	0.002
GetDEResults	0.559	0.000	0.559
GetMultiFC	6.396	0.003	6.404
GetMultiPP	5.754	0.000	5.755
GetNg	0.007	0.000	0.007
GetNormalizedMat	0.006	0.000	0.006
GetPP	0.377	0.000	0.377
GetPPMat	0.537	0.000	0.538
GetPatterns	0.001	0.000	0.001
IsoList	0.002	0.000	0.003
IsoMultiList	0.001	0.000	0.002
Likefun	0.000	0.000	0.001
LikefunMulti	0.001	0.000	0.001
LogN	0.001	0.000	0.001
LogNMulti	0.001	0.000	0.000
MedianNorm	0.005	0.000	0.004
MultiGeneMat	0.002	0.000	0.001
PlotPattern	0.006	0.000	0.007
PlotPostVsRawFC	0.744	0.000	0.744
PolyFitPlot	0.011	0.000	0.011
PostFC	0.641	0.000	0.641
QQP	2.625	0.004	2.630
QuantileNorm	0.004	0.000	0.004
RankNorm	0.011	0.000	0.012
beta.mom	0	0	0
crit_fun	0.605	0.000	0.604
f0	0	0	0
f1	0	0	0