BioC 3.2: CHECK report for EBSeq on zin1

Package: EBSeq

Version: 1.9.4

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings EBSeq_1.9.4.tar.gz

StartedAt: 2015-08-23 23:30:42 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:31:28 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 45.3 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_1.9.4.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 ‘1.9.4’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/26s] 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/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	3.156	0.011	3.197
EBMultiTest	4.861	0.000	4.861
EBSeq_NingLeng-package	0.414	0.000	0.414
EBTest	0.499	0.000	0.499
GeneMat	0.002	0.000	0.003
GetDEResults	0.408	0.000	0.408
GetMultiFC	4.842	0.000	4.867
GetMultiPP	4.916	0.000	4.912
GetNg	0.009	0.000	0.009
GetNormalizedMat	0.003	0.004	0.006
GetPP	0.439	0.000	0.440
GetPPMat	0.656	0.004	0.661
GetPatterns	0.001	0.000	0.002
IsoList	0.004	0.000	0.004
IsoMultiList	0.002	0.000	0.002
Likefun	0.001	0.000	0.001
LikefunMulti	0.001	0.000	0.000
LogN	0.000	0.000	0.001
LogNMulti	0	0	0
MedianNorm	0.006	0.000	0.006
MultiGeneMat	0.002	0.000	0.002
PlotPattern	0.009	0.000	0.008
PlotPostVsRawFC	0.982	0.004	1.006
PolyFitPlot	0.016	0.000	0.016
PostFC	0.662	0.000	0.665
QQP	3.104	0.000	3.118
QuantileNorm	0.005	0.000	0.006
RankNorm	0.015	0.000	0.015
beta.mom	0.000	0.000	0.001
crit_fun	0.791	0.000	0.792
f0	0.001	0.000	0.001
f1	0.000	0.000	0.001