BioC 3.1: CHECK report for EBSeq on petty

Package: EBSeq

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBSeq_1.8.0.tar.gz

StartedAt: 2015-10-08 22:46:25 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:47:51 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 85.9 seconds

RetCode: 0

Status:  OK

CheckDir: EBSeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBSeq_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/EBSeq.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.8.0’
* 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 ... [2s/2s] 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
'library' or 'require' call to ‘gplots’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘blockmodeling’ ‘gplots’
  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
EBMultiTest : <anonymous>: no visible global function definition for
  ‘nkpartitions’
EBMultiTest: no visible global function definition for ‘nkpartitions’
GetPatterns : <anonymous>: no visible global function definition for
  ‘nkpartitions’
PlotPostVsRawFC: no visible global function definition for ‘redgreen’
* 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 ... [41s/41s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
EBMultiTest 8.428  0.032   8.463
GetMultiFC  8.349  0.024   8.377
GetMultiPP  8.201  0.016   8.220
* 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
  ‘/Users/biocbuild/bbs-3.1-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	4.140	0.019	4.166
EBMultiTest	8.428	0.032	8.463
EBSeq_NingLeng-package	0.782	0.030	0.814
EBTest	0.721	0.013	0.733
GeneMat	0.003	0.001	0.005
GetDEResults	0.628	0.021	0.648
GetMultiFC	8.349	0.024	8.377
GetMultiPP	8.201	0.016	8.220
GetNg	0.020	0.001	0.021
GetNormalizedMat	0.012	0.001	0.013
GetPP	0.663	0.037	0.700
GetPPMat	0.930	0.021	0.951
GetPatterns	0.001	0.000	0.002
IsoList	0.004	0.001	0.005
IsoMultiList	0.002	0.001	0.003
Likefun	0.001	0.000	0.001
LikefunMulti	0.001	0.000	0.001
LogN	0.001	0.000	0.001
LogNMulti	0.000	0.000	0.001
MedianNorm	0.009	0.001	0.009
MultiGeneMat	0.004	0.001	0.004
PlotPattern	0.015	0.001	0.017
PlotPostVsRawFC	1.310	0.019	1.348
PolyFitPlot	0.021	0.001	0.022
PostFC	0.977	0.015	0.992
QQP	3.841	0.016	3.857
QuantileNorm	0.008	0.001	0.009
RankNorm	0.030	0.001	0.030
beta.mom	0.000	0.000	0.001
crit_fun	1.196	0.018	1.215
f0	0.001	0.000	0.001
f1	0.001	0.001	0.001